def default(taskname=None): """ reset given task to its default values : taskname -- Name of task """ try: myf=stack_frame_find( ) if taskname==None: taskname=myf['taskname'] myf['taskname']=taskname if type(taskname)!=str: taskname=taskname.__name__ myf['taskname']=taskname ###Check if task exists by checking if task_defaults is defined if ( not myf.has_key(taskname) and str(type(myf[taskname])) != "<type 'instance'>" and not hasattr(myf[taskname],"defaults") ): raise TypeError, "task %s is not defined " %taskname eval(myf['taskname']+'.defaults()') casalog.origin('default') taskstring=str(taskname).split()[0] casalog.post(' ####### Setting values to default for task: '+taskstring+' #######') except TypeError, e: print "default --error: ", e
def __set_default_parameters(b): myf=stack_frame_find( ) a=b elkey=a.keys() for k in range(len(a)): if (type(a[elkey[k]]) != dict): myf[elkey[k]]=a[elkey[k]] elif (type(a[elkey[k]]) == dict and len(a[elkey[k]])==0): myf[elkey[k]]=a[elkey[k]] else: subdict=a[elkey[k]] ##clear out variables of other options if they exist for j in range(1,len(subdict)): subkey=subdict[j].keys() for kk in range(len(subkey)): if((subkey[kk] != 'value') & (subkey[kk] != 'notvalue') ): if(myf.has_key(subkey[kk])): del myf[subkey[kk]] ### if(subdict[0].has_key('notvalue')): myf[elkey[k]]=subdict[0]['notvalue'] else: myf[elkey[k]]=subdict[0]['value'] subkey=subdict[0].keys() for j in range(0, len(subkey)): if((subkey[j] != 'value') & (subkey[j] != 'notvalue')): myf[subkey[j]]=subdict[0][subkey[j]]
def pointcal_defaults(param=None): myf = stack_frame_find() a = odict() a['vis'] = '' a['model'] = '' a['caltable'] = '' a['field'] = '' a['spw'] = '' a['selectdata'] = { 1: { 'value': False }, 0: odict([{ 'value': True }, { 'timerange': '' }, { 'uvrange': '' }, { 'antenna': '' }, { 'scan': '' }, { 'msselect': '' }]) } a['solint'] = 0.0 if (param == None): myf['__set_default_parameters'](a) elif (param == 'paramkeys'): return a.keys() else: if (a.has_key(param)): return a[param]
def filecatalog(): """ Open the File Catalog GUI: """ myf = stack_frame_find() myf['__last_task'] = 'filecatalog' ### #Handle globals or user over-ride of arguments #Python script if (os.uname()[0] == 'Darwin'): from Carbon.Launch import LSFindApplicationForInfo from Carbon.CoreFoundation import kCFURLPOSIXPathStyle kLSUnknownCreator = '\x00\x00\x00\x00' fsRef, cfURL = LSFindApplicationForInfo(kLSUnknownCreator, None, "casafilecatalog.app") filecatalog_path = os.path.join(fsRef.as_pathname(), 'Contents', 'MacOS', 'casafilecatalog') fcpid = os.spawnvp(os.P_NOWAIT, filecatalog_path, [filecatalog_path]) #logpid=os.system('open -a casalogger.app casa.log') elif (os.uname()[0] == 'Linux'): fcpid = os.spawnlp(os.P_NOWAIT, 'casafilecatalog', 'casafilecatalog') else: print 'Unrecognized OS: No filecatalog available' myf['fcpid'] = fcpid
def tput(taskname=None, outfile=''): myf=stack_frame_find( ) if taskname == None: taskname = myf['taskname'] if type(taskname) != str: taskname=taskname.__name__ myf['taskname'] = taskname outfile = myf['taskname']+'.last' saveinputs(taskname, outfile)
def setUp(self): self.g = stack_frame_find() if self.g.has_key('__rethrow_casa_exceptions'): self.rethrow_backup = self.g['__rethrow_casa_exceptions'] else: self.rethrow_backup = None self.g['__rethrow_casa_exceptions'] = True super(failureTestCase, self).setUp()
def inp(taskname=None, page=False): """ Function to browse input parameters of a given task taskname: name of task of interest page: use paging if True, useful if list of parameters is longer than terminal height """ try: ####paging contributed by user Ramiro Hernandez if (page): ######################### class TemporaryRedirect(object): def __init__(self, stdout=None, stderr=None): self._stdout = stdout or sys.stdout self._stderr = stderr or sys.stderr def __enter__(self): self.old_stdout, self.old_stderr = sys.stdout, sys.stderr self.old_stdout.flush() self.old_stderr.flush() sys.stdout, sys.stderr = self._stdout, self._stderr def __exit__(self, exc_type, exc_value, traceback): self._stdout.flush() self._stderr.flush() sys.stdout = self.old_stdout sys.stderr = self.old_stderr #######################end class tempfile = "__temp_input.casa" temporal = open(tempfile, 'w') with TemporaryRedirect(stdout=temporal): inp(taskname, False) temporal.close() os.system('more ' + tempfile) os.system('rm ' + tempfile) return #### myf = stack_frame_find() if ((taskname == None) and (not myf.has_key('taskname'))): print 'No task name defined for inputs display' return if taskname == None: taskname = myf['taskname'] myf['taskname'] = taskname if type(taskname) != str: taskname = taskname.__name__ myf['taskname'] = taskname try: parameter_checktype(['taskname'], taskname, str) except TypeError, e: print "inp -- TypeError: ", e return except ValueError, e: print "inp -- OptionError: ", e return
def tget_defaults(param=None): myf = stack_frame_find() a = odict() a['task'] = '' a['savefile'] = '' if (param == None): myf['__set_default_parameters'](a) elif (param == 'paramkeys'): return a.keys() else: if (a.has_key(param)): return a[param]
def tget_defaults(param=None): myf=stack_frame_find( ) a=odict() a['task']='' a['savefile']='' if(param == None): myf['__set_default_parameters'](a) elif(param == 'paramkeys'): return a.keys() else: if(a.has_key(param)): return a[param]
def taskparamgui(useGlobals=True): """ Show a parameter-setting GUI for all available tasks. """ import paramgui if useGlobals: paramgui.setGlobals(stack_frame_find( )) else: paramgui.setGlobals({}) paramgui.runAll(_ip) paramgui.setGlobals({})
def inp(taskname=None, page=False): """ Function to browse input parameters of a given task taskname: name of task of interest page: use paging if True, useful if list of parameters is longer than terminal height """ try: ####paging contributed by user Ramiro Hernandez if(page): ######################### class TemporaryRedirect(object): def __init__(self, stdout=None, stderr=None): self._stdout = stdout or sys.stdout self._stderr = stderr or sys.stderr def __enter__(self): self.old_stdout, self.old_stderr = sys.stdout, sys.stderr self.old_stdout.flush(); self.old_stderr.flush() sys.stdout, sys.stderr = self._stdout, self._stderr def __exit__(self, exc_type, exc_value, traceback): self._stdout.flush(); self._stderr.flush() sys.stdout = self.old_stdout sys.stderr = self.old_stderr #######################end class tempfile="__temp_input.casa" temporal = open(tempfile, 'w') with TemporaryRedirect(stdout=temporal): inp(taskname, False) temporal.close() os.system('more '+tempfile) os.system('rm '+tempfile) return #### myf=stack_frame_find( ) if((taskname==None) and (not myf.has_key('taskname'))): print 'No task name defined for inputs display' return if taskname==None: taskname=myf['taskname'] myf['taskname']=taskname if type(taskname)!=str: taskname=taskname.__name__ myf['taskname']=taskname try: parameter_checktype(['taskname'],taskname,str) except TypeError, e: print "inp -- TypeError: ", e return except ValueError, e: print "inp -- OptionError: ", e return
def defaults(self, param=None, ipython_globals=None, paramvalue=None, subparam=None): if not hasattr(self, "__globals__") or self.__globals__ == None: self.__globals__ = stack_frame_find() if ipython_globals == None: myf = self.__globals__ else: myf = ipython_globals a = odict() a['vis'] = '' a['spw'] = '' a['field'] = '' a['secsour'] = '' a['stddevfact'] = '' ### This function sets the default values but also will return the list of ### parameters or the default value of a given parameter if (param == None): myf['__set_default_parameters'](a) elif (param == 'paramkeys'): return a.keys() else: if (paramvalue == None and subparam == None): if (a.has_key(param)): return a[param] else: return self.itsdefault(param) else: retval = a[param] if (type(a[param]) == dict): for k in range(len(a[param])): valornotval = 'value' if (a[param][k].has_key('notvalue')): valornotval = 'notvalue' if ((a[param][k][valornotval]) == paramvalue): retval = a[param][k].copy() retval.pop(valornotval) if (subparam != None): if (retval.has_key(subparam)): retval = retval[subparam] else: retval = self.itsdefault(subparam) else: retval = self.itsdefault(subparam) return retval
def asap_init(): """ Initialize ASAP....: """ myf = stack_frame_find() casapath = os.environ['CASAPATH'] print('*** Loading ATNF ASAP Package...') import asap as sd #print('*** ... ASAP (%s rev#%s) import complete ***' % (sd.__version__,sd.__revision__)) print('*** ... ASAP (rev#%s) import complete ***' % (sd.__revision__)) os.environ['CASAPATH'] = casapath from sdimaging_cli import sdimaging_cli as sdimaging from sdfixscan_cli import sdfixscan_cli as sdfixscan from sdaverageold_cli import sdaverageold_cli as sdaverageold from sdbaselineold_cli import sdbaselineold_cli as sdbaselineold from sdbaseline2old_cli import sdbaseline2old_cli as sdbaseline2old from sdcalold_cli import sdcalold_cli as sdcalold from sdcal2old_cli import sdcal2old_cli as sdcal2old from sdcoaddold_cli import sdcoaddold_cli as sdcoaddold from sdfitold_cli import sdfitold_cli as sdfitold from sdflagold_cli import sdflagold_cli as sdflagold from sdflagmanagerold_cli import sdflagmanagerold_cli as sdflagmanagerold from sdgridold_cli import sdgridold_cli as sdgridold from sdlistold_cli import sdlistold_cli as sdlistold from sdmathold_cli import sdmathold_cli as sdmathold from sdplotold_cli import sdplotold_cli as sdplotold from sdreduceold_cli import sdreduceold_cli as sdreduceold from sdsaveold_cli import sdsaveold_cli as sdsaveold from sdscaleold_cli import sdscaleold_cli as sdscaleold from sdstatold_cli import sdstatold_cli as sdstatold myf['sd'] = sd myf['sdimaging'] = sdimaging myf['sdfixscan'] = sdfixscan myf['sdaverageold'] = sdaverageold myf['sdbaselineold'] = sdbaselineold myf['sdbaseline2old'] = sdbaseline2old myf['sdcalold'] = sdcalold myf['sdcal2old'] = sdcal2old myf['sdcoaddold'] = sdcoaddold myf['sdfitold'] = sdfitold myf['sdflagold'] = sdflagold myf['sdflagmanagerold'] = sdflagmanagerold myf['sdgridold'] = sdgridold myf['sdlistold'] = sdlistold myf['sdmathold'] = sdmathold myf['sdplotold'] = sdplotold myf['sdreduceold'] = sdreduceold myf['sdsaveold'] = sdsaveold myf['sdscaleold'] = sdscaleold myf['sdstatold'] = sdstatold
def asap_init(): """ Initialize ASAP....: """ myf=stack_frame_find( ) casapath=os.environ['CASAPATH'] print('*** Loading ATNF ASAP Package...') import asap as sd #print('*** ... ASAP (%s rev#%s) import complete ***' % (sd.__version__,sd.__revision__)) print('*** ... ASAP (rev#%s) import complete ***' % (sd.__revision__)) os.environ['CASAPATH']=casapath from sdimaging_cli import sdimaging_cli as sdimaging from sdimprocess_cli import sdimprocess_cli as sdimprocess from sdaverageold_cli import sdaverageold_cli as sdaverageold from sdbaselineold_cli import sdbaselineold_cli as sdbaselineold from sdbaseline2old_cli import sdbaseline2old_cli as sdbaseline2old from sdcalold_cli import sdcalold_cli as sdcalold from sdcal2old_cli import sdcal2old_cli as sdcal2old from sdcoaddold_cli import sdcoaddold_cli as sdcoaddold from sdfitold_cli import sdfitold_cli as sdfitold from sdflagold_cli import sdflagold_cli as sdflagold from sdflagmanagerold_cli import sdflagmanagerold_cli as sdflagmanagerold from sdgridold_cli import sdgridold_cli as sdgridold from sdlistold_cli import sdlistold_cli as sdlistold from sdmathold_cli import sdmathold_cli as sdmathold from sdplotold_cli import sdplotold_cli as sdplotold from sdreduceold_cli import sdreduceold_cli as sdreduceold from sdsaveold_cli import sdsaveold_cli as sdsaveold from sdscaleold_cli import sdscaleold_cli as sdscaleold from sdstatold_cli import sdstatold_cli as sdstatold myf['sd']=sd myf['sdimaging']=sdimaging myf['sdimprocess']=sdimprocess myf['sdaverageold']=sdaverageold myf['sdbaselineold']=sdbaselineold myf['sdbaseline2old']=sdbaseline2old myf['sdcalold']=sdcalold myf['sdcal2old']=sdcal2old myf['sdcoaddold']=sdcoaddold myf['sdfitold']=sdfitold myf['sdflagold']=sdflagold myf['sdflagmanagerold']=sdflagmanagerold myf['sdgridold']=sdgridold myf['sdlistold']=sdlistold myf['sdmathold']=sdmathold myf['sdplotold']=sdplotold myf['sdreduceold']=sdreduceold myf['sdsaveold']=sdsaveold myf['sdscaleold']=sdscaleold myf['sdstatold']=sdstatold
def go(taskname=None): """ Execute taskname: """ myf=stack_frame_find( ) if taskname==None: taskname=myf['taskname'] oldtaskname=taskname if(myf.has_key('taskname')): oldtaskname=myf['taskname'] #myf['taskname']=taskname if type(taskname)!=str: taskname=taskname.__name__ myf['taskname']=taskname try: parameter_checktype(['taskname'],[taskname],str) except TypeError, e: print "go -- TypeError: ",e return
def paramgui(self, useGlobals=True, ipython_globals=None): """ Opens a parameter GUI for this task. If useGlobals is true, then any relevant global parameter settings are used. """ import paramgui if not hasattr(self, "__globals__") or self.__globals__ == None: self.__globals__ = stack_frame_find() if useGlobals: if ipython_globals == None: myf = self.__globals__ else: myf = ipython_globals paramgui.setGlobals(myf) else: paramgui.setGlobals({}) paramgui.runTask('polconvert', myf['_ip']) paramgui.setGlobals({})
def filecatalog(): """ Open the File Catalog GUI: """ myf=stack_frame_find( ) myf['__last_task']='filecatalog' ### #Handle globals or user over-ride of arguments #Python script if (os.uname()[0]=='Darwin'): from Carbon.Launch import LSFindApplicationForInfo from Carbon.CoreFoundation import kCFURLPOSIXPathStyle kLSUnknownCreator = '\x00\x00\x00\x00' fsRef, cfURL = LSFindApplicationForInfo(kLSUnknownCreator, None, "casafilecatalog.app") filecatalog_path = os.path.join(fsRef.as_pathname(), 'Contents', 'MacOS', 'casafilecatalog') fcpid=os.spawnvp(os.P_NOWAIT, filecatalog_path, [filecatalog_path]) #logpid=os.system('open -a casalogger.app casa.log') elif (os.uname()[0]=='Linux'): fcpid=os.spawnlp(os.P_NOWAIT,'casafilecatalog','casafilecatalog') else: print 'Unrecognized OS: No filecatalog available' myf['fcpid']=fcpid
def importvla(archivefiles, vis, bandname, frequencytol, project, starttime, stoptime, applytsys, autocorr, antnamescheme, keepblanks, evlabands): i = 0 overwrite = True ok = True try: casalog.origin('importvla') if ((type(vis) != str) | (vis == '') | (os.path.exists(vis))): raise Exception, 'Need valid visibility file name (bad name or already exists)' if (os.path.exists(vis)): raise Exception, 'Visibility file already exists - remove or rename' for archivefile in archivefiles: if i > 0: overwrite = False myf = stack_frame_find() vftask = myf['vftask'] vlafiller = vftask.fill if ((type(archivefile) == str) & (os.path.exists(archivefile))): vlafiller(msname=vis, inputfile=archivefile, overwrite=overwrite, bandname=bandname, freqtol=frequencytol, project=project, start=starttime, stop=stoptime, applytsys=applytsys, keepautocorr=autocorr, antnamescheme=antnamescheme, keepblanks=keepblanks, evlabands=evlabands) i += 1 else: raise Exception, 'Archive file not found - please verify the name' except Exception, instance: print '*** Error importing %s to %s:' % (archivefiles, vis) raise Exception, instance
def pointcal_defaults(param=None): myf=stack_frame_find( ) a=odict() a['vis']='' a['model']='' a['caltable']='' a['field']='' a['spw']='' a['selectdata']={1:{'value':False}, 0:odict([{'value':True}, {'timerange':''}, {'uvrange':''}, {'antenna':''}, {'scan':''}, {'msselect':''}]) } a['solint']=0.0 if(param == None): myf['__set_default_parameters'](a) elif(param == 'paramkeys'): return a.keys() else: if(a.has_key(param)): return a[param]
def pointcal(vis=None,model=None,caltable=None, field=None,spw=None, selectdata=None,timerange=None,uvrange=None,antenna=None,scan=None,msselect=None, solint=None): """Solve for pointing error calibration: This program is under development. Please do not use. Keyword arguments: vis -- Name of input visibility file (MS) default: <unset>; example: vis='ngc5921.ms' model -- Name of input model (component list or image) default: <unset>; example: model='ngc5921.im' caltable -- Name of output Pointing calibration table default: <unset>; example: caltable='ngc5921.gcal' --- Data Selection (see help par.selectdata for more detailed information) field -- Select field using field id(s) or field name(s). [run listobs to obtain the list id's or names] default: ''=all fields If field string is a non-negative integer, it is assumed a field index otherwise, it is assumed a field name field='0~2'; field ids 0,1,2 field='0,4,5~7'; field ids 0,4,5,6,7 field='3C286,3C295'; field named 3C286 adn 3C295 field = '3,4C*'; field id 3, all names starting with 4C spw -- Select spectral window/channels default: ''=all spectral windows and channels spw='0~2,4'; spectral windows 0,1,2,4 (all channels) spw='<2'; spectral windows less than 2 (i.e. 0,1) spw='0:5~61'; spw 0, channels 5 to 61 spw='0,10,3:3~45'; spw 0,10 all channels, spw 3, channels 3 to 45. spw='0~2:2~6'; spw 0,1,2 with channels 2 through 6 in each. spw='0:0~10;15~60'; spectral window 0 with channels 0-10,15-60 spw='0:0~10,1:20~30,2:1;2;3'; spw 0, channels 0-10, spw 1, channels 20-30, and spw 2, channels, 1,2 and 3 selectdata -- Other data selection parameters default: True timerange -- Select data based on time range: default = '' (all); examples, timerange = 'YYYY/MM/DD/hh:mm:ss~YYYY/MM/DD/hh:mm:ss' Note: if YYYY/MM/DD is missing dat defaults to first day in data set timerange='09:14:0~09:54:0' picks 40 min on first day timerange= '25:00:00~27:30:00' picks 1 hr to 3 hr 30min on next day timerange='09:44:00' data within one integration of time timerange='>10:24:00' data after this time uvrange -- Select data within uvrange (default units kilo-lambda) default: '' (all); example: uvrange='0~1000'; uvrange from 0-1000 kilo-lamgda uvrange='>4';uvranges greater than 4 kilo lambda antenna -- Select data based on antenna/baseline default: '' (all) If antenna string is a non-negative integer, it is assumed an antenna index otherwise, it is assumed as an antenna name antenna='5&6'; baseline between antenna index 5 and index 6. antenna='VA05&VA06'; baseline between VLA antenna 5 and 6. antenna='5&6;7&8'; baseline 5-6 and 7-8 antenna='5'; all baselines with antenna 5 antenna='5,6,10'; all baselines with antennas 5 and 6 scan -- Scan number range - New, under developement msselect -- Optional complex data selection (ignore for now) solint -- Solution interval (sec) default: 0.0 (scan based); example: solint=60. """ myf=stack_frame_find( ) myf['taskname']='pointcal' ###fill unfilled parameters with defaults myf['update_params'](func=myf['taskname'], printtext=False) ####local params cb = myf['cb'] selectantenna=myf['selectantenna'] ### #Handle globals or user over-ride of arguments # function_signature_defaults=dict(zip(pointcal.func_code.co_varnames,pointcal.func_defaults)) for item in function_signature_defaults.iteritems(): key,val = item keyVal = eval(key) if (keyVal == None): #user hasn't set it - use global/default pass else: myf[key]=keyVal #user has set it - use over-ride vis=myf['vis'] model=myf['model'] caltable=myf['caltable'] field=myf['field'] spw=myf['spw'] selectdata=myf['selectdata'] if (selectdata): timerange=myf['timerange'] uvrange=myf['uvrange'] antenna=myf['antenna'] scan=myf['scan'] msselect=myf['msselect'] else: timerange='' uvrange='' antenna='' scan='' msselect='' solint=myf['solint'] #Add type/menu/range error checking here arg_names=['vis','model','caltable', 'field','spw', 'selectdata','timerange','uvrange','antenna','scan','msselect', 'solint'] arg_values=[vis,model,caltable, field,spw, selectdata,timerange,uvrange,antenna,scan,msselect, solint] arg_types=[str,str,str, str,str, bool,str,str,str,str,str, float] try: parameter_checktype(arg_names,arg_values,arg_types) except TypeError, e: print "pointcal -- TypeError: ", e return
