##################### generated by xml-casa (v2) from hif_uvcontfit.xml #############
##################### 93ce4e4b04efed7ca90a4d7f99ab9aa3 ##############################
from __future__ import absolute_import
from casashell.private.stack_manip import find_local as __sf__
from casashell.private.stack_manip import find_frame as _find_frame
from casatools.typecheck import validator as _pc
from casatools.coercetype import coerce as _coerce
from pipeline.hif.cli import hif_uvcontfit as _hif_uvcontfit_t
from collections import OrderedDict
import numpy
import sys
import os
import shutil
[docs]def static_var(varname, value):
def decorate(func):
setattr(func, varname, value)
return func
return decorate
class _hif_uvcontfit:
"""
hif_uvcontfit ---- Fit the continuum in the UV plane
This task estimates the continuum emission by fitting polynomials to
the real and imaginary parts of the spectral windows and channels
selected by spw and exclude spw. This fit represents a model of
the continuum in all channels. Fit orders less than 2 are strongly
recommended. Spw window combination is not currently supported.
--------- parameter descriptions ---------------------------------------------
vis The list of input MeasurementSets. Defaults to the list of
MeasurementSets specified in the h_init or hif_importdata task.
'': use all MeasurementSets in the context
Examples: 'ngc5921.ms', ['ngc5921a.ms', ngc5921b.ms', 'ngc5921c.ms']
caltable The list of output Mueller matrix calibration tables one per
input MS.
'': The output names default to the standard pipeline name
scheme
contfile Name of the input file of per source / spw continuum regions
'': Defaults first to the file named in the context, next to a
file called 'cont.dat' in the pipeline working directory.
field The list of field names or field ids for which UV continuum
fits are computed. Defaults to all fields.
Eexamples: '3C279', '3C279, M82'
intent A string containing a comma delimited list of intents against
which the selected fields are matched.
'': Defaults to all data with TARGET intent.
spw The list of spectral windows and channels for which uv
continuum fits are computed.
'', Defaults to all science spectral windows.
Example: '11,13,15,17'
combine Data axes to be combined for solving. Axes are 'scan', 'spw',
or ''.
This option is currently not supported.
solint Time scale for the continuum fit
fitorder Polynomial order for the continuum fits
pipelinemode The pipeline operating mode.
In 'automatic' mode the pipeline determines the values of all
context defined pipeline inputs automatically.
In 'interactive' mode the user can set the pipeline context
defined parameters manually.
In 'getinputs' mode the user can check the settings of all
pipeline parameters without running the task.
dryrun Run the task (False) or just display the command (True)
acceptresults Add the results of the task to the pipeline context (True) or
reject them (False).
--------- examples -----------------------------------------------------------
"""
_info_group_ = """pipeline"""
_info_desc_ = """Fit the continuum in the UV plane"""
__schema = {'vis': {'type': 'cStrVec', 'coerce': [_coerce.to_list,_coerce.to_strvec]}, 'caltable': {'type': 'cStrVec', 'coerce': [_coerce.to_list,_coerce.to_strvec]}, 'contfile': {'type': 'cStr', 'coerce': _coerce.to_str}, 'field': {'type': 'cStr', 'coerce': _coerce.to_str}, 'intent': {'type': 'cStr', 'coerce': _coerce.to_str}, 'spw': {'type': 'cStr', 'coerce': _coerce.to_str}, 'combine': {'type': 'cStr', 'coerce': _coerce.to_str}, 'solint': {'type': 'cVariant', 'coerce': [_coerce.to_variant]}, 'fitorder': {'type': 'cInt'}, 'pipelinemode': {'type': 'cStr', 'coerce': _coerce.to_str, 'allowed': [ 'automatic', 'interactive', 'getinputs' ]}, 'dryrun': {'type': 'cBool'}, 'acceptresults': {'type': 'cBool'}}
def __init__(self):
self.__stdout = None
self.__stderr = None
self.__root_frame_ = None
def __globals_(self):
if self.__root_frame_ is None:
self.__root_frame_ = _find_frame( )
assert self.__root_frame_ is not None, "could not find CASAshell global frame"
return self.__root_frame_
def __to_string_(self,value):
if type(value) is str:
return "'%s'" % value
else:
return str(value)
def __validate_(self,doc,schema):
return _pc.validate(doc,schema)
def __do_inp_output(self,param_prefix,description_str,formatting_chars):
out = self.__stdout or sys.stdout
description = description_str.split( )
prefix_width = 23 + 16 + 4
output = [ ]
addon = ''
first_addon = True
while len(description) > 0:
## starting a new line.....................................................................
if len(output) == 0:
## for first line add parameter information............................................
if len(param_prefix)-formatting_chars > prefix_width - 1:
output.append(param_prefix)
continue
addon = param_prefix + ' #'
first_addon = True
addon_formatting = formatting_chars
else:
## for subsequent lines space over prefix width........................................
addon = (' ' * prefix_width) + '#'
first_addon = False
addon_formatting = 0
## if first word of description puts us over the screen width, bail........................
if len(addon + description[0]) - addon_formatting + 1 > self.term_width:
## if we're doing the first line make sure it's output.................................
if first_addon: output.append(addon)
break
while len(description) > 0:
## if the next description word puts us over break for the next line...................
if len(addon + description[0]) - addon_formatting + 1 > self.term_width: break
addon = addon + ' ' + description[0]
description.pop(0)
output.append(addon)
out.write('\n'.join(output) + '\n')
#--------- return nonsubparam values ----------------------------------------------
def __fitorder_dflt( self, glb ):
return int(1)
def __fitorder( self, glb ):
if 'fitorder' in glb: return glb['fitorder']
return int(1)
def __solint_dflt( self, glb ):
return 'int'
def __solint( self, glb ):
if 'solint' in glb: return glb['solint']
return 'int'
def __pipelinemode_dflt( self, glb ):
return 'automatic'
def __pipelinemode( self, glb ):
if 'pipelinemode' in glb: return glb['pipelinemode']
return 'automatic'
#--------- return inp/go default --------------------------------------------------
def __dryrun_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return bool(False)
return None
def __field_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return ""
if self.__pipelinemode( glb ) == "getinputs": return ""
return None
def __intent_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return ""
if self.__pipelinemode( glb ) == "getinputs": return ""
return None
def __vis_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return []
if self.__pipelinemode( glb ) == "getinputs": return []
return None
def __acceptresults_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return bool(True)
return None
def __contfile_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return ""
if self.__pipelinemode( glb ) == "getinputs": return ""
return None
def __combine_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return ""
if self.__pipelinemode( glb ) == "getinputs": return ""
return None
def __caltable_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return []
if self.__pipelinemode( glb ) == "getinputs": return []
return None
def __spw_dflt( self, glb ):
if self.__pipelinemode( glb ) == "interactive": return ""
if self.__pipelinemode( glb ) == "getinputs": return ""
return None
#--------- return subparam values -------------------------------------------------
def __vis( self, glb ):
if 'vis' in glb: return glb['vis']
dflt = self.__vis_dflt( glb )
if dflt is not None: return dflt
return [ ]
def __caltable( self, glb ):
if 'caltable' in glb: return glb['caltable']
dflt = self.__caltable_dflt( glb )
if dflt is not None: return dflt
return [ ]
def __contfile( self, glb ):
if 'contfile' in glb: return glb['contfile']
dflt = self.__contfile_dflt( glb )
if dflt is not None: return dflt
return ''
def __field( self, glb ):
if 'field' in glb: return glb['field']
dflt = self.__field_dflt( glb )
if dflt is not None: return dflt
return ''
def __intent( self, glb ):
if 'intent' in glb: return glb['intent']
dflt = self.__intent_dflt( glb )
if dflt is not None: return dflt
return ''
def __spw( self, glb ):
if 'spw' in glb: return glb['spw']
dflt = self.__spw_dflt( glb )
if dflt is not None: return dflt
return ''
def __combine( self, glb ):
if 'combine' in glb: return glb['combine']
dflt = self.__combine_dflt( glb )
if dflt is not None: return dflt
return ''
def __dryrun( self, glb ):
if 'dryrun' in glb: return glb['dryrun']
dflt = self.__dryrun_dflt( glb )
if dflt is not None: return dflt
return False