def update_params(func, printtext=True, ipython_globals=None): from odict import odict if ipython_globals == None: myf=stack_frame_find( ) else: myf=ipython_globals ### set task to the one being called myf['taskname']=func obj=myf[func] if ( str(type(obj)) == "<type 'instance'>" and hasattr(obj,"check_params") ): hascheck = True else: hascheck = False noerror=True ###check if task has defined a task_check_params function if (hascheck): has_othertasks = myf.has_key('task_location') if(has_othertasks) : has_task = myf['task_location'].has_key(myf['taskname']) if (has_task) : pathname=myf['task_location'][myf['taskname']] else : pathname = os.environ.get('CASAPATH').split()[0]+'/'+os.environ.get('CASAPATH').split()[1]+'/xml' if not os.path.exists(pathname) : pathname = os.environ.get('CASAPATH').split()[0]+'/xml' if not os.path.exists(pathname) : pathname = os.environ.get('CASAPATH').split()[0]+'/Resources/xml' else : pathname = os.environ.get('CASAPATH').split()[0]+'/'+os.environ.get('CASAPATH').split()[1]+'/xml' if not os.path.exists(pathname) : pathname = os.environ.get('CASAPATH').split()[0]+'/xml' if not os.path.exists(pathname) : pathname = os.environ.get('CASAPATH').split()[0]+'/Resources/xml' if not os.path.exists(pathname) : sys.exit("ERROR: casapy.py update_params() can not locate xml file for task %s" % (taskname)) xmlfile=pathname+'/'+myf['taskname']+'.xml' if(os.path.exists(xmlfile)) : cu.setconstraints('file://'+xmlfile); else: # # SRankin: quick fix for CAS-5381 - needs review. # The task is not a CASA internal task. Extract the path from task_location. # This may not be robust. I have not tracked down all the code that could update task_location. task_path=task_location[taskname] xmlfile=task_path+'/'+myf['taskname']+'.xml' if(os.path.exists(xmlfile)) : cu.setconstraints('file://'+xmlfile); a=myf[myf['taskname']].defaults("paramkeys",myf) itsdef=myf[myf['taskname']].defaults itsparams=myf[myf['taskname']].parameters params=a #print 'itsparams:', itsparams for k in range(len(params)): paramval = obj.defaults(params[k], myf) notdict=True ###if a dictionary with key 0, 1 etc then need to peel-open ###parameters if(type(paramval)==dict): if(paramval.has_key(0)): notdict=False if(myf.has_key(params[k])): itsparams.update({params[k]:myf[params[k]]}) else: itsparams.update({params[k]:obj.itsdefault(params[k])}) if (notdict ): if(not myf.has_key(params[k])): myf.update({params[k]:paramval}) itsparams.update({params[k]:paramval}) if(printtext): #print 'params:', params[k], '; myf[params]:', myf[params[k]] if(hascheck): noerror = obj.check_params(params[k],myf[params[k]],myf) # RI this doesn't work with numpy arrays anymore. Noone seems # interested, so I'll be the red hen and try to fix it. #print 'params:', params[k], '; noerror:', noerror, '; myf[params]:', myf[params[k]] myfparamsk=myf[params[k]] if(type(myf[params[k]])==np.ndarray): myfparamsk=myfparamsk.tolist() #if(myf[params[k]]==paramval): if(myfparamsk==paramval): print_params_col(params[k],myf[params[k]],obj.description(params[k]), 'ndpdef', 'black',noerror) else: print_params_col(params[k],myf[params[k]],obj.description(params[k]), 'ndpnondef', 'black', noerror) itsparams[params[k]] = myf[params[k]] else: subdict=odict(paramval) ##printtext is False....called most probably to set ##undefined params..no harm in doing it anyways if(not printtext): ##locate which dictionary is user selected userdict={} subkeyupdated={} for somekey in paramval: somedict=dict(paramval[somekey]) subkeyupdated.update(dict.fromkeys(somedict, False)) if(somedict.has_key('value') and myf.has_key(params[k])): if(somedict['value']==myf[params[k]]): userdict=somedict elif(somedict.has_key('notvalue') and myf.has_key(params[k])): if(somedict['notvalue']!=myf[params[k]]): userdict=somedict ###The behaviour is to use the task.defaults ### for all non set parameters and parameters that ### have no meaning for this selection for j in range(len(subdict)): subkey=subdict[j].keys() for kk in range(len(subkey)): if( (subkey[kk] != 'value') & (subkey[kk] != 'notvalue') ): #if user selecteddict #does not have the key ##put default if(userdict.has_key(subkey[kk])): if(myf.has_key(subkey[kk])): itsparams.update({subkey[kk]:myf[subkey[kk]]}) else: itsparams.update({subkey[kk]:userdict[subkey[kk]]}) subkeyupdated[subkey[kk]]=True elif((not subkeyupdated[subkey[kk]])): itsparams.update({subkey[kk]:itsdef(params[k], None, itsparams[params[k]], subkey[kk])}) subkeyupdated[subkey[kk]]=True ### need to do default when user has not set val if(not myf.has_key(params[k])): if(paramval[0].has_key('notvalue')): itsparams.update({params[k]:paramval[0]['notvalue']}) myf.update({params[k]:paramval[0]['notvalue']}) else: itsparams.update({params[k]:paramval[0]['value']}) myf.update({params[k]:paramval[0]['value']}) userval=myf[params[k]] choice=0 notchoice=-1 valuekey='value' for j in range(len(subdict)): if(subdict[j].has_key('notvalue')): valuekey='notvalue' if(subdict[j]['notvalue'] != userval): notchoice=j; break else: if(subdict[j]['value']==userval): choice=j notchoice=j break subkey=subdict[choice].keys() if(hascheck): noerror=obj.check_params(params[k],userval,myf) if(printtext): if(myf[params[k]]==paramval[0][valuekey]): print_params_col(params[k],myf[params[k]],obj.description(params[k]),'dpdef','black', noerror) else: print_params_col(params[k],myf[params[k]],obj.description(params[k]),'dpnondef','black', noerror) itsparams[params[k]] = myf[params[k]] for j in range(len(subkey)): if((subkey[j] != valuekey) & (notchoice > -1)): ###put default if not there if(not myf.has_key(subkey[j])): myf.update({subkey[j]:subdict[choice][subkey[j]]}) paramval=subdict[choice][subkey[j]] if (j==(len(subkey)-1)): # last subparameter - need to add an extra line to allow cut/pasting comment='last' else: comment='blue' if(hascheck): noerror = obj.check_params(subkey[j],myf[subkey[j]],myf) if(printtext): if(myf[subkey[j]]==paramval): print_params_col(subkey[j],myf[subkey[j]],obj.description(subkey[j],userval),'spdef',comment, noerror) else: print_params_col(subkey[j],myf[subkey[j]],obj.description(subkey[j],userval),'spnondef',comment, noerror) itsparams[params[k]] = myf[params[k]]
def defaults(self, param=None, ipython_globals=None, paramvalue=None, subparam=None): if not hasattr(self, "__globals__") or self.__globals__ == None: self.__globals__ = stack_frame_find() if ipython_globals == None: myf = self.__globals__ else: myf = ipython_globals a = odict() a['IDI'] = '' a['OUTPUTIDI'] = '' a['DiFXinput'] = '' a['DiFXcalc'] = '' a['doIF'] = [] a['linAntIdx'] = [1] a['Range'] = [] a['ALMAant'] = '' a['spw'] = -1 a['calAPP'] = '' a['calAPPTime'] = [0., 5.] a['APPrefant'] = '' a['gains'] = [["NONE"]] a['interpolation'] = [] a['gainmode'] = [] a['XYavgTime'] = 0.0 a['dterms'] = ["NONE"] a['amp_norm'] = 0.01 a['XYadd'] = {} a['XYdel'] = {} a['XYratio'] = {} a['usePcal'] = [] a['swapXY'] = [False] a['swapRL'] = True a['feedRotation'] = [] a['correctParangle'] = False a['IDI_conjugated'] = False a['plotIF'] = -1 a['plotRange'] = [] a['plotAnt'] = -1 a['excludeAnts'] = [] a['excludeBaselines'] = [] a['doSolve'] = -1 a['solint'] = [1, 1] a['doTest'] = True a['npix'] = 50 a['solveAmp'] = True a['solveMethod'] = 'gradient' a['calstokes'] = [1., 0., 0., 0.] a['calfield'] = -1 ### This function sets the default values but also will return the list of ### parameters or the default value of a given parameter if (param == None): myf['__set_default_parameters'](a) elif (param == 'paramkeys'): return a.keys() else: if (paramvalue == None and subparam == None): if (a.has_key(param)): return a[param] else: return self.itsdefault(param) else: retval = a[param] if (type(a[param]) == dict): for k in range(len(a[param])): valornotval = 'value' if (a[param][k].has_key('notvalue')): valornotval = 'notvalue' if ((a[param][k][valornotval]) == paramvalue): retval = a[param][k].copy() retval.pop(valornotval) if (subparam != None): if (retval.has_key(subparam)): retval = retval[subparam] else: retval = self.itsdefault(subparam) else: retval = self.itsdefault(subparam) return retval
def saveinputs(taskname=None, outfile='', myparams=None, ipython_globals=None, scriptstr=['']): #parameter_printvalues(arg_names,arg_values,arg_types) """ Save current input values to file on disk for a specified task: taskname -- Name of task default: <unset>; example: taskname='bandpass' <Options: type tasklist() for the complete list> outfile -- Output file for the task inputs default: taskname.saved; example: outfile=taskname.orion """ try: if ipython_globals == None: myf=stack_frame_find( ) else: myf=ipython_globals if taskname==None: taskname=myf['taskname'] myf['taskname']=taskname if type(taskname)!=str: taskname=taskname.__name__ myf['taskname']=taskname parameter_checktype(['taskname','outfile'],[taskname,outfile],[str,str]) ###Check if task exists by checking if task_defaults is defined obj = False if ( not myf.has_key(taskname) and str(type(myf[taskname])) != "<type 'instance'>" and not hasattr(myf[taskname],"defaults") ): raise TypeError, "task %s is not defined " %taskname else: obj = myf[taskname] if taskname==None: taskname=myf['taskname'] myf['taskname']=taskname if outfile=='': outfile=taskname+'.saved' if(myf.has_key('__multibackup') and myf['__multibackup']): backupoldfile(outfile) ##make sure unfolded parameters get their default values myf['update_params'](func=myf['taskname'], printtext=False, ipython_globals=myf) ### do_save_inputs = False outpathdir = os.path.realpath(os.path.dirname(outfile)) outpathfile = outpathdir + os.path.sep + os.path.basename(outfile) if outpathfile not in casa['state']['unwritable'] and outpathdir not in casa['state']['unwritable']: try: taskparameterfile=open(outfile,'w') print >>taskparameterfile, '%-15s = "%s"'%('taskname', taskname) do_save_inputs = True except: print "********************************************************************************" print "Warning: no write permission for %s, cannot save task" % outfile if os.path.isfile(outfile): print " inputs in %s..." % outpathfile casa['state']['unwritable'].add(outpathfile) elif not os.path.isdir(outfile): print " inputs in dir %s..." % outpathdir casa['state']['unwritable'].add(outpathdir) else: print " inputs because given file (%s) is a dir..." % outpathfile print "********************************************************************************" f=zip(myf[taskname].__call__.func_code.co_varnames[1:],myf[taskname].__call__.func_defaults) scriptstring='#'+str(taskname)+'(' if myparams == None : myparams = {} l=0 for j in range(len(f)): k=f[j][0] if not myparams.has_key(k) and k != 'self' : myparams[k] = myf[taskname].parameters[k] if(k != 'self' and type(myparams[k])==str): if ( myparams[k].count( '"' ) < 1 ): # if the string doesn't contain double quotes then # use double quotes around it in the parameter file. if do_save_inputs: print >>taskparameterfile, '%-15s = "%s"'%(k, myparams[k]) scriptstring=scriptstring+k+'="'+myparams[k]+'",' else: # use single quotes. if do_save_inputs: print >>taskparameterfile, "%-15s = '%s'"%(k, myparams[k]) scriptstring=scriptstring+k+"='"+myparams[k]+"'," else : if ( j != 0 or k != "self" or str(type(myf[taskname])) != "<type 'instance'>" ) : if do_save_inputs: print >>taskparameterfile, '%-15s = %s'%(k, myparams[k]) scriptstring=scriptstring+k+'='+str(myparams[k])+',' ###Now delete varianle from global user space because ###the following applies: "It would be nice if one ### could tell the system to NOT recall ### previous non-default settings sometimes." if(not myf['casaglobals'] and myf.has_key(k)): del myf[k] l=l+1 if l%5==0: scriptstring=scriptstring+'\n ' scriptstring=scriptstring.rstrip() scriptstring=scriptstring.rstrip('\n') scriptstring=scriptstring.rstrip(',') scriptstring=scriptstring+')' scriptstr.append(scriptstring) scriptstring=scriptstring.replace(' ', '') scriptstring=scriptstring.replace('\n', '') if do_save_inputs: print >>taskparameterfile,scriptstring taskparameterfile.close() except TypeError, e: print "saveinputs --error: ", e
def importarchive( archivefiles=None, vis=None, bandname=None, freqtol=None, ): """Convert VLA archive file(s) to a CASA visibility data set (MS): ....Keyword arguments: ....archivefiles -- Name of input VLA archive file(s) ........default: <unset> ........example: archivefiles=['AP314_A950519.xp1','AP314_A950519.xp2'] ....vis -- Name of output visibility file (MS) ........default: <unset>; example: vis='NGC7538.ms' ....bandname -- VLA Frequency band ........default: <unset> - all bands; example: bandname='K' ........<Options: '4'=48-96 MHz,'P'=298-345 MHz,'L'=1.15-1.75 GHz, ........'C'=4.2-5.1 GHz,'X'=6.8-9.6 GHz,'U'=13.5-16.3 GHz, ........'K'=20.8-25.8 GHz,'Q'=38-51 GHz> ....#projectname -- Observing project name ....#....default: <unset>; example='AP314' ....freqtol -- Tolerance in frequency shift in naming spectral windows ........default: channel width of current spectral window in Hz ........example: 150000.0 .... ....""" myf = stack_frame_find( ) vftask = myf['vftask'] vlafiller = vftask.fill # fg = myf['fg'] aflocal = casac.agentflagger() # ## # Handle globals or user over-ride of arguments function_signature_defaults = \ dict(zip(importarchive.func_code.co_varnames, importarchive.func_defaults)) for item in function_signature_defaults.iteritems(): (key, val) = item keyVal = eval(key) if keyVal == None: # user hasn't set it - use global/default pass else: # user has set it - use over-ride myf[key] = keyVal archivefiles = myf['archivefiles'] vis = myf['vis'] bandname = myf['bandname'] freqtol = myf['freqtol'] # # ## # Add type/menu/range error checking here if type(archivefiles) == str: archivefiles = [archivefiles] arg_names = ['archivefiles', 'vis', 'bandname', 'freqtol'] arg_values = [archivefiles, vis, bandname, freqtol] arg_types = [list, str, str, float] try: parameter_checktype(arg_names, arg_values, arg_types) parameter_checkmenu('bandname', bandname, [ '4', 'P', 'L', 'C', 'X', 'U', 'K', 'Q', ]) except TypeError, e: print 'importarchive -- TypeError: ', e return
def __call__( self, raster=None, contour=None, zoom=None, axes=None, out=None ): """ Old parameters: infile=None,displaytype=None,channel=None,zoom=None,outfile=None, outscale=None,outdpi=None,outformat=None,outlandscape=None,gui=None The imview task will display images in raster, contour, vector or marker form. Images can be blinked, and movies are available for spectral-line image cubes. For measurement sets, many display and editing options are available. examples of usage: imview imview "myimage.im" imview "myrestorefile.rstr" imview "myimage.im", "contour" imview "'myimage1.im' - 2 * 'myimage2.im'", "lel" Executing imview( ) will bring up a display panel window, which can be resized. If no data file was specified, a Load Data window will also appear. Click on the desired data file and choose the display type; the rendered data should appear on the display panel. A Data Display Options window will also appear. It has drop-down subsections for related options, most of which are self-explanatory. The state of the imview task -- loaded data and related display options -- can be saved in a 'restore' file for later use. You can provide the restore filename on the command line or select it from the Load Data window. See the cookbook for more details on using the imview task. Keyword arguments: infile -- Name of file to visualize default: '' example: infile='ngc5921.image' If no infile is specified the Load Data window will appear for selecting data. displaytype -- (optional): method of rendering data visually (raster, contour, vector or marker). You can also set this parameter to 'lel' and provide an lel expression for infile (advanced). default: 'raster' example: displaytype='contour' Note: the filetype parameter is optional; typing of data files is now inferred. example: imview infile='my.im' implies: imview infile='my.im', filetype='raster' the filetype is still used to load contours, etc. """ myf=stack_frame_find( ) vi = myf['vi'] if myf.has_key('vi') else None ving = myf['ving'] if myf.has_key('ving') else None casalog.origin('imview') if (type(out) == str and len(out) != 0) or \ (type(out) == dict and len(out) != 0) : gui = False (out_file, out_format, out_scale, out_dpi, out_orientation) = self.__extract_outputinfo( out ) else: gui = True if gui and self.local_vi is None or \ not gui and self.local_ving is None: try: ## vi/ving might not be defined in taskinit if ## loading directly from python via casa.py... vwr = vi if gui else ving if type(vwr) == type(None) or type(vwr.cwd( )) != str: vwr = viewertool.viewertool( gui, True, (type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == type(os)) ) except: vwr = None if gui: self.local_vi = vwr else: self.local_ving = vwr else: vwr = self.local_vi if gui else self.local_ving if type(vwr) == type(None): casalog.post( "failed to find a viewertool...", 'SEVERE') raise Exception, "failed to find a viewertool..." self.__pushd( vwr, os.path.abspath(os.curdir) ) if (raster is None or len(raster) == 0) and \ (contour is None or len(contour) == 0) : panel = self.__panel(vwr) else: panel = self.__load_files( "raster", vwr, None, raster ) panel = self.__load_files( "contour", vwr, panel, contour ) self.__set_axes( vwr, panel, axes ) self.__zoom( vwr, panel, zoom ) self.__process_colorwedges( vwr, panel ) #vwr.unfreeze( panel ) if not gui: vwr.output(out,scale=out_scale,dpi=out_dpi,format=out_format,orientation=out_orientation,panel=panel) vwr.close(panel) self.__popd( vwr ) return None
# # User defined tasks setup. # Generated from buildmytask. # import sys from casa_stack_manip import stack_frame_find if sys.path[1] != '/home/marti/WORKAREA/ARC_TOOLS/PolConvert/LaunchPad/trunk': sys.path.insert( 1, '/home/marti/WORKAREA/ARC_TOOLS/PolConvert/LaunchPad/trunk') from odict import odict if not globals().has_key('mytasks'): mytasks = odict() mytasks[ 'polconvert'] = '\n\nVersion 1.7.3\n\nConverts VLBI visibilities from mixed-polarization basis (i.e., linear-to-circular) into circular basis. Works with single VLBI stations as well as with phased arrays (i.e., phased ALMA).\n\n' if not globals().has_key('task_location'): task_location = odict() task_location[ 'polconvert'] = '/home/marti/WORKAREA/ARC_TOOLS/PolConvert/LaunchPad/trunk' myglobals = stack_frame_find() tasksum = myglobals['tasksum'] for key in mytasks.keys(): tasksum[key] = mytasks[key] from polconvert_cli import polconvert_cli as polconvert
def __launch( self ): ## if we've already launched the viewer if type(self.__state['launched']) == bool and self.__state['launched'] == True: return if dbus_connection( ) == None: raise Exception, "dbus is not available; cannot script the viewer" myf=stack_frame_find( ) self.__rgm = myf['casac'].regionmanager() viewer_path = None if type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == dict : if myf['casa'].has_key('helpers') \ and type(myf['casa']['helpers']) == dict and myf['casa']['helpers'].has_key('viewer'): viewer_path = myf['casa']['helpers']['viewer'] #### set in casapy.py if len(os.path.dirname(viewer_path)) == 0: for dir in os.getenv('PATH').split(':') : dd = dir + os.sep + viewer_path if os.path.exists(dd) and os.access(dd,os.X_OK) : viewer_path = dd break args = [ viewer_path, "--casapy" ] else: for exe in ['casaviewer']: for dir in os.getenv('PATH').split(':') : dd = dir + os.sep + exe if os.path.exists(dd) and os.access(dd,os.X_OK) : viewer_path = dd break if viewer_path is not None: break args = [ viewer_path ] if myf['casa'].has_key('state') and myf['casa']['state'].has_key('init_version'): if myf['casa']['state']['init_version'] <= 0: args += [ '--daemon' ] else: args += [ '--daemon' ] if viewer_path == None or not os.access(viewer_path,os.X_OK): raise RuntimeError("cannot find casa viewer executable") if self.__state['gui']: args += [ '--server=' + self.__state['dbus name'] ] else: args += [ '--nogui=' + self.__state['dbus name'] ] if type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == dict and myf['casa'].has_key('files') \ and type(myf['casa']['files']) == dict and myf['casa']['files'].has_key('logfile'): args += [ '--casalogfile=' + myf['casa']['files']['logfile'] ] if type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == dict and myf['casa'].has_key('flags') \ and type(myf['casa']['flags']) == dict and myf['casa']['flags'].has_key('--rcdir'): args += [ "--rcdir=" + myf['casa']['flags']['--rcdir'] ] if (os.uname()[0]=='Darwin'): if myf['casa']['state']['init_version'] > 0: from casa_system import procmgr procmgr.create(self.__state['dbus name'],args) else: vwrpid=os.spawnvp( os.P_NOWAIT, viewer_path, args ) elif (os.uname()[0]=='Linux'): if myf['casa']['state']['init_version'] > 0: from casa_system import procmgr procmgr.create(self.__state['dbus name'],args) else: vwrpid=os.spawnlp( os.P_NOWAIT, viewer_path, *args ) else: raise Exception,'unrecognized operating system' self.__state['launched'] = True
import string import inspect import sys import os import shutil from casa_stack_manip import stack_frame_find myf=stack_frame_find( ) casalog=myf['casalog'] # # Utils # def note(message, priority="INFO", origin="regression_utility", ntime=None, postcli='F'): #if not ntime: #if (ntime==None): # ntime=time.asctime() #print ntime, priority, origin, message if postcli: print message casalog.postLocally(message, priority, origin) ### def info(message): #note(message,origin='regression_utility') #print message casalog.postLocally(message, priority="INFO", origin="regression_utility") def fail(message=""): casalog.postLocally(message, priority="SEVERE", origin='regression_utility') #print message raise RuntimeError, message ###
def __call__(self, infile=None,displaytype=None,channel=None,zoom=None,outfile=None,outscale=None,outdpi=None,outformat=None,outlandscape=None,gui=None): """ The viewer will display images in raster, contour, vector or marker form. Images can be blinked, and movies are available for spectral-line image cubes. For measurement sets, many display and editing options are available. examples of usage: viewer viewer "myimage.im" viewer "mymeasurementset.ms" viewer "myrestorefile.rstr" viewer "myimage.im", "contour" viewer "'myimage1.im' - 2 * 'myimage2.im'", "lel" The viewer can be run outside of casapy by typing <casaviewer>. Executing viewer <viewer> will bring up a display panel window, which can be resized. If no data file was specified, a Load Data window will also appear. Click on the desired data file and choose the display type; the rendered data should appear on the display panel. A Data Display Options window will also appear. It has drop-down subsections for related options, most of which are self-explanatory. The state of the viewer -- loaded data and related display options -- can be saved in a 'restore' file for later use. You can provide the restore filename on the command line or select it from the Load Data window. See the cookbook for more details on using the viewer. Keyword arguments: infile -- Name of file to visualize default: '' example: infile='ngc5921.image' If no infile is specified the Load Data window will appear for selecting data. displaytype -- (optional): method of rendering data visually (raster, contour, vector or marker). You can also set this parameter to 'lel' and provide an lel expression for infile (advanced). default: 'raster' example: displaytype='contour' Note: there is no longer a filetype parameter; typing of data files is now done automatically. example: viewer infile='my.ms' obsolete: viewer infile='my.ms', filetype='ms' """ myf=stack_frame_find( ) vi = myf['vi'] if myf.has_key('vi') else None ving = myf['ving'] if myf.has_key('ving') else None #Python script try: vwr = vi if type(gui) == bool and gui == False: vwr = ving if type(vwr.cwd( )) != str: vwr = None except: vwr = None if type(vwr) == type(None): need_gui = True if type(gui) == bool and gui == False: need_gui = False if need_gui : if self.local_vi is not None: vwr = self.local_vi else: vwr = viewertool.viewertool( True, True, (type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == type(os)) ) self.local_vi = vwr else: if self.local_ving is not None: vwr = self.local_ving else: vwr = viewertool.viewertool( False, True, (type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == type(os)) ) self.local_ving = vwr if type(vwr) != type(None) : ## ## (1) save current *viewer*server* path ## (2) have viewer() task follow casapy/python's cwd try: old_path = vwr.cwd( ) except: raise Exception, "viewer() failed to get the current working directory [" + str(sys.exc_info()[0]) + ": " + str(sys.exc_info()[1]) + "]" try: vwr.cwd(os.path.abspath(os.curdir)) except: raise Exception, "viewer() failed to change to the new working directory (" + os.path.abspath(os.curdir) + ") [" + str(sys.exc_info()[0]) + ": " + str(sys.exc_info()[1]) + "]" panel = vwr.panel("viewer") data = None if type(infile) == str and len(infile) > 0 : if type(displaytype) == str: data = vwr.load( infile, displaytype, panel=panel ) else: data = vwr.load( infile, panel=panel ) if type(channel) == int and channel > 0 : vwr.channel(channel,panel=panel) if type(zoom) == int and zoom != 1 : vwr.zoom(zoom,panel=panel) if type(outfile) == str and len(outfile) > 0 : scale=1.0 if type(outscale) == float : scale=outscale dpi=300 if type(outdpi) == int : dpi=outdpi format="jpg" if type(outformat) == str : format=outformat orientation="portrait" if type(outlandscape) == bool and outlandscape : orientation="landscape" vwr.output(outfile,scale=scale,dpi=dpi,format=format,orientation=orientation,panel=panel) else: vwr.popup( 'open', panel=panel ) # it makes no sense to leave a panel open with no way of interacting with it if type(gui) == bool and not gui: vwr.close(panel) ## (3) restore original path try: vwr.cwd(old_path) except: raise Exception, "viewer() failed to restore the old working directory (" + old_path + ") [" + str(sys.exc_info()[0]) + ": " + str(sys.exc_info()[1]) + "]" else: viewer_path = myf['casa']['helpers']['viewer'] #### set in casapy.py args = [ viewer_path ] if type(infile) == str: if type(displaytype) == str: args += [ infile, displaytype ] else: args += [ infile ] if (os.uname()[0]=='Darwin'): vwrpid=os.spawnvp( os.P_NOWAIT, viewer_path, args ) elif (os.uname()[0]=='Linux'): vwrpid=os.spawnlp( os.P_NOWAIT, viewer_path, *args ) else: print 'Unrecognized OS: No viewer available' return None
def pointcal(vis=None, model=None, caltable=None, field=None, spw=None, selectdata=None, timerange=None, uvrange=None, antenna=None, scan=None, msselect=None, solint=None): """Solve for pointing error calibration: This program is under development. Please do not use. Keyword arguments: vis -- Name of input visibility file (MS) default: <unset>; example: vis='ngc5921.ms' model -- Name of input model (component list or image) default: <unset>; example: model='ngc5921.im' caltable -- Name of output Pointing calibration table default: <unset>; example: caltable='ngc5921.gcal' --- Data Selection (see help par.selectdata for more detailed information) field -- Select field using field id(s) or field name(s). [run listobs to obtain the list id's or names] default: ''=all fields If field string is a non-negative integer, it is assumed a field index otherwise, it is assumed a field name field='0~2'; field ids 0,1,2 field='0,4,5~7'; field ids 0,4,5,6,7 field='3C286,3C295'; field named 3C286 adn 3C295 field = '3,4C*'; field id 3, all names starting with 4C spw -- Select spectral window/channels default: ''=all spectral windows and channels spw='0~2,4'; spectral windows 0,1,2,4 (all channels) spw='<2'; spectral windows less than 2 (i.e. 0,1) spw='0:5~61'; spw 0, channels 5 to 61 spw='0,10,3:3~45'; spw 0,10 all channels, spw 3, channels 3 to 45. spw='0~2:2~6'; spw 0,1,2 with channels 2 through 6 in each. spw='0:0~10;15~60'; spectral window 0 with channels 0-10,15-60 spw='0:0~10,1:20~30,2:1;2;3'; spw 0, channels 0-10, spw 1, channels 20-30, and spw 2, channels, 1,2 and 3 selectdata -- Other data selection parameters default: True timerange -- Select data based on time range: default = '' (all); examples, timerange = 'YYYY/MM/DD/hh:mm:ss~YYYY/MM/DD/hh:mm:ss' Note: if YYYY/MM/DD is missing dat defaults to first day in data set timerange='09:14:0~09:54:0' picks 40 min on first day timerange= '25:00:00~27:30:00' picks 1 hr to 3 hr 30min on next day timerange='09:44:00' data within one integration of time timerange='>10:24:00' data after this time uvrange -- Select data within uvrange (default units kilo-lambda) default: '' (all); example: uvrange='0~1000'; uvrange from 0-1000 kilo-lamgda uvrange='>4';uvranges greater than 4 kilo lambda antenna -- Select data based on antenna/baseline default: '' (all) If antenna string is a non-negative integer, it is assumed an antenna index otherwise, it is assumed as an antenna name antenna='5&6'; baseline between antenna index 5 and index 6. antenna='VA05&VA06'; baseline between VLA antenna 5 and 6. antenna='5&6;7&8'; baseline 5-6 and 7-8 antenna='5'; all baselines with antenna 5 antenna='5,6,10'; all baselines with antennas 5 and 6 scan -- Scan number range - New, under developement msselect -- Optional complex data selection (ignore for now) solint -- Solution interval (sec) default: 0.0 (scan based); example: solint=60. """ myf = stack_frame_find() myf['taskname'] = 'pointcal' ###fill unfilled parameters with defaults myf['update_params'](func=myf['taskname'], printtext=False) ####local params cb = myf['cb'] selectantenna = myf['selectantenna'] ### #Handle globals or user over-ride of arguments # function_signature_defaults = dict( zip(pointcal.func_code.co_varnames, pointcal.func_defaults)) for item in function_signature_defaults.iteritems(): key, val = item keyVal = eval(key) if (keyVal == None): #user hasn't set it - use global/default pass else: myf[key] = keyVal #user has set it - use over-ride vis = myf['vis'] model = myf['model'] caltable = myf['caltable'] field = myf['field'] spw = myf['spw'] selectdata = myf['selectdata'] if (selectdata): timerange = myf['timerange'] uvrange = myf['uvrange'] antenna = myf['antenna'] scan = myf['scan'] msselect = myf['msselect'] else: timerange = '' uvrange = '' antenna = '' scan = '' msselect = '' solint = myf['solint'] #Add type/menu/range error checking here arg_names = [ 'vis', 'model', 'caltable', 'field', 'spw', 'selectdata', 'timerange', 'uvrange', 'antenna', 'scan', 'msselect', 'solint' ] arg_values = [ vis, model, caltable, field, spw, selectdata, timerange, uvrange, antenna, scan, msselect, solint ] arg_types = [str, str, str, str, str, bool, str, str, str, str, str, float] try: parameter_checktype(arg_names, arg_values, arg_types) except TypeError, e: print "pointcal -- TypeError: ", e return
def csvclean(vis, imagename,field, spw, advise, mode, nchan, width, imsize, cell, phasecenter, niter, weighting, restoringbeam, interactive): """ This task does an invert of the visibilities and deconvolve in the image plane. It does not do a uvdata subtraction (aka Cotton-Schwab major cycle) of model visibility as in clean. - For ALMA Commissioning vis -- Name of input visibility file default: none; example: vis='ngc5921.ms' imagename -- Name of output CASA image. (only the prefix) default: none; example: imagename='m2' output images are: m2.image; cleaned and restored image With or without primary beam correction m2dirty.image; dirty image m2psf.image; point-spread function (dirty beam) m2.model; image of clean components m2.mask; image containing clean regions, when interative=True field -- Select fields in MS. Use field id(s) or field name(s). ['go listobs' to obtain the list id's or names] default: ''= all fields If field string is a non-negative integer, it is assumed to be a field index otherwise, it is assumed to be a field name field='0~2'; field ids 0,1,2 field='0,4,5~7'; field ids 0,4,5,6,7 field='3C286,3C295'; field named 3C286 and 3C295 field = '3,4C*'; field id 3, all names starting with 4C spw --Select spectral window/channels NOTE: This selects the data passed as the INPUT to mode default: ''=all spectral windows and channels spw='0~2,4'; spectral windows 0,1,2,4 (all channels) spw='0:5~61'; spw 0, channels 5 to 61 spw='<2'; spectral windows less than 2 (i.e. 0,1) spw='0,10,3:3~45'; spw 0,10 all channels, spw 3, channels 3 to 45. spw='0~2:2~6'; spw 0,1,2 with channels 2 through 6 in each. spw='0:0~10;15~60'; spectral window 0 with channels 0-10,15-60 spw='0:0~10,1:20~30,2:1;2;3'; spw 0, channels 0-10, spw 1, channels 20-30, and spw 2, channels, 1,2 and 3 imsize -- Image pixel size (x,y). DOES NOT HAVE TO BE A POWER OF 2 default = [256,256]; example: imsize=[350,350] imsize = 500 is equivalent to [500,500] Avoid odd-numbered imsize. cell -- Cell size (x,y) default= '1.0arcsec'; example: cell=['0.5arcsec,'0.5arcsec'] or cell=['1arcmin', '1arcmin'] cell = '1arcsec' is equivalent to ['1arcsec','1arcsec'] NOTE:cell = 2.0 => ['2arcsec', '2arcsec'] phasecenter -- direction measure or fieldid for the mosaic center default: '' => first field selected ; example: phasecenter=6 or phasecenter='J2000 19h30m00 -40d00m00' niter -- Maximum number iterations, if niter=0, then no CLEANing is done ("invert" only) default: 500; example: niter=5000 weighting -- Weighting to apply to visibilities: default='natural'; example: weighting='uniform'; Options: 'natural','uniform','briggs', 'superuniform','briggsabs','radial' restoringbeam -- Output Gaussian restoring beam for CLEAN image [bmaj, bmin, bpa] elliptical Gaussian restoring beam default units are in arc-seconds for bmaj,bmin, degrees for bpa default: restoringbeam=[]; Use PSF calculated from dirty beam. example: restoringbeam=['10arcsec'] or restorinbeam='10arcsec', circular Gaussian. FWHM 10 arcseconds example: restoringbeam=['10.0','5.0','45.0deg'] 10"x5" at 45 degrees interactive -- Create a mask interactively or not. default=False; example: interactive=True The viewer will open with the image displayed. Select the region for the mask and double click in the middle of it. """ #Python script try: casalog.origin('csvclean') ms = casac.ms() parsummary = 'vis="'+str(vis)+'", imagename="'+str(imagename)+'", ' parsummary += 'field="'+str(field)+'", spw="'+str(spw)+'", ' parsummary = 'cell="'+str(cell)+'",' parsummary = 'phasecenter='+str(phasecenter)+',' parsummary += 'imsize='+str(imsize)+', niter='+str(niter)+', ' parsummary += 'weighting="'+str(weighting)+'", ' parsummary += 'restoringbeam="'+str(restoringbeam)+'", ' parsummary += 'interactive='+str(interactive)+'' casalog.post(parsummary,'INFO') # if (not (type(vis)==str) & (os.path.exists(vis))): # raise Exception, 'Visibility data set not found - please verify the name' if ((type(vis)==str) & (os.path.exists(vis))): ms.open(vis) else: raise Exception, 'Visibility data set not found - please verify the name' if(not advise): if (imagename == ""): # ms.close() raise Exception, "Must provide output image name in parameter imagename." if os.path.exists(imagename): # ms.close() raise Exception, "Output image %s already exists - will not overwrite." % imagename if (field == ''): field = '*' if (spw == ''): spw = '*' if ((type(imsize)==int)): imsize=[imsize,imsize] if ((len(imsize)==1)): imsize=[imsize[0],imsize[0]] nx = imsize[0] ny = imsize[1] if ((type(cell)==int) | (type(cell)==float) | (type(cell)==str)): cell=[cell,cell] if ((len(cell)==1)): cell=[cell[0],cell[0]] cellx=cell[0] celly=cell[1] if((type(cell[0])==int) or (type(cell[0])==float)): cellx=qa.quantity(cell[0], 'arcsec') celly=qa.quantity(cell[1], 'arcsec') if(type(phasecenter)==str): ### blank means take field[0] if (phasecenter==''): fieldoo=field if(fieldoo==''): fieldoo='0' phasecenter=int(ms.msseltoindex(vis,field=fieldoo)['field'][0]) else: tmppc=phasecenter try: if(len(ms.msseltoindex(vis, field=phasecenter)['field']) > 0): tmppc = int(ms.msseltoindex(vis, field=phasecenter)['field'][0]) ##succesful must be string like '0' or 'NGC*' except Exception, instance: #failed must be a string type J2000 18h00m00 10d00m00 tmppc = phasecenter phasecenter = tmppc if restoringbeam == [''] or len(restoringbeam) == 0: # calculate from fit below bmaj = '' bmin = '' bpa = '' else: if (type(restoringbeam)==str): restoringbeam=[restoringbeam,restoringbeam,'0deg'] if (type(restoringbeam)==list and (len(restoringbeam)==1)): restoringbeam=[restoringbeam[0],restoringbeam[0],'0deg'] if (type(restoringbeam)==list and (len(restoringbeam)==2)): restoringbeam=[restoringbeam[0],restoringbeam[1],'0deg'] if (type(restoringbeam)==list and (len(restoringbeam)==2)): restoringbeam=[restoringbeam[0],restoringbeam[1],restoringbeam[2]] if(qa.quantity(restoringbeam[0])['unit'] == ''): restoringbeam[0]=restoringbeam[0]+'arcsec' if(qa.quantity(restoringbeam[1])['unit'] == ''): restoringbeam[1]=restoringbeam[1]+'arcsec' if(qa.quantity(restoringbeam[2])['unit'] == ''): restoringbeam[2]=restoringbeam[2]+'deg' bmaj = restoringbeam[0] bmin = restoringbeam[1] bpa = restoringbeam[2] # Create output names based on imagename parameter dirtyim = imagename+'dirty.image' psfim = imagename+'psf.image' modelname = imagename+'.model' imname = imagename+'.image' # Make sure all tables and images are closed # ms.close() # Add scratch columns if they don't exist #tb.open(vis) #hasit = tb.colnames().count('CORRECTED_DATA')>0 #tb.close() #if not hasit: # cb.open(vis) # cb.close() # make the dirty image and psf im.open(vis, usescratch=True) im.selectvis(spw=spw, field=field) spwsel=ms.msseltoindex(vis=vis, spw=spw)['spw'] ch=ms.msseltoindex(vis=vis, spw=spw)['channel'] if(nchan < 1): nchan=0 for k in range(len(spwsel)): nchan += ch[k,2]-ch[k,1]+1 nchan=nchan/width if(nchan < 1): nchan=1 if(advise): tb.open(vis+'/SPECTRAL_WINDOW') allreffreq=tb.getcol('REF_FREQUENCY') reffreq=0.0 if(len(allreffreq) > 1): reffreq=0.0; for f in allreffreq: reffreq+=f reffreq=reffreq/float(len(allreffreq)) else: reffreq=allreffreq[0] tb.done() tb.open(vis+'/ANTENNA') diams=tb.getcol('DISH_DIAMETER') diam=np.min(diams) tb.done() fov=qa.quantity(3.0e8/reffreq/diam, 'rad') adv=im.advise(fieldofview=fov) cellx=qa.tos(adv[2], prec=4) celly=cellx myf = stack_frame_find( ) myf['cell']=[cellx,cellx] myf['imsize']=[adv[1], adv[1]] nx=ny=adv[1] myf['advise']=False return redopsf=True redokounter=0 immode='mfs' start=ch[0,1] if(mode=='cube'): immode='channel' if(width >1): start=start+ width/2 while(redopsf): im.defineimage(nx=nx, ny=ny, cellx=cellx, celly=celly, phasecenter=phasecenter, spw=spwsel.tolist(), mode=immode, start=start, step=width, nchan=nchan) im.weight(weighting) try: im.makeimage(type='corrected', image=dirtyim) im.makeimage(type='psf', image=psfim) ###make an empty model im.make(modelname) if((redokounter==2) and (np.min(nx,ny) > 25)): #pdb.set_trace() ia.open(psfim) csys=ia.coordsys() rg.setcoordinates(csys=csys.torecord()) shp=ia.shape() blc=['10pix', '10pix', '0pix', '0pix'] trc=[str(shp[0]-10)+'pix',str(shp[1]-10)+'pix', str(shp[2]-1)+'pix', str(shp[3]-1)+'pix'] reg=rg.wbox(blc=blc, trc=trc) ia.set(pixels=0, region=rg.complement(reg)) ia.done() #im.done() # Calculate bpa, bmin, bmaj if not given if restoringbeam == [''] or len(restoringbeam) == 0: cx = nx/2 cy = ny/2 box = '' #if (nx > 100 and ny > 100): # rrg = [cx-10, cy-10, cx+10, cy+10] # box = '%s,%s,%s,%s'%(rrg[0],rrg[1],rrg[2],rrg[3]) #ia.open(psfim) #shp=ia.shape() #coords = ia.fitcomponents(box=box) #ia.close() #if(coords['converged'] == True): coords=im.fitpsf(psfim) if(coords[0]): bmaj=coords[1] bmin=coords[2] bpa=coords[3] redopsf=False else: redopsf=True nx=nx+1 ny=ny+1 redokounter += 1 if(redokounter==3): casalog.post('Failed to find a decent psf','SEVERE') return False else: casalog.post('Trying new image with 1 extra pixel','WARN') except : redopsf=True nx=nx+1 ny=ny+1 redokounter += 1 if(redokounter==3): casalog.post('Failed to find a decent psf','SEVERE') im.done() return False else: casalog.post('Trying new image with 1 extra pixel','WARN') im.done() parsummary = 'restoringbeam values = [\'%s\',\'%s\',\'%s\']'%(qa.tos(bmaj),qa.tos(bmin),qa.tos(bpa)) casalog.post(parsummary,'INFO') # Make a mask maskname='' if(interactive): maskname=imagename+'.mask' if(os.path.exists(maskname)): ia.open(dirtyim) csys=ia.coordsys() shp=ia.shape() ia.done() ia.open(maskname) ia.regrid(outfile='__tmpmask__', shape=shp, csys=csys.torecord(), axes=[0,1], asvelocity=False) ia.remove(True) ia.done() shutil.move('__tmpmask__', maskname) im.drawmask(dirtyim, maskname) # use deconvolver to do image plane deconvolution # using a mask image as the mask dc.open(dirty=dirtyim, psf=psfim) # NOTE: use the parameter mask which can be an empty # string if no mask dc.clean(niter=niter, model=modelname, mask=maskname) # create the restored image if restoringbeam == [''] or len(restoringbeam) == 0: dc.restore(model=modelname, image=imname, bmaj=bmaj, bmin=bmin, bpa=bpa) else: dc.restore(model=modelname, image=imname, bmaj=restoringbeam[0], bmin=restoringbeam[1], bpa=restoringbeam[2]) dc.done() return True
def __launch( self ): ## if we've already launched the viewer if type(self.__state['launched']) == bool and self.__state['launched'] == True: return if dbus_connection( ) == None: raise Exception, "dbus is not available; cannot script the viewer" myf=stack_frame_find( ) self.__rgm = __casac__.regionmanager.regionmanager( ) viewer_path = None if type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == dict : if myf['casa'].has_key('helpers') \ and type(myf['casa']['helpers']) == dict and myf['casa']['helpers'].has_key('viewer'): viewer_path = myf['casa']['helpers']['viewer'] #### set in casapy.py if len(os.path.dirname(viewer_path)) == 0: for dir in os.getenv('PATH').split(':') : dd = dir + os.sep + viewer_path if os.path.exists(dd) and os.access(dd,os.X_OK) : viewer_path = dd break args = [ viewer_path, "--casapy" ] else: for exe in ['casaviewer']: for dir in os.getenv('PATH').split(':') : dd = dir + os.sep + exe if os.path.exists(dd) and os.access(dd,os.X_OK) : viewer_path = dd break if viewer_path is not None: break args = [ viewer_path ] if myf['casa'].has_key('state') and myf['casa']['state'].has_key('init_version'): if myf['casa']['state']['init_version'] <= 0: args += [ '--daemon' ] else: args += [ '--daemon' ] if viewer_path == None or not os.access(viewer_path,os.X_OK): raise RuntimeError("cannot find casa viewer executable") if self.__state['gui']: args += [ '--server=' + self.__state['dbus name'] ] else: args += [ '--nogui=' + self.__state['dbus name'] ] if type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == dict and myf['casa'].has_key('files') \ and type(myf['casa']['files']) == dict and myf['casa']['files'].has_key('logfile'): args += [ '--casalogfile=' + myf['casa']['files']['logfile'] ] if type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == dict and myf['casa'].has_key('flags') \ and type(myf['casa']['flags']) == dict and myf['casa']['flags'].has_key('--rcdir'): args += [ "--rcdir=" + myf['casa']['flags']['--rcdir'] ] if (os.uname()[0]=='Darwin'): if myf['casa']['state']['init_version'] > 0: from casa_system import procmgr procmgr.create(self.__state['dbus name'],args,procmgr.output_option.DISCARD) else: vwrpid=os.spawnvp( os.P_NOWAIT, viewer_path, args ) elif (os.uname()[0]=='Linux'): if myf['casa']['state']['init_version'] > 0: from casa_system import procmgr procmgr.create(self.__state['dbus name'],args,procmgr.output_option.DISCARD) else: vwrpid=os.spawnlp( os.P_NOWAIT, viewer_path, *args ) else: raise Exception,'unrecognized operating system' self.__state['launched'] = True
def importarchive( archivefiles=None, vis=None, bandname=None, freqtol=None, ): """Convert VLA archive file(s) to a CASA visibility data set (MS): ....Keyword arguments: ....archivefiles -- Name of input VLA archive file(s) ........default: <unset> ........example: archivefiles=['AP314_A950519.xp1','AP314_A950519.xp2'] ....vis -- Name of output visibility file (MS) ........default: <unset>; example: vis='NGC7538.ms' ....bandname -- VLA Frequency band ........default: <unset> - all bands; example: bandname='K' ........<Options: '4'=48-96 MHz,'P'=298-345 MHz,'L'=1.15-1.75 GHz, ........'C'=4.2-5.1 GHz,'X'=6.8-9.6 GHz,'U'=13.5-16.3 GHz, ........'K'=20.8-25.8 GHz,'Q'=38-51 GHz> ....#projectname -- Observing project name ....#....default: <unset>; example='AP314' ....freqtol -- Tolerance in frequency shift in naming spectral windows ........default: channel width of current spectral window in Hz ........example: 150000.0 .... ....""" myf = stack_frame_find() vftask = myf['vftask'] vlafiller = vftask.fill # fg = myf['fg'] aflocal = casac.agentflagger() # ## # Handle globals or user over-ride of arguments function_signature_defaults = \ dict(zip(importarchive.func_code.co_varnames, importarchive.func_defaults)) for item in function_signature_defaults.iteritems(): (key, val) = item keyVal = eval(key) if keyVal == None: # user hasn't set it - use global/default pass else: # user has set it - use over-ride myf[key] = keyVal archivefiles = myf['archivefiles'] vis = myf['vis'] bandname = myf['bandname'] freqtol = myf['freqtol'] # # ## # Add type/menu/range error checking here if type(archivefiles) == str: archivefiles = [archivefiles] arg_names = ['archivefiles', 'vis', 'bandname', 'freqtol'] arg_values = [archivefiles, vis, bandname, freqtol] arg_types = [list, str, str, float] try: parameter_checktype(arg_names, arg_values, arg_types) parameter_checkmenu('bandname', bandname, [ '4', 'P', 'L', 'C', 'X', 'U', 'K', 'Q', ]) except TypeError, e: print 'importarchive -- TypeError: ', e return
import shutil import unittest import os import sys from tasks import flagdata, flagmanager from taskinit import aftool, tbtool from __main__ import default import exceptions import __builtin__ from parallel.parallel_task_helper import ParallelTaskHelper from casa_stack_manip import stack_frame_find import flaghelper as fh # to rethrow exception import inspect g = stack_frame_find( ) g['__rethrow_casa_exceptions'] = True # Path for data datapath = os.environ.get('CASAPATH').split()[0] + "/data/regression/unittest/flagdata/" # Pick up alternative data directory to run tests on MMSs testmms = False if os.environ.has_key('TEST_DATADIR'): DATADIR = str(os.environ.get('TEST_DATADIR'))+'/flagdata/' if os.path.isdir(DATADIR): testmms = True datapath = DATADIR print 'flagmanager tests will use data from '+datapath
def tget(task=None, savefile=''): """ Get last input values from file on disk for a specified task: task -- Name of task default: <unset>; example: task='bandpass' <Options: type tasklist() for the complete list> savefile -- Output file for the task inputs default: task.last then task.saved example: savefile=task.orion """ try: myf=stack_frame_find( ) if task==None : if myf.has_key('task') : task=myf['task'] else : if myf.has_key('taskname') : task=myf['taskname'] myf['taskname']=task myf['task']=task if type(task)!=str: task=task.__name__ myf['task']=task myf['taskname']=task parameter_checktype(['task','savefile'],[task,savefile],[str,str]) parameter_checkmenu('task',task,tasksum.keys()) ###Check if task exists by checking if task_defaults is defined if ( not myf.has_key(task) and str(type(myf[task])) != "<type 'instance'>" and not hasattr(myf[task],"defaults") ): raise TypeError, "task %s is not defined " %task if task==None: task=myf['task'] myf['task']=task #f=zip(myf[taskname].func_code.co_varnames,myf[taskname].func_defaults) #for j in range(len(f)): # k=f[j][0] # print 'k is ',k # stst = myf[k] # if ( type(stst) == str ): # sex = k+"='"+stst+"'" # else: # sex = k+"="+str(stst) # exec(sex) if savefile=='': savefile=task+'.last' try: taskparameterfile=open(savefile,'r') except: savefile=task+'.saved' try: taskparameterfile=open(savefile,'r') except: print "Sorry - no task.last or .saved" return taskparameterfile.close() execfile(savefile) # Put the task parameters back into the global namespace f=zip(myf[task].__call__.func_code.co_varnames[1:],myf[task].__call__.func_defaults) missing_ks = [] for j in f: k = j[0] if k != 'self': try: myf[k] = eval(k) except NameError: missing_ks.append(k) if missing_ks: print "Did not find a saved value for", if len(missing_ks) > 1: print ', '.join(missing_ks[:-1]), print 'or', missing_ks[-1] else: print missing_ks[0] print "The set of task parameters has probably changed" print "since", savefile, "was written." print "Restored parameters from file "+savefile except TypeError, e: print "tget --error: ", e
def __call__(self, infile=None,displaytype=None,channel=None,zoom=None,outfile=None,outscale=None,outdpi=None,outformat=None,outlandscape=None,gui=None): """ The msview will display measurement sets in raster form Many display and editing options are available. examples of usage: msview msview "mymeasurementset.ms" msview "myrestorefile.rstr" Executing the msview task will bring up a display panel window, which can be resized. If no data file was specified, a Load Data window will also appear. Click on the desired data file and choose the display type; the rendered data should appear on the display panel. A Data Display Options window will also appear. It has drop-down subsections for related options, most of which are self-explanatory. The state of the msview task -- loaded data and related display options -- can be saved in a 'restore' file for later use. You can provide the restore filename on the command line or select it from the Load Data window. See the cookbook for more details on using the msview task. Keyword arguments: infile -- Name of file to visualize default: '' example: infile='my.ms' If no infile is specified the Load Data window will appear for selecting data. displaytype -- (optional): method of rendering data visually (raster, contour, vector or marker). You can also set this parameter to 'lel' and provide an lel expression for infile (advanced). default: 'raster' Note: there is no longer a filetype parameter; typing of data files is now done automatically. example: msview infile='my.ms' obsolete: msview infile='my.ms', filetype='ms' """ myf=stack_frame_find( ) vi = myf['vi'] if myf.has_key('vi') else None ving = myf['ving'] if myf.has_key('ving') else None #Python script try: ## vi might not be defined in taskinit if loading ## directly from python via casa.py... vwr = vi if type(gui) == bool and gui == False: vwr = ving if type(vwr.cwd( )) != str: vwr = None except: vwr = None if type(vwr) == type(None): need_gui = True if type(gui) == bool and gui == False: need_gui = False if need_gui : if self.local_vi is not None: vwr = self.local_vi else: vwr = viewertool.viewertool( True, True, (type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == type(os)) ) self.local_vi = vwr else: if self.local_ving is not None: vwr = self.local_ving else: vwr = viewertool.viewertool( False, True, (type(myf) == dict and myf.has_key('casa') and type(myf['casa']) == type(os)) ) self.local_ving = vwr if type(vwr) != type(None) : ## ## (1) save current *viewer*server* path ## (2) have viewer() task follow casapy/python's cwd try: old_path = vwr.cwd( ) except: raise Exception, "msview() failed to get the current working directory" try: vwr.cwd(os.path.abspath(os.curdir)) except: raise Exception, "msview() failed to change to the new working directory" data = None if type(infile) == str and len(infile) > 0 : info = vwr.fileinfo(infile); if info['type'] != 'ms' : if info['type'] == 'image' : raise Exception, "msview() only displays images, try 'imview()'..." elif info['type'] == 'nonexistent' : raise Exception, "ms (" + infile + ") could not be found..." else : raise Exception, "unknow error..." panel = vwr.panel("viewer") if type(displaytype) == str: data = vwr.load( infile, displaytype, panel=panel ) else: data = vwr.load( infile, panel=panel ) if type(channel) == int and channel > 0 : vwr.channel(channel,panel=panel) if type(zoom) == int and zoom != 1 : vwr.zoom(zoom,panel=panel) if type(outfile) == str and len(outfile) > 0 : scale=1.0 if type(outscale) == float : scale=outscale dpi=300 if type(outdpi) == int : dpi=outdpi format="jpg" if type(outformat) == str : format=outformat orientation="portrait" if type(outlandscape) == bool and outlandscape : orientation="landscape" vwr.output(outfile,scale=scale,dpi=dpi,format=format,orientation=orientation,panel=panel) else: panel = vwr.panel("viewer") vwr.popup( 'open', panel=panel ) # it makes no sense to leave a panel open with no way of interacting with it if type(gui) == bool and not gui: vwr.close(panel) ## (3) restore original path try: vwr.cwd(old_path) except: raise Exception, "msview() failed to restore the old working directory" else: viewer_path = myf['casa']['helpers']['viewer'] #### set in casapy.py args = [ viewer_path ] if type(infile) == str: if type(displaytype) == str: args += [ infile, displaytype ] else: args += [ infile ] if (os.uname()[0]=='Darwin'): vwrpid=os.spawnvp( os.P_NOWAIT, viewer_path, args ) elif (os.uname()[0]=='Linux'): vwrpid=os.spawnlp( os.P_NOWAIT, viewer_path, *args ) else: print 'Unrecognized OS: No msview available' return None
def __call__( self, vis=None, spw=None, field=None, secsour=None, stddevfact=None, ): """Find line free channels to use in continuum imaging. Detailed Description: Find spectral channels free of spectral line emission to aid in the processes of continuum imaging. Arguments : vis: name of input visibility file Default Value: spw: Spectral window Default Value: field: Field Name Default Value: secsour: File with positions and properties of Secondary Sources Default Value: stddevfact: Standard deviation factor Default Value: Returns: void Example : Task to find channels free of molecular emission lines to provide users with line free channels to use in continuum only imaging. Outputs proposed line free channels to [field]_SPW_[spw]_LineFreeChans.txt Intended to be used within the ALMA data directory structure, as downloaded from the ALMA Archive. vis -- Name of fully calibrated input visibility file, within the 'calibrated' directory of an ALMA Archive product default: none; example: vis='ngc5921.ms' field -- Select field in which to find lines. Use field name(s) *ONLY*. spw -- Select a *single* spectral window in which to find lines secsour -- User defined file for extracting spectra a position "sourceX RA[hh:mm:ss.000] Dec[dd:mm:ss.000] Bmaj* Bmin* BPA*" " *fitted 2D Gaussian major, minor axis and position angle." stddevfact -- Standard deviation factor for sigma clipping. default = 1.5 """ if not hasattr(self, "__globals__") or self.__globals__ == None: self.__globals__ = stack_frame_find() #casac = self.__globals__['casac'] casalog = self.__globals__['casalog'] casa = self.__globals__['casa'] #casalog = casac.casac.logsink() self.__globals__['__last_task'] = 'lumberjack' self.__globals__['taskname'] = 'lumberjack' ### self.__globals__['update_params'](func=self.__globals__['taskname'], printtext=False, ipython_globals=self.__globals__) ### ### #Handle globals or user over-ride of arguments # if type(self.__call__.func_defaults) is NoneType: function_signature_defaults = {} else: function_signature_defaults = dict( zip(self.__call__.func_code.co_varnames[1:], self.__call__.func_defaults)) useLocalDefaults = False for item in function_signature_defaults.iteritems(): key, val = item keyVal = eval(key) if (keyVal == None): #user hasn't set it - use global/default pass else: #user has set it - use over-ride if (key != 'self'): useLocalDefaults = True myparams = {} if useLocalDefaults: for item in function_signature_defaults.iteritems(): key, val = item keyVal = eval(key) exec('myparams[key] = keyVal') self.parameters[key] = keyVal if (keyVal == None): exec('myparams[key] = ' + key + ' = self.itsdefault(key)') keyVal = eval(key) if (type(keyVal) == dict): if len(keyVal) > 0: exec('myparams[key] = ' + key + ' = keyVal[len(keyVal)-1][\'value\']') else: exec('myparams[key] = ' + key + ' = {}') else: print '' myparams['vis'] = vis = self.parameters['vis'] myparams['spw'] = spw = self.parameters['spw'] myparams['field'] = field = self.parameters['field'] myparams['secsour'] = secsour = self.parameters['secsour'] myparams['stddevfact'] = stddevfact = self.parameters['stddevfact'] result = None # # The following is work around to avoid a bug with current python translation # mytmp = {} mytmp['vis'] = vis mytmp['spw'] = spw mytmp['field'] = field mytmp['secsour'] = secsour mytmp['stddevfact'] = stddevfact pathname = "file:///raid1/scratch/aavison/LJ_2020/" trec = casac.casac.utils().torecord(pathname + 'lumberjack.xml') casalog.origin('lumberjack') try: #if not trec.has_key('lumberjack') or not casac.casac.utils().verify(mytmp, trec['lumberjack']) : #return False casac.casac.utils().verify(mytmp, trec['lumberjack'], True) scriptstr = [''] saveinputs = self.__globals__['saveinputs'] # Save .last file for this task execution. MPI servers don't write it (CASR-329). from mpi4casa.MPIEnvironment import MPIEnvironment do_full_logging = MPIEnvironment.is_mpi_disabled_or_client() if type(self.__call__.func_defaults) is NoneType: saveinputs = '' else: saveinputs('lumberjack', 'lumberjack.last', myparams, self.__globals__, scriptstr=scriptstr, do_save_inputs=do_full_logging) tname = 'lumberjack' spaces = ' ' * (18 - len(tname)) casalog.post('\n##########################################' + '\n##### Begin Task: ' + tname + spaces + ' #####') # Don't do telemetry from MPI servers (CASR-329) if do_full_logging and casa['state']['telemetry-enabled']: #casalog.poststat('Begin Task: ' + tname) task_starttime = str(datetime.datetime.now()) if type(self.__call__.func_defaults) is NoneType: casalog.post(scriptstr[0] + '\n', 'INFO') else: casalog.post(scriptstr[1][1:] + '\n', 'INFO') # Effective call to the task as defined in gcwrap/python/scripts/task_* result = lumberjack(vis, spw, field, secsour, stddevfact) if do_full_logging and casa['state']['telemetry-enabled']: task_endtime = str(datetime.datetime.now()) casalog.poststat('Task ' + tname + ' complete. Start time: ' + task_starttime + ' End time: ' + task_endtime) casalog.post('##### End Task: ' + tname + ' ' + spaces + ' #####' + '\n##########################################') except Exception, instance: if (self.__globals__.has_key('__rethrow_casa_exceptions') and self.__globals__['__rethrow_casa_exceptions']): raise else: #print '**** Error **** ',instance tname = 'lumberjack' casalog.post('An error occurred running task ' + tname + '.', 'ERROR') pass
def simanalyze( project=None, image=None, # if image==False: imagename=None, skymodel=None, # else: vis=None, modelimage=None, imsize=None, imdirection=None, cell=None, interactive=None, niter=None, threshold=None, weighting=None, mask=None, outertaper=None, pbcor=None, stokes=None, featherimage=None, # endif analyze=None, showuv=None, showpsf=None, showmodel=None, showconvolved=None, showclean=None, showresidual=None, showdifference=None, showfidelity=None, graphics=None, verbose=None, overwrite=None, dryrun=False, logfile=None ): #def simanalyze(project='sim', image=True, imagename='default', skymodel='', vis='default', modelimage='', imsize=[128, 128], imdirection='', cell='', interactive=False, niter=0, threshold='0.1mJy', weighting='natural', mask=[], outertaper=[''], stokes='I', featherimage='', analyze=False, showuv=True, showpsf=True, showmodel=True, showconvolved=False, showclean=True, showresidual=False, showdifference=True, showfidelity=True, graphics='both', verbose=False, overwrite=True, dryrun=False): # Collect a list of parameter values to save inputs in_params = locals() import re import glob casalog.origin('simanalyze') if verbose: casalog.filter(level="DEBUG2") myf = stack_frame_find( ) # create the utility object: myutil = simutil() if logfile: myutil.reportfile=logfile myutil.openreport() if verbose: myutil.verbose = True msg = myutil.msg from simutil import is_array_type # put output in directory called "project" fileroot = project if not os.path.exists(fileroot): msg(fileroot+" directory doesn't exist - the task expects to find results from creating the datasets there, like the skymodel.",priority="error") # msg should raise an exception for priority=error saveinputs = myf['saveinputs'] saveinputs('simanalyze',fileroot+"/"+project+".simanalyze.last") # myparams=in_params) if (not image) and (not analyze): casalog.post("No operation to be done. Exiting from task.", "WARN") return True grscreen = False grfile = False if graphics == "both": grscreen = True grfile = True if graphics == "screen": grscreen = True if graphics == "file": grfile = True try: # Predefined parameters pbcoeff = 1.13 ## PB defined as pbcoeff*lambda/d # handle '$project' in modelimage modelimage = modelimage.replace('$project',project) featherimage = featherimage.replace('$project',project) #========================= # things we need: model_cell, model_direction if user doesn't specify - # so find those first, and get information using util.modifymodel # with skymodel=newmodel # we need to parse either the mslist or imagename (if image=False) # first, so that we can pick the appropriate skymodel, # if there are several. skymodel_searchstring="NOT SPECIFIED" if not (image or dryrun): user_imagename=imagename if user_imagename=="default" or len(user_imagename)<=0: images= glob.glob(fileroot+"/*image") if len(images)<1: msg("can't find any image in project directory",priority="error") return False if len(images)>1: msg("found multiple images in project directory",priority="warn") msg("using "+images[0],priority="warn") imagename=images[0] # trim .image suffix: imagename= imagename.replace(".image","") # if the user hasn't specified a sky model image, we can try to # see if their imagename contains something like the project and # configuration, as it would if simobserve created it. user_skymodel=skymodel if not os.path.exists(user_skymodel): if os.path.exists(fileroot+"/"+user_skymodel): user_skymodel=fileroot+"/"+user_skymodel elif len(user_skymodel)>0: raise Exception,"Can't find your specified skymodel "+user_skymodel # try to strip a searchable identifier tmpstring=user_skymodel.split("/")[-1] skymodel_searchstring=tmpstring.replace(".image","") if image: # check for default measurement sets: default_mslist = glob.glob(fileroot+"/*ms") n_default=len(default_mslist) # is the user requesting this ms? default_requested=[] for i in range(n_default): default_requested.append(False) # parse ms parameter and check for existance; # initial ms list if vis=="default" or len(vis)==0: mslist0=default_mslist else: mslist0 = vis.split(',') # verified found ms list mslist = [] mstype = [] mstoimage=[] tpmstoimage=None for ms0 in mslist0: if not len(ms0): continue ms1 = ms0.replace('$project',project) # MSes in fileroot/ have priority if os.path.exists(fileroot+"/"+ms1): ms1 = fileroot + "/" + ms1 if os.path.exists(ms1)or dryrun: mslist.append(ms1) # mark as requested if default_mslist.count(ms1): i=default_mslist.index(ms1) default_requested[i]=True # check if noisy in name if re.search('noisy.',ms1): ms1_raw=str.join("",re.split('noisy.',ms1)) if default_mslist.count(ms1_raw): i=default_mslist.index(ms1_raw) default_requested[i]=True else: # not noisy if ms1.endswith(".sd.ms"): ms1_noisy=re.split('.sd.ms',ms1)[0]+'.noisy.sd.ms' else: ms1_noisy=re.split('.ms',ms1)[0]+'.noisy.ms' if default_mslist.count(ms1_noisy): i=default_mslist.index(ms1_noisy) default_requested[i]=True if vis == "default": continue msg("You requested "+ms1+" but there is a noisy version of the ms in your project directory - if your intent is to model noisy data you may want to check inputs",priority="warn") # check if the ms is tp data or not. if dryrun: # HACK mstype.append('INT') mstoimage.append(ms1) elif myutil.ismstp(ms1,halt=False): mstype.append('TP') tpmstoimage = ms1 # XXX TODO more than one TP ms will not be handled # correctly msg("Found a total power measurement set, %s." % ms1,origin='simanalyze') else: mstype.append('INT') mstoimage.append(ms1) msg("Found a synthesis measurement set, %s." % ms1,origin='simanalyze') else: msg("measurement set "+ms1+" not found -- removing from imaging list") # check default mslist for unrequested ms: for i in range(n_default): if not default_requested[i]: msg("Project directory contains "+default_mslist[i]+" but you have not requested to include it in your simulated image.") if not mstoimage and len(tpmstoimage) == 0: raise Exception,"No MS found to image" # now try to parse the mslist for an identifier string that # we can use to find the right skymodel if there are several if len(mstoimage) == 0 and len(tpmstoimage) > 0: tmpstring = tpmstoimage.split("/")[-1] else: tmpstring=(mstoimage[0]).split("/")[-1] skymodel_searchstring=tmpstring.replace(".ms","") # more than one to image? if len(mstoimage) > 1: msg("Multiple interferometric ms found:",priority="info",origin='simanalyze') for i in range(len(mstoimage)): msg(" "+mstoimage[i],priority="info",origin='simanalyze') msg(" will be concated and simultaneously deconvolved; if something else is desired, please specify vis, or image manually and use image=F",priority="info",origin='simanalyze') concatms=project+"/"+project+".concat.ms" from concat import concat weights = get_concatweights(mstoimage) msg(" concat("+str(mstoimage)+",concatvis='"+concatms+"',visweightscale="+str(weights)+")",origin='simanalyze') if not dryrun: concat(mstoimage,concatvis=concatms,visweightscale=weights) mstoimage=[concatms] #======================================================== # now we can search for skymodel, and if there are several, # pick the one that is closest to either the imagename, # or the first MS if there are several MS to image. components_only=False # first look for skymodel, if not then compskymodel skymodels=glob.glob(fileroot+"/"+project+"*.skymodel")+glob.glob(fileroot+"/"+project+"*.newmodel") nmodels=len(skymodels) skymodel_index=0 if nmodels>1: msg("Found %i sky model images:" % nmodels,origin='simanalyze') # use the skymodel_searchstring to try to pick the right one # print them out for the user while we're at it. for i in range(nmodels): msg(" "+skymodels[i]) if skymodels[i].count(skymodel_searchstring)>0: skymodel_index=i msg("Using skymodel "+skymodels[skymodel_index],origin='simanalyze') if nmodels>=1: skymodel=skymodels[skymodel_index] else: skymodel="" if os.path.exists(skymodel): msg("Sky model image "+skymodel+" found.",origin='simanalyze') else: skymodels=glob.glob(fileroot+"/"+project+"*.compskymodel") nmodels=len(skymodels) if nmodels>1: msg("Found %i sky model images:" % nmodels,origin='simanalyze') for ff in skymodels: msg(" "+ff) msg("Using "+skymodels[0],origin='simanalyze') if nmodels>=1: skymodel=skymodels[0] else: skymodel="" if os.path.exists(skymodel): msg("Sky model image "+skymodel+" found.",origin='simanalyze') components_only=True elif not dryrun: msg("Can't find a model image in your project directory, named skymodel or compskymodel - output image will be created, but comparison with the input model is not possible.",priority="warn",origin='simanalyze') analyze=False modelflat = skymodel+".flat" if os.path.exists(skymodel): if not (os.path.exists(modelflat) or dryrun): myutil.flatimage(skymodel,verbose=verbose) # modifymodel just collects info if skymodel==newmodel (model_refdir,model_cell,model_size, model_nchan,model_center,model_width, model_stokes) = myutil.modifymodel(skymodel,skymodel, "","","","","",-1, flatimage=False) cell_asec=qa.convert(model_cell[0],'arcsec')['value'] ##################################################################### # clean if desired, use noisy image for further calculation if present # todo suggest a cell size from psf? ##################################################################### if image: # make sure cell is defined if is_array_type(cell): if len(cell) > 0: cell0 = cell[0] else: cell0 = "" else: cell0 = cell if len(cell0)<=0: cell = model_cell if is_array_type(cell): if len(cell) == 1: cell = [cell[0],cell[0]] else: cell = [cell,cell] # cells are positive by convention cell = [qa.abs(cell[0]),qa.abs(cell[1])] # and imsize if is_array_type(imsize): if len(imsize) > 0: imsize0 = imsize[0] if len(imsize) > 1: imsize1 = imsize[1] else: imsize1 = imsize0 else: imsize0 = -1 else: imsize0 = imsize if imsize0 <= 0: imsize = [int(pl.ceil(qa.convert(qa.div(model_size[0],cell[0]),"")['value'])), int(pl.ceil(qa.convert(qa.div(model_size[1],cell[1]),"")['value']))] else: imsize=[imsize0,imsize1] if len(mstoimage) == 0: if tpmstoimage: sd_only = True else: msg("no measurement sets found to image",priority="error",origin='simanalyze') else: sd_only = False # get some quantities from the interferometric ms # TODO use something like aU.baselineStats for this, and the 90% baseline maxbase=0. if len(mstoimage)>1 and dryrun: msg("imaging multiple ms not possible in dryrun mode",priority="warn",origin="simanalyze") # TODO make work better for multiple MS for msfile in mstoimage: if os.path.exists(msfile): tb.open(msfile) rawdata = tb.getcol("UVW") tb.done() maxbase = max([max(rawdata[0,]),max(rawdata[1,])]) # in m psfsize = 0.3/qa.convert(qa.quantity(model_center),'GHz')['value']/maxbase*3600.*180/pl.pi # lambda/b converted to arcsec minimsize = 8* int(psfsize/cell_asec) elif dryrun: minimsize = min(imsize) psfsize = qa.mul(cell[0],3) # HACK else: raise Exception,mstoimage+" not found." if imsize[0] < minimsize: msg("The number of image pixel in x-axis, %d, is small to cover 8 x PSF. Setting x pixel number, %d." % (imsize[0], minimsize), priority='warn',origin='simanalyze') imsize[0] = minimsize if imsize[1] < minimsize: msg("The number of image pixel in y-axis, %d, is small to cover 8 x PSF. Setting y pixel number, %d" % (imsize[1], minimsize), priority='warn',origin='simanalyze') imsize[1] = minimsize tpimage=None # Do single dish imaging first if tpmstoimage exists. if tpmstoimage and os.path.exists(tpmstoimage): msg('creating image from ms: '+tpmstoimage,origin='simanalyze') #if len(mstoimage): # tpimage = project + '.sd.image' #else: # tpimage = project + '.image' tpimage = project + '.sd.image' tpimage = fileroot + "/" + tpimage if len(mstoimage): if len(modelimage) and tpimage != modelimage and \ tpimage != fileroot+"/"+modelimage: msg("modelimage parameter set to "+modelimage+" but also creating a new total power image "+tpimage,priority="warn",origin='simanalyze') msg("assuming you know what you want, and using modelimage="+modelimage+" in deconvolution",priority="warn",origin='simanalyze') elif len(featherimage) and tpimage != featherimage and \ tpimage != fileroot+"/"+featherimage: msg("featherimage parameter set to "+featherimage+" but also creating a new total power image "+tpimage,priority="warn",origin='simanalyze') msg("assuming you know what you want, and using featherimage="+featherimage+" in feather",priority="warn",origin='simanalyze') # Get PB size of TP Antenna # !! aveant will only be set if modifymodel or setpointings and in # any case it will the the aveant of the INTERFM array - we want the SD if os.path.exists(tpmstoimage): # antenna diameter tb.open(tpmstoimage+"/ANTENNA") diams = tb.getcol("DISH_DIAMETER") tb.close() aveant = pl.mean(diams) # theoretical antenna beam size import sdbeamutil pb_asec = sdbeamutil.primaryBeamArcsec(qa.tos(qa.convert(qa.quantity(model_center),'GHz')),aveant,(0.75 if aveant==12.0 else 0.0),10.0) elif dryrun: aveant = 12.0 pb_asec = pbcoeff*0.29979/qa.convert(qa.quantity(model_center),'GHz')['value']/aveant*3600.*180/pl.pi else: raise Exception, tpmstoimage+" not found." # default PSF from PB of antenna imbeam = {'major': qa.quantity(pb_asec,'arcsec'), 'minor': qa.quantity(pb_asec,'arcsec'), 'positionangle': qa.quantity(0.0,'deg')} # Common imaging parameters sdim_param = dict(infiles=[tpmstoimage], overwrite=overwrite, phasecenter=model_refdir, mode='channel', nchan=model_nchan, start=0, width=1) if True: #SF gridding msg("Generating TP image using 'SF' kernel.",origin='simanalyze') beamsamp = 9 sfcell_asec = pb_asec/beamsamp sfcell = qa.tos(qa.quantity(sfcell_asec, "arcsec")) cell_asec = [qa.convert(cell[0],"arcsec")['value'], qa.convert(cell[1],"arcsec")['value']] if cell_asec[0] > sfcell_asec or \ cell_asec[1] > sfcell_asec: # imregrid() may not work properly for regrid of # small to large cell msg("The requested cell size is too large to invoke SF gridding. Please set cell size <= %f arcsec or grid TP MS '%s' manually" % (sfcell_asec, tpmstoimage),priority="error",origin='simanalyze') sfsupport = 6 temp_out = tpimage+"0" temp_cell = [sfcell, sfcell] # too small - is imsize too small to start with? # needs to cover all pointings. temp_imsize = [int(pl.ceil(cell_asec[0]/sfcell_asec*imsize[0])), int(pl.ceil(cell_asec[1]/sfcell_asec*imsize[1]))] msg("Using predefined algorithm to define grid parameters.",origin='simanalyze') msg("SF gridding summary",origin='simanalyze') msg("- Antenna primary beam: %f arcsec" % pb_asec,origin='simanalyze') msg("- Image pixels per antenna PB (predefined): %f" % beamsamp,origin='simanalyze') msg("- Cell size (arcsec): [%s, %s]" % (temp_cell[0], temp_cell[1]),origin='simanalyze') msg("- Imsize to cover final TP image area: [%d, %d] (type: %s)" % (temp_imsize[0], temp_imsize[1], type(temp_imsize[0])),origin='simanalyze') msg("- convolution support: %d" % sfsupport,origin='simanalyze') # kernel specific imaging parameters sdim_param['gridfunction'] = 'SF' sdim_param['convsupport'] = sfsupport sdim_param['outfile'] = temp_out sdim_param['imsize'] = temp_imsize sdim_param['cell'] = temp_cell msg(get_taskstr('sdimaging', sdim_param), priority="info") if not dryrun: sdimaging(**sdim_param) if not os.path.exists(temp_out): raise RuntimeError, "TP imaging failed." # Scale image by convolved beam / antenna primary beam ia.open(temp_out) imbeam = ia.restoringbeam() ia.close() beam_area_ratio = qa.getvalue(qa.convert(imbeam['major'], "arcsec")) \ * qa.getvalue(qa.convert(imbeam['minor'], "arcsec")) \ / pb_asec**2 msg("Scaling TP image intensity by %f." % (beam_area_ratio),origin='simanalyze') temp_in = temp_out temp_out = temp_out + ".scaled" immath(imagename=temp_in, mode='evalexpr', expr="IM0*%f" % (beam_area_ratio), outfile=temp_out) if not os.path.exists(temp_out): raise RuntimeError, "TP image scaling failed." # Regrid TP image to final resolution msg("Regridding TP image to final resolution",origin='simanalyze') msg("- cell size (arecsec): [%s, %s]" % (cell[0], cell[1]),origin='simanalyze') msg("- imsize: [%d, %d]" % (imsize[0], imsize[1]),origin='simanalyze') if not dryrun: ia.open(temp_out) newcsys = ia.coordsys() ia.close() dir_idx = newcsys.findcoordinate("direction")['world'] newcsys.setreferencepixel([imsize[0]/2., imsize[1]/2.], type="direction") incr = newcsys.increment(type='direction')['numeric'] newincr = [incr[0]*cell_asec[0]/sfcell_asec, incr[1]*cell_asec[1]/sfcell_asec,] newcsys.setincrement(newincr, type="direction") # sdtemplate = imregrid(imagename=temp_out, template="get") sdtemplate['csys'] = newcsys.torecord() for idx in range(len(dir_idx)): sdtemplate['shap'][ dir_idx[idx] ] = imsize[idx] imregrid(imagename=temp_out, interpolation="cubic", template=sdtemplate, output=tpimage, overwrite=overwrite) del newcsys, sdtemplate, incr, newincr, dir_idx del temp_out, temp_cell, temp_imsize, sfcell_asec, cell_asec else: #PB grid msg("Generating TP image using 'PB' kernel.",origin='simanalyze') # Final TP cell and image size. # imsize and cell are already int and quantum arrays sdimsize = imsize sdcell = [qa.tos(cell[0]), qa.tos(cell[1])] ### TODO: need to set phasecenter properly based on imdirection # kernel specific imaging parameters sdim_param['gridfunction'] = 'PB' sdim_param['outfile'] = tpimage sdim_param['imsize'] = sdimsize sdim_param['cell'] = sdcell msg(get_taskstr('sdimaging', sdim_param), priority="info") if not dryrun: sdimaging(**sdim_param) del sdimsize, sdcell # TODO: Define PSF of image here # for now use default # get image beam size form TP image if os.path.exists(tpimage): ia.open(tpimage) beam = ia.restoringbeam() ia.close() if sd_only: bmarea = beam['major']['value']*beam['minor']['value']*1.1331 #arcsec2 bmarea = bmarea/(cell[0]['value']*cell[1]['value']) # bm area in pix else: del beam #del beam msg('generation of total power image '+tpimage+' complete.',origin='simanalyze') # update TP ms name the for following steps sdmsfile = tpmstoimage sd_any = True imagename = re.split('.image$',tpimage)[0] # End of single dish imaging part outflat_current = False convsky_current = False if image and len(mstoimage) > 0: # for reruns foo=mstoimage[0] foo=foo.replace(".ms","") foo=foo.replace(project,"") foo=foo.replace("/","") project=project+foo imagename = fileroot + "/" + project # get nfld, sourcefieldlist, from (interfm) ms if it was not just created # TODO make work better for multiple mstoimage (figures below) if os.path.exists(mstoimage[0]): tb.open(mstoimage[0]+"/SOURCE") code = tb.getcol("CODE") sourcefieldlist = pl.where(code=='OBJ')[0] nfld = len(sourcefieldlist) tb.done() elif dryrun: nfld=1 # HACK msfile = mstoimage[0] # set cleanmode automatically (for interfm) if nfld == 1: cleanmode = "csclean" else: cleanmode = "mosaic" # clean insists on using an existing model if its present if os.path.exists(imagename+".image"): shutil.rmtree(imagename+".image") if os.path.exists(imagename+".model"): shutil.rmtree(imagename+".model") # An image in fileroot/ has priority if len(modelimage) > 0 and os.path.exists(fileroot+"/"+modelimage): modelimage = fileroot + "/" + modelimage msg("Found modelimage, %s." % modelimage,origin='simanalyze') # in simdata we use imdirection instead of model_refdir if not myutil.isdirection(imdirection,halt=False): imdirection=model_refdir myutil.imclean(mstoimage,imagename, cleanmode,cell,imsize,imdirection, interactive,niter,threshold,weighting, outertaper,pbcor,stokes, #sourcefieldlist=sourcefieldlist, modelimage=modelimage,mask=mask,dryrun=dryrun) # create imagename.flat and imagename.residual.flat: if not dryrun: myutil.flatimage(imagename+".image",verbose=verbose) myutil.flatimage(imagename+".residual",verbose=verbose) outflat_current = True # feather if featherimage: if not os.path.exists(featherimage): raise Exception,"Could not find featherimage "+featherimage else: featherimage="" if tpimage: # if you set modelimage, then it won't force tpimage into # featherimage. this could be hard to explain # to the user. if os.path.exists(tpimage) and not os.path.exists(modelimage): featherimage=tpimage if os.path.exists(featherimage): msg("feathering the interfermetric image "+imagename+".image with "+featherimage,origin='simanalyze',priority="info") from feather import feather # TODO call with params? msg("feather('"+imagename+".feather.image','"+imagename+".image','"+featherimage+"')",priority="info") if not dryrun: feather(imagename+".feather.image",imagename+".image",featherimage) # copy residual flat image shutil.copytree(imagename+".residual.flat",imagename+".feather.residual.flat") imagename=imagename+".feather" # but replace combined flat image myutil.flatimage(imagename+".image",verbose=verbose) if verbose: msg(" ") msg("done inverting and cleaning",origin='simanalyze') if not is_array_type(cell): cell = [cell,cell] if len(cell) <= 1: cell = [qa.quantity(cell[0]),qa.quantity(cell[0])] else: cell = [qa.quantity(cell[0]),qa.quantity(cell[1])] cell = [qa.abs(cell[0]),qa.abs(cell[0])] # get beam from output clean image if verbose: msg("getting beam from "+imagename+".image",origin='simanalyze') if os.path.exists(imagename+".image"): ia.open(imagename+".image") beam = ia.restoringbeam() ia.close() # model has units of Jy/pix - calculate beam area from clean image # (even if we are not plotting graphics) bmarea = beam['major']['value']*beam['minor']['value']*1.1331 #arcsec2 bmarea = bmarea/(cell[0]['value']*cell[1]['value']) # bm area in pix msg("synthesized beam area in output pixels = %f" % bmarea,origin='simanalyze') if image: # show model, convolved model, clean image, and residual if grfile: file = fileroot + "/" + project + ".image.png" else: file = "" else: mslist=[] if dryrun: grscreen=False grfile=False analyze=False if image and len(mstoimage) > 0: if grscreen or grfile: myutil.newfig(multi=[2,2,1],show=grscreen) # create regridded and convolved sky model image myutil.convimage(modelflat,imagename+".image.flat") convsky_current = True # don't remake this for analysis in this run disprange = [] # passing empty list causes return of disprange # original sky regridded to output pixels but not convolved with beam discard = myutil.statim(modelflat+".regrid",disprange=disprange,showstats=False) myutil.nextfig() # convolved sky model - units of Jy/bm disprange = [] discard = myutil.statim(modelflat+".regrid.conv",disprange=disprange) myutil.nextfig() # clean image - also in Jy/beam # although because of DC offset, better to reset disprange disprange = [] discard = myutil.statim(imagename+".image.flat",disprange=disprange) myutil.nextfig() if len(mstoimage) > 0: myutil.nextfig() # clean residual image - Jy/bm discard = myutil.statim(imagename+".residual.flat",disprange=disprange) myutil.endfig(show=grscreen,filename=file) ##################################################################### # analysis if analyze: if not os.path.exists(imagename+".image"): if os.path.exists(fileroot+"/"+imagename+".image"): imagename=fileroot+"/"+imagename else: msg("Can't find a simulated image - expecting "+imagename,priority="error") return False # we should have skymodel.flat created above if not image: if not os.path.exists(imagename+".image"): msg("you must image before analyzing.",priority="error") return False # get beam from output clean image if verbose: msg("getting beam from "+imagename+".image",origin="analysis") ia.open(imagename+".image") beam = ia.restoringbeam() ia.close() # model has units of Jy/pix - calculate beam area from clean image cell = myutil.cellsize(imagename+".image") cell= [ qa.convert(cell[0],'arcsec'), qa.convert(cell[1],'arcsec') ] # (even if we are not plotting graphics) bmarea = beam['major']['value']*beam['minor']['value']*1.1331 #arcsec2 bmarea = bmarea/(cell[0]['value']*cell[1]['value']) # bm area in pix msg("synthesized beam area in output pixels = %f" % bmarea) # flat output:? if the user manually cleaned, this may not exist outflat = imagename + ".image.flat" if (not outflat_current) or (not os.path.exists(outflat)): # create imagename.flat and imagename.residual.flat myutil.flatimage(imagename+".image",verbose=verbose) if os.path.exists(imagename+".residual"): myutil.flatimage(imagename+".residual",verbose=verbose) else: if showresidual: msg(imagename+".residual not found -- residual will not be plotted",priority="warn") showresidual = False outflat_current = True # regridded and convolved input:? if not convsky_current: myutil.convimage(modelflat,imagename+".image.flat") convsky_current = True # now should have all the flat, convolved etc even if didn't run "image" # make difference image. # immath does Jy/bm if image but only if ia.setbrightnessunit("Jy/beam") in convimage() convolved = modelflat + ".regrid.conv" difference = imagename + '.diff' diff_ia = ia.imagecalc(difference, "'%s' - '%s'" % (convolved, outflat), overwrite=True) diff_ia.setbrightnessunit("Jy/beam") # get rms of difference image for fidelity calculation #ia.open(difference) diffstats = diff_ia.statistics(robust=True, verbose=False,list=False) diff_ia.close() del diff_ia maxdiff = diffstats['medabsdevmed'] if maxdiff != maxdiff: maxdiff = 0. if type(maxdiff) != type(0.): if maxdiff.__len__() > 0: maxdiff = maxdiff[0] else: maxdiff = 0. # Make fidelity image. absdiff = imagename + '.absdiff' calc_ia = ia.imagecalc(absdiff, "max(abs('%s'), %f)" % (difference, maxdiff/pl.sqrt(2.0)), overwrite=True) calc_ia.close() fidelityim = imagename + '.fidelity' calc_ia = ia.imagecalc(fidelityim, "abs('%s') / '%s'" % (convolved, absdiff), overwrite=True) calc_ia.close() msg("fidelity image calculated",origin="analysis") # scalar fidelity absconv = imagename + '.absconv' calc_ia = ia.imagecalc(absconv, "abs('%s')" % convolved, overwrite=True) if ia.isopen(): ia.close() #probably not necessary calc_ia.close() del calc_ia ia.open(absconv) modelstats = ia.statistics(robust=True, verbose=False,list=False) maxmodel = modelstats['max'] if maxmodel != maxmodel: maxmodel = 0. if type(maxmodel) != type(0.): if maxmodel.__len__() > 0: maxmodel = maxmodel[0] else: maxmodel = 0. ia.close() scalarfidel = maxmodel/maxdiff msg("fidelity range (max model / rms difference) = "+str(scalarfidel),origin="analysis") # now, what does the user want to actually display? # need MS for showuv and showpsf if not image: msfile = fileroot + "/" + project + ".ms" elif sd_only: # imaged and single dish only msfile = tpmstoimage # psf is not available for SD only sim if os.path.exists(msfile) and myutil.ismstp(msfile,halt=False): if showpsf: msg("single dish simulation -- psf will not be plotted",priority='warn') showpsf = False if (not image) and (not os.path.exists(msfile)): if showpsf or showuv: msg("No image is generated in this run. Default MS, '%s', does not exist -- uv and psf will not be plotted" % msfile,priority='warn') showpsf = False showuv = False # if the order in the task input changes, change it here too figs = [showuv,showpsf,showmodel,showconvolved,showclean,showresidual,showdifference,showfidelity] nfig = figs.count(True) if nfig > 6: msg("only displaying first 6 selected panels in graphic output",priority="warn") if nfig <= 0: return True if nfig < 4: multi = [1,nfig,1] else: if nfig == 4: multi = [2,2,1] else: multi = [2,3,1] if grfile: file = fileroot + "/" + project + ".analysis.png" else: file = "" if grscreen or grfile: myutil.newfig(multi=multi,show=grscreen) # if order in task parameters changes, change here too if showuv: # TODO loop over all ms - show all UV including zero if len(mslist)>1: msg("Using only "+msfile+" for uv plot",priority="warn",origin='simanalyze') tb.open(msfile) rawdata = tb.getcol("UVW") tb.done() pl.box() maxbase = max([max(rawdata[0,]),max(rawdata[1,])]) # in m klam_m = 300/qa.convert(model_center,'GHz')['value'] pl.plot(rawdata[0,]/klam_m,rawdata[1,]/klam_m,'b,') pl.plot(-rawdata[0,]/klam_m,-rawdata[1,]/klam_m,'b,') ax = pl.gca() ax.yaxis.LABELPAD = -4 pl.xlabel('u[klambda]',fontsize='x-small') pl.ylabel('v[klambda]',fontsize='x-small') pl.axis('equal') # Add zero-spacing (single dish) if not yet plotted # TODO make this a check over all ms # if predict_sd and not myutil.ismstp(msfile,halt=False): # pl.plot([0.],[0.],'r,') myutil.nextfig() if showpsf: if image: psfim = imagename + ".psf" else: psfim = project + ".quick.psf" if not os.path.exists(psfim): if len(mslist)>1: msg("Using only "+msfile+" for psf generation",priority="warn") im.open(msfile) # TODO spectral parms im.defineimage(cellx=qa.tos(model_cell[0]),nx=max([minimsize,128])) if os.path.exists(psfim): shutil.rmtree(psfim) im.approximatepsf(psf=psfim) # beam is set above (even in "analyze" only) # note that if image, beam has fields 'major' whereas if not, it # has fields like 'bmaj'. # beam=im.fitpsf(psf=psfim) im.done() ia.open(psfim) beamcs = ia.coordsys() beam_array = ia.getchunk(axes=[beamcs.findcoordinate("spectral")['pixel'][0],beamcs.findcoordinate("stokes")['pixel'][0]],dropdeg=True) nn = beam_array.shape xextent = nn[0]*cell_asec*0.5 xextent = [xextent,-xextent] yextent = nn[1]*cell_asec*0.5 yextent = [-yextent,yextent] flipped_array = beam_array.transpose() ttrans_array = flipped_array.tolist() ttrans_array.reverse() pl.imshow(ttrans_array,interpolation='bilinear',cmap=pl.cm.jet,extent=xextent+yextent,origin="bottom") psfim.replace(project+"/","") pl.title(psfim,fontsize="x-small") b = qa.convert(beam['major'],'arcsec')['value'] pl.xlim([-3*b,3*b]) pl.ylim([-3*b,3*b]) ax = pl.gca() pl.text(0.05,0.95,"bmaj=%7.1e\nbmin=%7.1e" % (beam['major']['value'],beam['minor']['value']),transform = ax.transAxes,bbox=dict(facecolor='white', alpha=0.7),size="x-small",verticalalignment="top") ia.close() myutil.nextfig() disprange = [] # first plot will define range if showmodel: discard = myutil.statim(modelflat+".regrid",incell=cell,disprange=disprange,showstats=False) myutil.nextfig() disprange = [] if showconvolved: discard = myutil.statim(modelflat+".regrid.conv") # if disprange gets set here, it'll be Jy/bm myutil.nextfig() if showclean: # own scaling because of DC/zero spacing offset discard = myutil.statim(imagename+".image.flat") myutil.nextfig() if showresidual: # it gets its own scaling discard = myutil.statim(imagename+".residual.flat") myutil.nextfig() if showdifference: # it gets its own scaling. discard = myutil.statim(imagename+".diff") myutil.nextfig() if showfidelity: # it gets its own scaling. discard = myutil.statim(imagename+".fidelity",showstats=False) myutil.nextfig() myutil.endfig(show=grscreen,filename=file) sim_min,sim_max,sim_rms,sim_units = myutil.statim(imagename+".image.flat",plot=False) # if not displaying still print stats: # 20100505 ia.stats changed to return Jy/bm: msg('Simulation rms: '+str(sim_rms/bmarea)+" Jy/pix = "+ str(sim_rms)+" Jy/bm",origin="analysis") msg('Simulation max: '+str(sim_max/bmarea)+" Jy/pix = "+ str(sim_max)+" Jy/bm",origin="analysis") #msg('Simulation rms: '+str(sim_rms)+" Jy/pix = "+ # str(sim_rms*bmarea)+" Jy/bm",origin="analysis") #msg('Simulation max: '+str(sim_max)+" Jy/pix = "+ # str(sim_max*bmarea)+" Jy/bm",origin="analysis") msg('Beam bmaj: '+str(beam['major']['value'])+' bmin: '+str(beam['minor']['value'])+' bpa: '+str(beam['positionangle']['value']),origin="analysis") # cleanup - delete newmodel, newmodel.flat etc # flat kept by user request CAS-5509 # if os.path.exists(imagename+".image.flat"): # shutil.rmtree(imagename+".image.flat") if os.path.exists(imagename+".residual.flat"): shutil.rmtree(imagename+".residual.flat") # .flux.pbcoverage is nessesary for feather. #if os.path.exists(imagename+".flux.pbcoverage"): # shutil.rmtree(imagename+".flux.pbcoverage") absdiff = imagename + '.absdiff' if os.path.exists(absdiff): shutil.rmtree(absdiff) absconv = imagename + '.absconv' if os.path.exists(absconv): shutil.rmtree(absconv) # if os.path.exists(imagename+".diff"): # shutil.rmtree(imagename+".diff") if os.path.exists(imagename+".quick.psf") and os.path.exists(imagename+".psf"): shutil.rmtree(imagename+".quick.psf") finalize_tools() if myutil.isreport(): myutil.closereport() except TypeError, e: finalize_tools() #msg("simanalyze -- TypeError: %s" % e,priority="error") casalog.post("simanalyze -- TypeError: %s" % e, priority="ERROR") raise TypeError, e return
def plotms(vis=None, gridrows=None, gridcols=None, rowindex=None, colindex=None, plotindex=None, xaxis=None, xdatacolumn=None, yaxis=None, ydatacolumn=None, yaxislocation=None, selectdata=None, field=None, spw=None, timerange=None, uvrange=None, antenna=None, scan=None, correlation=None, array=None, observation=None, intent=None, feed=None, msselect=None, averagedata=None, avgchannel=None, avgtime=None, avgscan=None, avgfield=None, avgbaseline=None, avgantenna=None, avgspw=None, scalar=None, transform=None, freqframe=None, restfreq=None, veldef=None, shift=None, extendflag=None, extcorr=None, extchannel=None, iteraxis=None, xselfscale=None, yselfscale=None, xsharedaxis=None, ysharedaxis=None, customsymbol=None, symbolshape=None, symbolsize=None, symbolcolor=None, symbolfill=None, symboloutline=None, coloraxis=None, customflaggedsymbol=None, flaggedsymbolshape=None, flaggedsymbolsize=None, flaggedsymbolcolor=None, flaggedsymbolfill=None, flaggedsymboloutline=None, plotrange=None, title=None, titlefont=None, xlabel=None, xaxisfont=None, ylabel=None, yaxisfont=None, showmajorgrid=None, majorwidth=None, majorstyle=None, majorcolor=None, showminorgrid=None, minorwidth=None, minorstyle=None, minorcolor=None, showlegend=None, legendposition=None, plotfile=None, expformat=None, exprange=None, highres=None, dpi=None, width=None, height=None, overwrite=None, showgui=None, clearplots=None, callib=None, headeritems=None): # we'll add these later # extspw=None, extantenna=None, # exttime=None, extscans=None, extfield=None, """ Task for plotting and interacting with visibility data. A variety of axes choices (including data column) along with MS selection and averaging options are provided for data selection. Flag extension parameters are also available for flagging operations in the plotter. All of the provided parameters can also be set using the GUI once the application has been launched. Additional and more specific operations are available through the GUI and/or through the plotms tool (pm). Keyword arguments: vis -- input visibility dataset default: '' gridrows -- Number of subplot rows. default: 1 gridcols -- Number of subplot columns. default: 1 rowindex -- Row location of the subplot (0-based). default: 0 colindex -- Column location of the subplot (0-based). default: 0 plotindex -- Index to address a subplot (0-based). default: 0 xaxis, yaxis -- what to plot on the two axes default: '' (uses PlotMS defaults/current set). >>> xaxis, yaxis expandable parameters xdatacolumn, ydatacolumn -- which data column to use for data axes default: '' (uses PlotMS default/current set). yaxislocation -- whether the data should be plotted using the left or right y-axis default: '' (uses PlotMS default). iteraxis -- what axis to iterate on when doing iteration plots default: '' >>> xsharedaxis, ysharedaxis, xselfscale, yselfscale expandable parameters xselfscale -- If true, iterated plots should share a common x-axis label per column. default: False. yselfscale -- If true, iterated plots should share a common y-axis label per row. default: False. xsharedaxis -- use a common x-axis for vertically aligned plots (must also set xselfscale=True) default: False. ysharedaxis -- use a common y-axis for horizontally aligned plots (must also set yselfscale=True) default: False. selectdata -- data selection parameters flag (see help par.selectdata for more detailed information) default: False >>> selectdata expandable parameters field -- select using field ID(s) or field name(s) default: '' (all). spw -- select using spectral window/channels default: '' (all) timerange -- select using time range default: '' (all). uvrange -- select using uvrange default: '' (all). antenna -- select using antenna/baseline default: '' (all). scan -- select using scan number default: '' (all). correlation -- select using correlations default: '' (all). array -- select using (sub)-array range default: '' (all). observation -- select by observation ID(s). default: '' (all). intent -- select observing intent default: '' (no selection by intent) intent='*BANDPASS*' (selects data labelled with BANDPASS intent) feed -- select feed ID default: '' (all) feed='1~2' msselect -- TaQL selection expression default: '' (all). averagedata -- data averaging parameters flag default: False. >>> averagedata expandable parameters avgchannel -- average over channel? either blank for none, or a value in channels. default: '' (none). avgtime -- average over time? either blank for none, or a value in seconds. default: '' (none). avgscan -- average over scans? only valid if time averaging is turned on. default: False. avgfield -- average over fields? only valid if time averaging is turned on. default: False. avgbaseline -- average over all baselines? mutually exclusive with avgantenna. default: False. avgantenna -- average by per-antenna? mutually exclusive with avgbaseline. default: False. avgspw -- average over all spectral windows? default: False. extendflag -- have flagging extend to other data points? default: False. >>> extendflag expandable parameters extcorr -- extend flags based on correlation? blank = none. default: ''. extchannel -- extend flags based on channel? default: False. extspw -- extend flags based on spw? default: False. extantenna -- extend flags based on antenna? should be either blank, 'all' for all baselines, or an antenna-based value. default: ''. exttime -- extend flags based on time (within scans)? default: False. extscans -- extend flags based on scans? only valid if time extension is turned on. default: False. extfield -- extend flags based on field? only valid if time extension is turned on. default: False. showgui -- Whether or not to display the plotting GUI default: True; example showgui=False coloraxis -- which axis to use for colorizing default: '' (ignored - same as colorizing off) title -- title along top of plot (called "canvas" in some places) titlefont -- plot title font size default: 0 (autosize depending on grid) exprange -- Export all iteration plots ('all') or only the current one. default: '' (only export the current iteration plot) xlabel, ylabel -- text to label horiz. and vert. axes, with formatting (%% and so on) xaxisfont, yaxisfont -- int for axis font size showlegend -- show a legend on the plot default: False legendposition -- position for the legend. Legends can be interior or exterior to the plot Interior legends can be located in the upper right, lower right, upper left, or lower left. Exterior legends can be located on the right, left, top, or bottom. default: 'upperright' clearplots -- clear existing plots so that the new ones coming in can replace them. callib -- calibration library string, list of strings, or filename for on-the-fly calibration headeritems -- string of comma-separated page header items keywords """ # Check if DISPLAY environment variable is set. if os.getenv('DISPLAY') == None: casalog.post( 'ERROR: DISPLAY environment variable is not set! Cannot open plotms.', 'SEVERE') return False if plotfile: if not os.path.dirname(plotfile): # CAS-7148: Use dir that user cd'ed to in casapy session # instead of dir that plotfile = os.path.join(os.getcwd(), plotfile) if (os.path.exists(plotfile) and not overwrite): casalog.post( "Plot file " + plotfile + " exists and overwrite is false, cannot write the file", "SEVERE") return False try: # Check synonyms # format is: synonym['new_term'] = 'existing_term', with # the existing term being what's coded in PlotMSConstants.h (case insensitive) # CAS-8532 match capitalization in axis names in GUI synonyms = {} synonyms['Scan'] = 'scan' synonyms['Field'] = 'field' synonyms['Time'] = 'time' synonyms['timeinterval'] = synonyms['timeint'] = synonyms[ 'time_interval'] = synonyms['Interval'] = 'interval' synonyms['Spw'] = 'spw' synonyms['chan'] = synonyms['Channel'] = 'channel' synonyms['freq'] = synonyms['Frequency'] = 'frequency' synonyms['vel'] = synonyms['Velocity'] = 'velocity' synonyms['correlation'] = synonyms['Corr'] = 'corr' synonyms['ant1'] = synonyms['Antenna1'] = 'antenna1' synonyms['ant2'] = synonyms['Antenna2'] = 'antenna2' synonyms['Baseline'] = 'baseline' synonyms['Row'] = 'row' synonyms['Observation'] = 'observation' synonyms['Intent'] = 'intent' synonyms['Feed1'] = 'feed1' synonyms['Feed2'] = 'feed2' synonyms['amplitude'] = synonyms['Amp'] = 'amp' synonyms['Phase'] = 'phase' synonyms['Real'] = 'real' synonyms['imaginary'] = synonyms['Imag'] = 'imag' synonyms['weight'] = synonyms['Wt'] = synonyms['Weight'] = 'wt' synonyms['wtamp'] = synonyms['Wt*Amp'] = 'wtamp' synonyms['weightspectrum'] = synonyms['WtSp'] = synonyms[ 'WeightSpectrum'] = 'wtsp' synonyms['Sigma'] = 'sigma' synonyms['sigmaspectrum'] = synonyms['SigmaSpectrum'] = synonyms[ 'SigmaSp'] = 'sigmasp' synonyms['Flag'] = 'flag' synonyms['FlagRow'] = 'flagrow' synonyms['UVdist'] = 'uvdist' synonyms['uvdistl'] = synonyms['uvdist_l'] = synonyms[ 'UVwave'] = 'uvwave' synonyms['U'] = 'u' synonyms['V'] = 'v' synonyms['W'] = 'w' synonyms['Uwave'] = 'uwave' synonyms['Vwave'] = 'vwave' synonyms['Wwave'] = 'wwave' synonyms['Azimuth'] = 'azimuth' synonyms['Elevation'] = 'elevation' synonyms['hourang'] = synonyms['HourAngle'] = 'hourangle' synonyms['parang'] = synonyms['parallacticangle'] = synonyms[ 'ParAngle'] = 'parangle' synonyms['ant'] = synonyms['Antenna'] = 'antenna' synonyms['Ant-Azimuth'] = 'ant-azimuth' synonyms['Ant-Elevation'] = 'ant-elevation' synonyms['ant-parallacticangle'] = synonyms['ant-parang'] = synonyms[ 'Ant-ParAngle'] = 'ant-parangle' synonyms['gamp'] = synonyms['gainamp'] = synonyms[ 'GainAmp'] = 'Gain Amplitude' synonyms['gphase'] = synonyms['gainphase'] = synonyms[ 'GainPhase'] = 'Gain Phase' synonyms['greal'] = synonyms['gainreal'] = synonyms[ 'GainReal'] = 'Gain Real' synonyms['gimag'] = synonyms['gainimag'] = synonyms[ 'GainImag'] = 'Gain Imag' synonyms['del'] = synonyms['delay'] = synonyms['Delay'] = 'delay' synonyms['swp'] = synonyms['swpower'] = synonyms[ 'switchedpower'] = synonyms['SwPower'] = synonyms[ 'spgain'] = 'swpower' synonyms['tsys'] = synonyms['Tsys'] = synonyms['TSYS'] = 'tsys' synonyms['opac'] = synonyms['opacity'] = synonyms['Opac'] = 'opac' synonyms['snr'] = synonyms['SNR'] = 'SNR' synonyms['radialvelocity'] = synonyms[ 'Radial Velocity'] = 'Radial Velocity [km/s]' synonyms['rho'] = synonyms['Distance'] = 'Distance (rho) [km]' if (synonyms.has_key(xaxis)): xaxis = synonyms[xaxis] if type(yaxis) is str: if (synonyms.has_key(yaxis)): yaxis = synonyms[yaxis] elif type(yaxis) is list: for index, axis in enumerate(yaxis): if (synonyms.has_key(axis)): yaxis[index] = synonyms[axis] if type(coloraxis) is str: if (synonyms.has_key(coloraxis)): coloraxis = synonyms[coloraxis] # synonyms for data columns (only one, so just hardcode it) if (xdatacolumn == 'cor' or xdatacolumn == 'corr'): xdatacolumn = 'corrected' if (ydatacolumn == 'cor' or ydatacolumn == 'corr'): ydatacolumn = 'corrected' vis = vis.strip() if len(vis) > 0: vis = os.path.abspath(vis) if not os.path.exists(vis): casalog.post('\n'.join(['Input file not found:', vis]), "SEVERE") return False if not plotindex: plotindex = 0 if plotindex < 0: casalog.post("A negative plotindex is not valid.", "SEVERE") return False if clearplots and plotindex > 0: casalog.post( "A nonzero plotindex is not valid when clearing plots.", "SEVERE") return False # start plotms with the procmgr, use logfile myframe = stack_frame_find() if myframe['casa']['state']['init_version'] > 0: from casa_system import procmgr pmsrun = procmgr.running("plotms") pms = procmgr.fetch("plotms") try: if pmsrun and not pms.is_alive(): # crash! pms.stop() pmsrun = False except AttributeError: # fetch failed: pms=None pass if not pmsrun: # start (or restart) plotmsApp = 'casaplotms' for dir in os.getenv('PATH').split(':'): dd = dir + os.sep + plotmsApp if os.path.exists(dd) and os.access(dd, os.X_OK): plotmsApp = dd break try: logfile = myframe['casa']['files']['logfile'] except KeyError: logfile = "" procmgr.create("plotms", [ plotmsApp, "--nogui", "--nopopups", "--casapy", "--logfilename=" + logfile ]) if procmgr.running("plotms"): # connect future calls to this plotms procpid = procmgr.fetch('plotms').pid pm.setPlotmsPid(procpid) # Determine whether this is going to be a scripting client or # a full GUI supporting user interaction. This must be done # before other properties are set because it affects the # constructor of plotms. pm.setShowGui(showgui) if pm.isDrawing() and clearplots: casalog.post( "Plotms is running in GUI mode and cannot be run again until the current drawing completes.", "SEVERE") return False #Clear any existing plots. if clearplots: pm.clearPlots() gridChange = False if gridrows > 0 or gridcols > 0: gridChange = True if not gridrows: gridrows = 1 if not gridcols: gridcols = 1 if gridChange: pm.setGridSize(gridrows, gridcols) pm.setPlotMSFilename(vis, False, plotindex) if type(yaxis) is tuple: yaxis = yaxis[0] if not yaxis or type(yaxis) is str: if not yaxislocation or not type(yaxislocation) is str: yaxislocation = 'left' if not ydatacolumn or not type(ydatacolumn) is str: ydatacolumn = '' if not yaxis: yaxis = '' pm.setPlotAxes(xaxis, yaxis, xdatacolumn, ydatacolumn, yaxislocation, False, plotindex, 0) else: yAxisCount = len(yaxis) yDataCount = 0 if ydatacolumn != ['']: yDataCount = len(ydatacolumn) yLocationCount = 0 if yaxislocation != ['']: yLocationCount = len(yaxislocation) '''Make sure all the y-axis values are unique.''' uniqueY = True for i in range(0, yAxisCount): yDataColumnI = '' if i < yDataCount: yDataColumnI = ydatacolumn[i] for j in range(0, i): if yaxis[j] == yaxis[i]: yDataColumnJ = '' if j < yDataCount: yDataColumnJ = ydatacolumn[j] if yDataColumnI == yDataColumnJ: uniqueY = False break if not uniqueY: break if (uniqueY): for i in range(0, yAxisCount): yDataColumn = '' if i < yDataCount: yDataColumn = ydatacolumn[i] yAxisLocation = 'left' if i < yLocationCount: yAxisLocation = yaxislocation[i] pm.setPlotAxes(xaxis, yaxis[i], xdatacolumn, yDataColumn, yAxisLocation, False, plotindex, i) else: raise Exception, 'Please remove duplicate y-axes.' # Set selection if (selectdata and os.path.exists(vis)): pm.setPlotMSSelection(field, spw, timerange, uvrange, antenna, scan, correlation, array, str(observation), intent, feed, msselect, False, plotindex) else: pm.setPlotMSSelection('', '', '', '', '', '', '', '', '', '', '', '', False, plotindex) # Set averaging if not averagedata: avgchannel = avgtime = '' avgscan = avgfield = avgbaseline = avgantenna = avgspw = False scalar = False if avgbaseline and avgantenna: casalog.post( 'Averaging over baselines is mutually exclusive with per-antenna averaging.', "SEVERE") return False if avgchannel and (float(avgchannel) < 0.0): casalog.post('Cannot average negative number of channels', "SEVERE") return False try: if avgtime and (float(avgtime) < 0.0): casalog.post('Cannot average negative time value', "SEVERE") return False except ValueError: casalog.post( 'avgtime value must be numerical string in seconds (no units)', "SEVERE") return False pm.setPlotMSAveraging(avgchannel, avgtime, avgscan, avgfield, avgbaseline, avgantenna, avgspw, scalar, False, plotindex) # Set transformations if not transform: freqframe = '' restfreq = '' veldef = 'RADIO' shift = [0.0, 0.0] pm.setPlotMSTransformations(freqframe, veldef, restfreq, shift[0], shift[1], False, plotindex) # Set calibration: None, string (filename), dictionary useCallib = False callibString = '' if isinstance(callib, str): # Determine if filename or string of params if '=' in callib: useCallib = True callibString = callib else: callibFile = callib.strip() if len(callibFile) > 0: callibFile = os.path.abspath(callib) if os.path.exists(callibFile): useCallib = True callibString = callibFile else: casalog.post("Callib file does not exist") raise RuntimeError("Callib file does not exist") elif isinstance(callib, list): if len(callib[0] ) > 0: # no param is a list (default in plotms.xml?) useCallib = True callibString = ",".join(callib) pm.setPlotMSCalibration(useCallib, callibString, False, plotindex) # Set flag extension # for now, some options here are not available: # pm.setFlagExtension(extendflag, extcorrelation, extchannel, extspw, extantenna, exttime, extscans, extfield) extcorrstr = '' if extcorr: extcorrstr = 'all' pm.setFlagExtension(extendflag, extcorrstr, extchannel) # Export range if not exprange or exprange == "": exprange = 'current' pm.setExportRange(exprange) if not dpi: dpi = -1 if not width: width = -1 if not height: height = -1 # Set stuff that informs the plot on additional axes # (iteration, colorization, etc.) # (Iteration) if not iteraxis: iteraxis = "" if iteraxis == "": xselfscale = yselfscale = False xsharedaxis = ysharedaxis = False if not rowindex: rowindex = 0 if not colindex: colindex = 0 if not xselfscale: xselfscale = False if not yselfscale: yselfscale = False if not xsharedaxis: xsharedaxis = False if not ysharedaxis: ysharedaxis = False if not xselfscale and xsharedaxis: casalog.post( "Plots cannot share an x-axis unless they use the same x-axis scale.", "ERROR") return False if not yselfscale and ysharedaxis: casalog.post( "Plots cannot share a y-axis unless they use the same y-axis scale.", "ERROR") return False pm.setPlotMSIterate(iteraxis, rowindex, colindex, xselfscale, yselfscale, xsharedaxis, ysharedaxis, False, plotindex) # (Colorization) if coloraxis: pm.setColorAxis(coloraxis, False, plotindex) # Set custom symbol # Make the custom symbol into a list if it is not already. if type(customsymbol) is bool and customsymbol: customSymbolValue = customsymbol customsymbol = [customSymbolValue] if type(symbolshape) is str: symbolValue = symbolshape symbolshape = [symbolValue] if type(symbolsize) is int: symbolValue = symbolsize symbolsize = [symbolValue] if type(symbolcolor) is str: symbolValue = symbolcolor symbolcolor = [symbolValue] if type(symbolfill) is str: symbolValue = symbolfill symbolfill = [symbolValue] if type(symboloutline) is bool: symbolValue = symboloutline symboloutline = [symbolValue] if type(customsymbol) is list: customSymbolCount = len(customsymbol) for i in range(0, customSymbolCount): if i >= len(symbolshape) or not symbolshape[i]: symbolShapeI = 'autoscaling' else: symbolShapeI = symbolshape[i] symbolShape = symbolShapeI if customsymbol[i]: if i >= len(symbolsize) or not symbolsize[i]: symbolSizeI = 2 else: symbolSizeI = symbolsize[i] symbolSize = symbolSizeI if i >= len(symbolcolor) or not symbolcolor[i]: symbolColorI = '0000ff' else: symbolColorI = symbolcolor[i] symbolColor = symbolColorI if i >= len(symbolfill) or not symbolfill[i]: symbolFillI = 'fill' else: symbolFillI = symbolfill[i] symbolFill = symbolFillI if type(symboloutline) is bool: symbolOutlineI = symboloutline elif type(symboloutline) is list: if i >= len(symboloutline) or not symboloutline[i]: symbolOutlineI = False else: symbolOutlineI = symboloutline[i] else: symbolOutlineI = False symbolOutline = symbolOutlineI else: symbolSize = 2 symbolColor = '0000ff' symbolFill = 'fill' symbolOutline = False pm.setSymbol(symbolShape, symbolSize, symbolColor, symbolFill, symbolOutline, False, plotindex, i) # Set custom flagged symbol if type(customflaggedsymbol) is bool and customflaggedsymbol: customSymbolValue = customflaggedsymbol customflaggedsymbol = [customSymbolValue] if type(flaggedsymbolshape) is str: symbolValue = flaggedsymbolshape flaggedsymbolshape = [symbolValue] if type(flaggedsymbolsize) is int: symbolValue = flaggedsymbolsize flaggedsymbolsize = [symbolValue] if type(flaggedsymbolcolor) is str: symbolValue = flaggedsymbolcolor flaggedsymbolcolor = [symbolValue] if type(flaggedsymbolfill) is str: symbolValue = flaggedsymbolfill flaggedsymbolfill = [symbolValue] if type(flaggedsymboloutline) is bool: symbolValue = flaggedsymboloutline flaggedsymboloutline = [symbolValue] if type(customflaggedsymbol) is list: customSymbolCount = len(customflaggedsymbol) for i in range(0, customSymbolCount): if i >= len(flaggedsymbolshape) or not flaggedsymbolshape[i]: flaggedSymbolShapeI = 'nosymbol' else: flaggedSymbolShapeI = flaggedsymbolshape[i] flaggedSymbolShape = flaggedSymbolShapeI if customflaggedsymbol[i]: if i >= len(flaggedsymbolsize) or not flaggedsymbolsize[i]: flaggedSymbolSizeI = 2 else: flaggedSymbolSizeI = flaggedsymbolsize[i] flaggedSymbolSize = flaggedSymbolSizeI if i >= len( flaggedsymbolcolor) or not flaggedsymbolcolor[i]: flaggedSymbolColorI = 'ff0000' else: flaggedSymbolColorI = flaggedsymbolcolor[i] flaggedSymbolColor = flaggedSymbolColorI if i >= len(flaggedsymbolfill) or not flaggedsymbolfill[i]: flaggedSymbolFillI = 'fill' else: flaggedSymbolFillI = flaggedsymbolfill[i] flaggedSymbolFill = flaggedSymbolFillI if type(flaggedsymboloutline) is bool: flaggedSymbolOutlineI = flaggedsymboloutline elif type(flaggedsymboloutline) is list: if i >= len(flaggedsymboloutline ) or not flaggedsymboloutline[i]: flaggedSymbolOutlineI = False else: flaggedSymbolOutlineI = flaggedsymboloutline[i] else: flaggedSymbolOutlineI = False flaggedSymbolOutline = flaggedSymbolOutlineI else: flaggedSymbolSize = 2 flaggedSymbolColor = 'ff0000' flaggedSymbolFill = 'fill' flaggedSymbolOutline = False pm.setFlaggedSymbol(flaggedSymbolShape, flaggedSymbolSize, flaggedSymbolColor, flaggedSymbolFill, flaggedSymbolOutline, False, plotindex, i) #Determine if there should be a legend. if not showlegend: showlegend = False if not legendposition: legendposition = 'upperRight' pm.setLegend(showlegend, legendposition, False, plotindex) # Set various user-directed appearance parameters pm.setTitle(title, False, plotindex) pm.setTitleFont(titlefont, False, plotindex) pm.setXAxisLabel(xlabel, False, plotindex) pm.setXAxisFont(xaxisfont, False, plotindex) pm.setYAxisLabel(ylabel, False, plotindex) pm.setYAxisFont(yaxisfont, False, plotindex) pm.setGridParams(showmajorgrid, majorwidth, majorstyle, majorcolor, showminorgrid, minorwidth, minorstyle, minorcolor, False, plotindex) #Plot range if (len(plotrange) != 4): if (len(plotrange) == 0): plotrange = [0.0, 0.0, 0.0, 0.0] else: raise Exception, 'plotrange parameter has incorrect number of elements.' xrange = plotrange[1] - plotrange[0] yrange = plotrange[3] - plotrange[2] pm.setXRange((xrange <= 0.), plotrange[0], plotrange[1], False, plotindex) pm.setYRange((yrange <= 0.), plotrange[2], plotrange[3], False, plotindex) # Page Header Items # Python keywords for specifying header items are defined in CAS-8082, # Erik's comment dated 9-jun-2016 # Python / C++ header items keywords map # format is header_cpp_kw['python_keyword'] = 'c++_keyword', where # the c++ keyword is what's coded in PlotMSPageHeaderParam.h header_cpp_kw = {} header_cpp_kw['filename'] = 'filename' header_cpp_kw['ycolumn'] = 'y_columns' header_cpp_kw['obsdate'] = 'obs_start_date' header_cpp_kw['obstime'] = 'obs_start_time' header_cpp_kw['observer'] = 'obs_observer' header_cpp_kw['projid'] = 'obs_project' header_cpp_kw['telescope'] = 'obs_telescope_name' header_cpp_kw['targname'] = 'target_name' header_cpp_kw['targdir'] = 'target_direction' if type(headeritems) is str: cpp_headeritems = [] for headeritem_word in headeritems.split(','): py_headeritem = headeritem_word.strip() if py_headeritem == "": continue if py_headeritem in header_cpp_kw: ccp_headeritem = header_cpp_kw[py_headeritem] cpp_headeritems.append(ccp_headeritem) else: casalog.post( "Ignoring invalid page header item: " + py_headeritem, "WARN") pm.setPlotMSPageHeaderItems(','.join(cpp_headeritems), False, plotindex) # Update plotUpdated = pm.update() if not plotUpdated: casalog.post("There was a problem updating the plot.") else: # write file if requested if (plotfile != ""): casalog.post("Plot file " + plotfile, 'NORMAL') time.sleep(0.5) if (pm.isDrawing()): casalog.post( "Will wait until drawing of the plot has completed before exporting it", 'NORMAL') while (pm.isDrawing()): time.sleep(1.0) casalog.post("Exporting the plot.", 'NORMAL') casalog.post("Calling pm.save", 'NORMAL') plotUpdated = pm.save(plotfile, expformat, highres, dpi, width, height) except Exception, instance: plotUpdated = False print "Exception during plotms task: ", instance
import sys import os import string from locatescript import copydata from locatescript import locatescript from casa_stack_manip import stack_frame_find gl = stack_frame_find() # Short description def description(): return "Test of a complete ALMA SV data analysis (2 ASDMs from Sept 2011)" pass_on = { "asdm_dataset_name": "uid___A002_X2a5c2f_X54", "asdm_dataset2_name": "uid___A002_X2a5c2f_X220", "tsys_table": 'cal-tsys_X54.fdm', "tsys_table2": 'cal-tsys_X220.fdm', "mask1": 'M100cont-orig.mask', "mask2": 'M100line-orig.mask', "mask3": 'test-M100line-orig.mask' } def data(): ### return the data files that are needed by the regression script return [ pass_on["asdm_dataset_name"], pass_on["asdm_dataset2_name"], pass_on["tsys_table"], pass_on["tsys_table2"], pass_on["mask1"],
def tget(task=None, savefile=''): """ Get last input values from file on disk for a specified task: task -- Name of task default: <unset>; example: task='bandpass' <Options: type tasklist() for the complete list> savefile -- Output file for the task inputs default: task.last then task.saved example: savefile=task.orion """ try: myf = stack_frame_find() if task == None: if myf.has_key('task'): task = myf['task'] else: if myf.has_key('taskname'): task = myf['taskname'] myf['taskname'] = task myf['task'] = task if type(task) != str: task = task.__name__ myf['task'] = task myf['taskname'] = task parameter_checktype(['task', 'savefile'], [task, savefile], [str, str]) parameter_checkmenu('task', task, tasksum.keys()) ###Check if task exists by checking if task_defaults is defined if (not myf.has_key(task) and str(type(myf[task])) != "<type 'instance'>" and not hasattr(myf[task], "defaults")): raise TypeError, "task %s is not defined " % task if task == None: task = myf['task'] myf['task'] = task #f=zip(myf[taskname].func_code.co_varnames,myf[taskname].func_defaults) #for j in range(len(f)): # k=f[j][0] # print 'k is ',k # stst = myf[k] # if ( type(stst) == str ): # sex = k+"='"+stst+"'" # else: # sex = k+"="+str(stst) # exec(sex) if savefile == '': savefile = task + '.last' try: taskparameterfile = open(savefile, 'r') except: savefile = task + '.saved' try: taskparameterfile = open(savefile, 'r') except: print "Sorry - no task.last or .saved" return taskparameterfile.close() execfile(savefile) # Put the task parameters back into the global namespace f = zip(myf[task].__call__.func_code.co_varnames[1:], myf[task].__call__.func_defaults) missing_ks = [] for j in f: k = j[0] if k != 'self': try: myf[k] = eval(k) except NameError: missing_ks.append(k) if missing_ks: print "Did not find a saved value for", if len(missing_ks) > 1: print ', '.join(missing_ks[:-1]), print 'or', missing_ks[-1] else: print missing_ks[0] print "The set of task parameters has probably changed" print "since", savefile, "was written." print "Restored parameters from file " + savefile except TypeError, e: print "tget --error: ", e
def __call__( self, IDI=None, OUTPUTIDI=None, DiFXinput=None, DiFXcalc=None, doIF=None, linAntIdx=None, Range=None, ALMAant=None, spw=None, calAPP=None, calAPPTime=None, APPrefant=None, gains=None, interpolation=None, gainmode=None, XYavgTime=None, dterms=None, amp_norm=None, XYadd=None, XYdel=None, XYratio=None, usePcal=None, swapXY=None, swapRL=None, feedRotation=None, correctParangle=None, IDI_conjugated=None, plotIF=None, plotRange=None, plotAnt=None, excludeAnts=None, excludeBaselines=None, doSolve=None, solint=None, doTest=None, npix=None, solveAmp=None, solveMethod=None, calstokes=None, calfield=None, ): """\n\nVersion 1.8.2 -- Converts VLBI visibilities polarization basis. Detailed Description: \n\nVersion 1.8.2 -- Converts VLBI visibilities from mixed-polarization (linear-circular) into circular basis. Works with single VLBI stations as well as with calibrated phased arrays (i.e., phased ALMA).\n\n Arguments : IDI: Input FITS-IDI file with VLBI visibilities. It can also be a direcotry containing SWIN files from DiFX. Default Value: OUTPUTIDI: Output FITS-IDI file (or SWIN directory). If equal to IDI, the file(s) will be overwritten Default Value: DiFXinput: If SWIN files are being converted, this must be the *.input file used by DiFX. Default Value: DiFXcalc: If SWIN files are being converted, this must be the *.calc file used by DiFX. This is optional, but if it is not provided, the cross-polarization gain estimates may be incorrect if doSolve>0. Default Value: doIF: List of IFs to convert. Default means all. Default Value: [] linAntIdx: List of indices of the linear-polarization antennas in the IDI file (lowest index starts with 1) Default Value: [1] Range: Time range to convert (integer list; AIPS format). Default means all data Default Value: [] ALMAant: If ALMA has been used, this is the antenna table from the MS with the intra-ALMA visibilities. Default Value: spw: Spectral window in ALMAvis that contains the VLBI band. If negative, the program will derive it automatically. Default Value: -1 calAPP: If ALMA has been used, this is the combined ASDM_CALAPPPHASE table from the ASDM. The list of measurement sets can also be given (so the table is concatenated from all of them). Default Value: calAPPTime: Time shift and time tolerance (in sec) for the CALAPPPHASE table obtained from the ASDM. Default Value: [0.,5.] APPrefant: If not empty, re-reference the TelCal phases, assuming that the X-Y phase-difference table provided in \'gains\' (see keyword below) uses APPrefant as the reference antenna. Notice that the name of the gain table with the X-Y phase differences has to contain the string \'.XY0\'. Default Value: gains: Gain tables to pre-calibrate the linear-pol VLBI stations (one list of gains per linear-pol station). Default Value: [["NONE"]] interpolation: Interpolation type to use (one per calibration table). Tells whether to apply linear or nearest interpolation. Default is to use linear for all tables. Default Value: [] gainmode: Mode of gain calibration to impose (one per calibration table). Default is \'T\' for all tables, unless either the string \'XY0\', \'bandpass\' or \'Gxyamp\' appears in the table name. The gain types can be either \'G\' (i.e., split gains per polarization) or \'T\' (i.e., combine polarizations). Default Value: [] XYavgTime: Re-compute the G-mode gains by adding a time smoothing of X-Y differences to the T-mode gains. Default is NOT to do this (i.e., use the G-mode gains as given). If positive, use a running time average with this size (in seconds). Default Value: 0.0 dterms: D-term tables to pre-calibrate the linear-pol VLBI stations (one table per linear-pol station). Default Value: ["NONE"] amp_norm: If positive, normalize the amplitude correction to the X-Y average, and save the scaling factor (vs time) in an external (ASCII) file (ANTAB format, assuming a DPFU=amp_norm). If zero, or negative, apply the amplitude correction as is. Default Value: 0.01 XYadd: Add manually a phase between X and Y before conversion (in deg.). Either a list with one value per linear-pol station OR a list of lists (i.e., one value per IF for each antenna) OR a list of lists of lists (one value per channel, for each IF, for each linear-polarization antenna). Default Value: {} XYdel: Add manually a multiband delay between X and Y before conversion (in deg./chanel). One value per linear-pol station. Default Value: {} XYratio: Add manually an amplitude ratio between X and Y before conversion (R=X/Y). Follows the same format as XYadd. If a negative value is given for an antenna, the X/Y ratio will be estimated from its autocorrelations (the spectrum for antenna i will be computed using a running-median filter of width equal to -1/XYratio[i] of the IF bandwidth). If 0.0 is given for an antenna, the ratio will be estimated from the phasecal amplitudes (as long as usePcal is True). Default Value: {} usePcal: List of booleans (one boolean per linear-polarization station). If True, use the X-Y difference of phasecal tones as an estimate of the X-Y cross-polarization phase. Default means to NOT use the phasecals. Default Value: [] swapXY: Swap X-Y before conversion. One boolean per linear-pol VLBI station. Default Value: [False] swapRL: Swap R-L of the OTHER antenna(s) when plotting the fringes. Default Value: True feedRotation: Rotation angle of the feed (one value per antenna, in degrees). Default means zero degrees (so that X is truly horizontal for the linear-pol. antennas). These angles are used in the gain-solver step. Default Value: [] correctParangle: If True, the correction for parallactic angle is applied to the converted antenna(s). Default Value: False IDI_conjugated: Assume a swap in the baseline defintion (i.e., conjugation) of the FITS-IDI file. This has NO effect on SWIN files. Default Value: False plotIF: IF index(es) to plot. Default means to NOT plot. An empty list, [], means to plot ALL IFs being converted (but do not forget to set plotRange and plotAnt!). Default Value: -1 plotRange: Time range to plot (integer list; AIPS format). Default means to NOT plot Default Value: [] plotAnt: Index of the other antenna in the baseline to plot. Default means to NOT plot. Default Value: -1 excludeAnts: List of antennas (i.e., list of antenna codenames) to NOT use in the cross-polarization gain estimates. Default Value: [] excludeBaselines: List of baselines (i.e., a list of lists of two antenna codenames) to NOT use in the cross-polarization gain estimates. Default Value: [] doSolve: If negative, do not estimate the cross-polarization gains. If positive or zero, estimate the gains using a Global Cross-Pol Fringe Fitting (GCPFF). The gains are fitted with an error function (Chi Square) defined as:\n\n sum( doSolve*(RR/LL-1)^2 + (RL^2 + LR^2) ),\n\n so that doSolve=0 minimizes the cross-hand polarizations (so it assumes a small linear polarization of the source), whereas doSolve>>1 assumes a negligible Stokes V. Default Value: -1 solint: If solint[0] null or negative, solve the cross-polarization phase plus a multi-band delay (MBD). If not, solve in bandpass mode by averaging solint[0] channels per solution.\n Divide the solution time range (per scan) in solint[1] chunks (i.e., in solint[1] subscans). I.e., if solint[1]==1, the fringes are fully averaged in time for each scan (but corrected for the scan fringe rates) before the GPLFF condition is computed. solint[2] is the minimum time jump (in seconds) to split the data into different scans (default: 100 seconds). Default Value: [1,1] doTest: If true, only compute (and eventually plot), the data, but leave OUTPUTIDI untouched. Default Value: True npix: Number of pixels for the fringe plots (and fringe search). Default Value: 50 solveAmp: if the cross-polarization gains are being estimated, solve also for the X/Y amplitude ratios. Default Value: True solveMethod: Method for the minimization of the Chi squared in the GCPFF. Can be \'gradient\', \'Levenberg-Marquardt\' or \'COBYLA\'. Default Value: gradient calstokes: Stokes parameters, [I,Q,U,V] of the calibrator (of course, this is only used if doSolve is not negative). The total intensity is not needed in the calibration (i.e., calstokes[0] can be left to 1.0, so that the other parameters will correspond to fractional polarization). Default Value: [1.,0.,0.,0.] calfield: If not negative, field ID of the calibrator (useful if a time range covering several scans is being used in the GCPFF). If negative, use all data in the time range, regardless of the field ID. Default Value: -1 Returns: bool Example : For more information about the internals of PolConvert, please read: Marti-Vidal et al. 2016, Astronomy and Astrophysics, 587, 143 PROCEDURE: If a VLBI antenna used linear-feed receivers, PolConvert must first estimate the X-Y cross gain for that antenna (phase, amplitude, and multi-band delay) before the final conversion. Use the plotting option of PolConvert to plot a selected scan of a given baseline and that scan will be used to estimate the cross-polarization gains. PolConvert returns a list with the amplitude and phase cross-gains for all the antennas, as long as it is run in plotting mode. The user can then set these gain lists to XYadd and XYratio for a second run of PolConvert. Given an FITS-IDI file (or set of SWIN DiFX files) with phased-ALMA observations, the user must first calibrate completely (i.e., in full polarization) the corresponding ALMA measurement set. It is important to create it using asis='CALAPPPHASE' in the importasdm task. If more than one asdm was created in the observations, the user must concatenate all the CALAPPPHASE tables of each asdm, for PolConvert to work properly. This can be done with the following commands (we assume here that MSLIST is a python list with the names of the measurement sets for each asdm): for i,myms in enumerate(MSLIST): if i==0: os.system('cp -rf %s/ASDM_CALAPPPHASE ./CALAPPPHASE.tab'%myms) else: tb.open('%s/ASDM_CALAPPPHASE'%myms) tb.copyrows('./CALAPPPHASE.tab') tb.close() These lines will create the table './CALAPPPHASE.tab', to be used by PolConvert (i.e., the table specified in the 'calAPP' keyword). PolConvert can also do this for you, if you set calAPP = MSLIST. But check carefully the information that it will print, regarding the time coverage of both the CALAPPPHASE table and the MSs. Let us assume that the calibration tables are named 'gain.tb' and 'bandpass.tb' (there can be many others, for delay, XY-phase, etc.) and the D-term table is called 'dterms.tb'. Then, with this assumption: - If ALMA is the only station with linear receivers (let's say it is station number 1 in the FITS-IDI file), the call to PolConvert should be done with the following keyword values: - linAntIdx = [1] - Range = [] # i.e., all data will be converted - ALMAvis = 'TheALMAvisibilities.ms' - spw = 0 # it may be a good idea to split first the science spw, # before concatenating and calibrating the ms - calAPP = './CALAPPPHASE.tab' - calAPPTime = [0., 5.0] # The CALAPP entries sometime start and end # with time lags in between. The time tolerance # of 5 seconds should avoid problems related # to this. - gains = [['gain.tb','bandpass.tb']] - dterms = ['dterms.tb'] - doTest = False # to actually APPLY the changes, not only compute them! ################### SPECIAL CASE 1: If there was a second antenna with linear-polarization receivers, it can also be converted, but has to be listed after ALMA. Let us assume that this antenna has id=4 in the FITS-IDI file. Then: - linAntIdx = [1,4] # i.e., ALMA plus the other linear-pol. station. - gains = [ ['gain.tb','bandpass.tb'] , ['NONE'] ] # Notice that 'NONE' can be used to tell PolConvert not to apply # any calibration to antenna #4 before conversion. - dterms = [ 'dterms.dt' , 'NONE'] ################### SPECIAL CASE 2: If the user wants to check the conversion before applying it, PolConvert can plot the fringes for a given IF, baseline and time range. Let us assume we want to plot the baseline to antenna 2 (i.e., baseline 1-2) in the time range 0-07:30:00 to 0-07:31:00 (AIPS format). Then: - doTest = True # i.e., do NOT write on the FITS-IDI file! - plotIF = 1 # i.e., first IF in FITS-IDI file. - plotRange = [0,7,30,0,0,7,31,0] - Range = [0,7,30,0,0,7,31,0] # i.e., to not waste resources computing # things that we will not save nor plot. - plotAnt = 2 ################### SPECIAL CASE 2: For the two linear-pol antennas, use the pcal tones to correct the phase difference between X and Y. In addition to this, for the first antenna, the X/Y relative amplitude is estimated from the phasecal tones. For the second antenna, the X/Y amplitude spectrum is estimated from the autocorrelations, using a running median filter of 51 channels (if the number of channels per IF is 510): - usePcal = [True,True] - XYratio = [-10., 0.0] Notice that, if the GCPFF algorithm is used to solve for the X/Y gains, these will be stored in the 'XYratio' and 'XYadd' keys of the returned dictionary, whereas the a-priori gains computed from the pcals and the autocorrelations will be stored as complex arrays in 'aPrioriXYGain'. ################### OTHER SPECIAL CASES (NOT FULLY TESTED): 1.- If two antennas have linear-pol receivers (i.e., ALMA plus another one) and the second one was correlated with the pol. channels swapped, then: - swapXY = [False, True] If it was ALMA the antenna with swapped pol. channels, then: - swapXY = [True, False] 2.- If the second antenna with linear-pol receivers had an offset of, say, 65 degrees between X and Y, this offset can be corrected before conversion: - XYadd = [0.0, 65.] If there are 4 IFs and the X-Y phases for the second antenna differ among IFs, we can set them in the following way: - XYadd = [[0.0, 0.0, 0.0, 0.0], [65., 30., 25., 10.]] NOTICE THAT POLCONVERT CAN ESTIMATE THE XYADD AND XYRATIO, FROM THE SCAN THAT YOU ASK IT TO PLOT. IF IT IS A SCAN OF A STRONG CALIBRATOR, POLCONVERT CAN ESTIMATE ALL THESE QUANTITIES FOR YOUR VLBI STATIONS WITH LINEAR FEEDS. ######################################### ######################################### ##### A TYPICAL ALMA DATA REDUCTION ##### 1.- Import all ASDMs into measurement sets. BEWARE THAT YOU SET asis='CalAppPhase' 2.- Find out the spw that matches the VLBI frequency setup. Split it for each measurement set. 3.- Concatenate the splitted measurement sets. 4.- Concatenate the 'ASDM_CALAPPPHASE' tables of the measurement sets into a new CALAPPPHASE TABLE (see help above). 5.- Calibrate the concatenated measurement set (full-polarization calibration) using standard ALMA procedures. 6.- Execute polconvert, feeding it with the calibration tables and the CALAPPPHASE table, in mode "doTest = True", and applying it only to a short (say, 1-2 minutes) scan of a strong source (e.g., the phase calibrator). Select a given IF and antenna to plot (it's better to select a short VLBI baseline to ALMA). 7.- The program will plot the fringes and print an estimate of the extra X/Y phase that should be added to ALMA. This number should be small, as long as the calibration is OK. If a large number is found, and you see large cross-hand polarizations, add this extra X-Y phase to polconvert, via the keyword "XYadd" 8.- Re-execute polconvert in test mode. Check whether the conversion is satisfactory. 9.- Once satisfied with the conversion of the selected calibrator scan, execute polconvert over the shole dataset with "doTest = False". 10.- It may be a good idea to do extra sanity checks, like the possible dependence of XYadd with IF and/or its eventual time evolution. All these effects should have been properly corrected if the measurement set calibration was successful. Different XYadd phases can be added to different IFs by converting each IF separately. # END OF POLCONVERT DOCUMENTATION ####################################### """ if not hasattr(self, "__globals__") or self.__globals__ == None: self.__globals__ = stack_frame_find() #casac = self.__globals__['casac'] casalog = self.__globals__['casalog'] casa = self.__globals__['casa'] #casalog = casac.casac.logsink() self.__globals__['__last_task'] = 'polconvert' self.__globals__['taskname'] = 'polconvert' ### self.__globals__['update_params'](func=self.__globals__['taskname'], printtext=False, ipython_globals=self.__globals__) ### ### #Handle globals or user over-ride of arguments # if type(self.__call__.func_defaults) is NoneType: function_signature_defaults = {} else: function_signature_defaults = dict( zip(self.__call__.func_code.co_varnames[1:], self.__call__.func_defaults)) useLocalDefaults = False for item in function_signature_defaults.iteritems(): key, val = item keyVal = eval(key) if (keyVal == None): #user hasn't set it - use global/default pass else: #user has set it - use over-ride if (key != 'self'): useLocalDefaults = True myparams = {} if useLocalDefaults: for item in function_signature_defaults.iteritems(): key, val = item keyVal = eval(key) exec('myparams[key] = keyVal') self.parameters[key] = keyVal if (keyVal == None): exec('myparams[key] = ' + key + ' = self.itsdefault(key)') keyVal = eval(key) if (type(keyVal) == dict): if len(keyVal) > 0: exec('myparams[key] = ' + key + ' = keyVal[len(keyVal)-1][\'value\']') else: exec('myparams[key] = ' + key + ' = {}') else: print '' myparams['IDI'] = IDI = self.parameters['IDI'] myparams['OUTPUTIDI'] = OUTPUTIDI = self.parameters['OUTPUTIDI'] myparams['DiFXinput'] = DiFXinput = self.parameters['DiFXinput'] myparams['DiFXcalc'] = DiFXcalc = self.parameters['DiFXcalc'] myparams['doIF'] = doIF = self.parameters['doIF'] myparams['linAntIdx'] = linAntIdx = self.parameters['linAntIdx'] myparams['Range'] = Range = self.parameters['Range'] myparams['ALMAant'] = ALMAant = self.parameters['ALMAant'] myparams['spw'] = spw = self.parameters['spw'] myparams['calAPP'] = calAPP = self.parameters['calAPP'] myparams['calAPPTime'] = calAPPTime = self.parameters['calAPPTime'] myparams['APPrefant'] = APPrefant = self.parameters['APPrefant'] myparams['gains'] = gains = self.parameters['gains'] myparams['interpolation'] = interpolation = self.parameters[ 'interpolation'] myparams['gainmode'] = gainmode = self.parameters['gainmode'] myparams['XYavgTime'] = XYavgTime = self.parameters['XYavgTime'] myparams['dterms'] = dterms = self.parameters['dterms'] myparams['amp_norm'] = amp_norm = self.parameters['amp_norm'] myparams['XYadd'] = XYadd = self.parameters['XYadd'] myparams['XYdel'] = XYdel = self.parameters['XYdel'] myparams['XYratio'] = XYratio = self.parameters['XYratio'] myparams['usePcal'] = usePcal = self.parameters['usePcal'] myparams['swapXY'] = swapXY = self.parameters['swapXY'] myparams['swapRL'] = swapRL = self.parameters['swapRL'] myparams['feedRotation'] = feedRotation = self.parameters[ 'feedRotation'] myparams['correctParangle'] = correctParangle = self.parameters[ 'correctParangle'] myparams['IDI_conjugated'] = IDI_conjugated = self.parameters[ 'IDI_conjugated'] myparams['plotIF'] = plotIF = self.parameters['plotIF'] myparams['plotRange'] = plotRange = self.parameters['plotRange'] myparams['plotAnt'] = plotAnt = self.parameters['plotAnt'] myparams['excludeAnts'] = excludeAnts = self.parameters[ 'excludeAnts'] myparams['excludeBaselines'] = excludeBaselines = self.parameters[ 'excludeBaselines'] myparams['doSolve'] = doSolve = self.parameters['doSolve'] myparams['solint'] = solint = self.parameters['solint'] myparams['doTest'] = doTest = self.parameters['doTest'] myparams['npix'] = npix = self.parameters['npix'] myparams['solveAmp'] = solveAmp = self.parameters['solveAmp'] myparams['solveMethod'] = solveMethod = self.parameters[ 'solveMethod'] myparams['calstokes'] = calstokes = self.parameters['calstokes'] myparams['calfield'] = calfield = self.parameters['calfield'] result = None # # The following is work around to avoid a bug with current python translation # mytmp = {} mytmp['IDI'] = IDI mytmp['OUTPUTIDI'] = OUTPUTIDI mytmp['DiFXinput'] = DiFXinput mytmp['DiFXcalc'] = DiFXcalc mytmp['doIF'] = doIF mytmp['linAntIdx'] = linAntIdx mytmp['Range'] = Range mytmp['ALMAant'] = ALMAant mytmp['spw'] = spw mytmp['calAPP'] = calAPP mytmp['calAPPTime'] = calAPPTime mytmp['APPrefant'] = APPrefant mytmp['gains'] = gains mytmp['interpolation'] = interpolation mytmp['gainmode'] = gainmode mytmp['XYavgTime'] = XYavgTime mytmp['dterms'] = dterms mytmp['amp_norm'] = amp_norm mytmp['XYadd'] = XYadd mytmp['XYdel'] = XYdel mytmp['XYratio'] = XYratio mytmp['usePcal'] = usePcal mytmp['swapXY'] = swapXY mytmp['swapRL'] = swapRL mytmp['feedRotation'] = feedRotation mytmp['correctParangle'] = correctParangle mytmp['IDI_conjugated'] = IDI_conjugated mytmp['plotIF'] = plotIF mytmp['plotRange'] = plotRange mytmp['plotAnt'] = plotAnt mytmp['excludeAnts'] = excludeAnts mytmp['excludeBaselines'] = excludeBaselines mytmp['doSolve'] = doSolve mytmp['solint'] = solint mytmp['doTest'] = doTest mytmp['npix'] = npix mytmp['solveAmp'] = solveAmp mytmp['solveMethod'] = solveMethod mytmp['calstokes'] = calstokes mytmp['calfield'] = calfield pathname = "file:///home/marti/WORKAREA/LAUNCHPAD/PolConvert/polconvertsd/" trec = casac.casac.utils().torecord(pathname + 'polconvert.xml') casalog.origin('polconvert') try: #if not trec.has_key('polconvert') or not casac.casac.utils().verify(mytmp, trec['polconvert']) : #return False casac.casac.utils().verify(mytmp, trec['polconvert'], True) scriptstr = [''] saveinputs = self.__globals__['saveinputs'] # Save .last file for this task execution. MPI servers don't write it (CASR-329). from mpi4casa.MPIEnvironment import MPIEnvironment do_full_logging = MPIEnvironment.is_mpi_disabled_or_client() if type(self.__call__.func_defaults) is NoneType: saveinputs = '' else: saveinputs('polconvert', 'polconvert.last', myparams, self.__globals__, scriptstr=scriptstr, do_save_inputs=do_full_logging) tname = 'polconvert' spaces = ' ' * (18 - len(tname)) casalog.post('\n##########################################' + '\n##### Begin Task: ' + tname + spaces + ' #####') # Don't do telemetry from MPI servers (CASR-329) if do_full_logging and casa['state']['telemetry-enabled']: #casalog.poststat('Begin Task: ' + tname) task_starttime = str(datetime.datetime.now()) if type(self.__call__.func_defaults) is NoneType: casalog.post(scriptstr[0] + '\n', 'INFO') else: casalog.post(scriptstr[1][1:] + '\n', 'INFO') # Effective call to the task as defined in gcwrap/python/scripts/task_* result = polconvert( IDI, OUTPUTIDI, DiFXinput, DiFXcalc, doIF, linAntIdx, Range, ALMAant, spw, calAPP, calAPPTime, APPrefant, gains, interpolation, gainmode, XYavgTime, dterms, amp_norm, XYadd, XYdel, XYratio, usePcal, swapXY, swapRL, feedRotation, correctParangle, IDI_conjugated, plotIF, plotRange, plotAnt, excludeAnts, excludeBaselines, doSolve, solint, doTest, npix, solveAmp, solveMethod, calstokes, calfield) if do_full_logging and casa['state']['telemetry-enabled']: task_endtime = str(datetime.datetime.now()) casalog.poststat('Task ' + tname + ' complete. Start time: ' + task_starttime + ' End time: ' + task_endtime) casalog.post('##### End Task: ' + tname + ' ' + spaces + ' #####' + '\n##########################################') except Exception, instance: if (self.__globals__.has_key('__rethrow_casa_exceptions') and self.__globals__['__rethrow_casa_exceptions']): raise else: #print '**** Error **** ',instance tname = 'polconvert' casalog.post('An error occurred running task ' + tname + '.', 'ERROR') pass