def __acceptresults( self, glb ):
if 'acceptresults' in glb: return glb['acceptresults']
dflt = self.__acceptresults_dflt( glb )
if dflt is not None: return dflt
return True
#--------- subparam inp output ----------------------------------------------------
def __vis_inp(self):
if self.__vis_dflt( self.__globals_( ) ) is not None:
description = 'The name of the input visibility file'
value = self.__vis( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'vis': value},{'vis': self.__schema['vis']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('vis',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __caltable_inp(self):
if self.__caltable_dflt( self.__globals_( ) ) is not None:
description = 'The list of output Mueller matrix calibration tables'
value = self.__caltable( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'caltable': value},{'caltable': self.__schema['caltable']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('caltable',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __contfile_inp(self):
if self.__contfile_dflt( self.__globals_( ) ) is not None:
description = 'Name of the input file of per source / spw continuum regions'
value = self.__contfile( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'contfile': value},{'contfile': self.__schema['contfile']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('contfile',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __field_inp(self):
if self.__field_dflt( self.__globals_( ) ) is not None:
description = 'Select field(s) using id(s) or name(s)'
value = self.__field( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'field': value},{'field': self.__schema['field']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('field',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __intent_inp(self):
if self.__intent_dflt( self.__globals_( ) ) is not None:
description = 'Select intents'
value = self.__intent( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'intent': value},{'intent': self.__schema['intent']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('intent',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __spw_inp(self):
if self.__spw_dflt( self.__globals_( ) ) is not None:
description = 'Spectral window / channels for fitting the continuum'
value = self.__spw( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'spw': value},{'spw': self.__schema['spw']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('spw',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __combine_inp(self):
if self.__combine_dflt( self.__globals_( ) ) is not None:
description = 'Data axes to combine for the continuum estimation (none, spw and/or scan)'
value = self.__combine( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'combine': value},{'combine': self.__schema['combine']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('combine',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __solint_inp(self):
description = 'Time scale for the continuum fit'
value = self.__solint( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'solint': value},{'solint': self.__schema['solint']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output('%-16.16s = %s%-23s%s' % ('solint',pre,self.__to_string_(value),post),description,0+len(pre)+len(post))
def __fitorder_inp(self):
description = 'Polynomial order for the continuum fits'
value = self.__fitorder( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'fitorder': value},{'fitorder': self.__schema['fitorder']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output('%-16.16s = %s%-23s%s' % ('fitorder',pre,self.__to_string_(value),post),description,0+len(pre)+len(post))
def __pipelinemode_inp(self):
description = 'The pipeline operating mode'
value = self.__pipelinemode( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'pipelinemode': value},{'pipelinemode': self.__schema['pipelinemode']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output('\x1B[1m\x1B[47m%-16.16s =\x1B[0m %s%-23s%s' % ('pipelinemode',pre,self.__to_string_(value),post),description,13+len(pre)+len(post))
def __dryrun_inp(self):
if self.__dryrun_dflt( self.__globals_( ) ) is not None:
description = 'Run the task (False) or just display the command (True)'
value = self.__dryrun( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'dryrun': value},{'dryrun': self.__schema['dryrun']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('dryrun',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
def __acceptresults_inp(self):
if self.__acceptresults_dflt( self.__globals_( ) ) is not None:
description = 'Add the results to the pipeline context'
value = self.__acceptresults( self.__globals_( ) )
(pre,post) = ('','') if self.__validate_({'acceptresults': value},{'acceptresults': self.__schema['acceptresults']}) else ('\x1B[91m','\x1B[0m')
self.__do_inp_output(' \x1B[92m%-13.13s =\x1B[0m %s%-23s%s' % ('acceptresults',pre,self.__to_string_(value),post),description,9+len(pre)+len(post))
#--------- global default implementation-------------------------------------------
@static_var('state', __sf__('casa_inp_go_state'))
def set_global_defaults(self):
self.set_global_defaults.state['last'] = self
glb = self.__globals_( )
if 'dryrun' in glb: del glb['dryrun']
if 'field' in glb: del glb['field']
if 'pipelinemode' in glb: del glb['pipelinemode']
if 'intent' in glb: del glb['intent']
if 'vis' in glb: del glb['vis']
if 'acceptresults' in glb: del glb['acceptresults']
if 'fitorder' in glb: del glb['fitorder']
if 'contfile' in glb: del glb['contfile']
if 'combine' in glb: del glb['combine']
if 'solint' in glb: del glb['solint']
if 'caltable' in glb: del glb['caltable']
if 'spw' in glb: del glb['spw']
#--------- inp function -----------------------------------------------------------
def inp(self):
print("# hif_uvcontfit -- %s" % self._info_desc_)
self.term_width, self.term_height = shutil.get_terminal_size(fallback=(80, 24))
self.__vis_inp( )
self.__caltable_inp( )
self.__contfile_inp( )
self.__field_inp( )
self.__intent_inp( )
self.__spw_inp( )
self.__combine_inp( )
self.__solint_inp( )
self.__fitorder_inp( )
self.__pipelinemode_inp( )
self.__dryrun_inp( )
self.__acceptresults_inp( )
#--------- tget function ----------------------------------------------------------
@static_var('state', __sf__('casa_inp_go_state'))
def tget(self,file=None):
from casashell.private.stack_manip import find_frame
from runpy import run_path
filename = None
if file is None:
if os.path.isfile("hif_uvcontfit.last"):
filename = "hif_uvcontfit.last"
elif isinstance(file, str):
if os.path.isfile(file):
filename = file
if filename is not None:
glob = find_frame( )
newglob = run_path( filename, init_globals={ } )
for i in newglob:
glob[i] = newglob[i]
self.tget.state['last'] = self
else:
print("could not find last file, setting defaults instead...")
self.set_global_defaults( )
def __call__( self, vis=None, caltable=None, contfile=None, field=None, intent=None, spw=None, combine=None, solint=None, fitorder=None, pipelinemode=None, dryrun=None, acceptresults=None ):
def noobj(s):
if s.startswith('<') and s.endswith('>'):
return "None"
else:
return s
_prefile = os.path.realpath('hif_uvcontfit.pre')
_postfile = os.path.realpath('hif_uvcontfit.last')
_return_result_ = None
_arguments = [vis,caltable,contfile,field,intent,spw,combine,solint,fitorder,pipelinemode,dryrun,acceptresults]
_invocation_parameters = OrderedDict( )
if any(map(lambda x: x is not None,_arguments)):
# invoke python style
# set the non sub-parameters that are not None
local_global = { }
if solint is not None: local_global['solint'] = solint
if fitorder is not None: local_global['fitorder'] = fitorder
if pipelinemode is not None: local_global['pipelinemode'] = pipelinemode
# the invocation parameters for the non-subparameters can now be set - this picks up those defaults
_invocation_parameters['solint'] = self.__solint( local_global )
_invocation_parameters['fitorder'] = self.__fitorder( local_global )
_invocation_parameters['pipelinemode'] = self.__pipelinemode( local_global )
# the sub-parameters can then be set. Use the supplied value if not None, else the function, which gets the appropriate default
_invocation_parameters['vis'] = self.__vis( _invocation_parameters ) if vis is None else vis
_invocation_parameters['caltable'] = self.__caltable( _invocation_parameters ) if caltable is None else caltable
_invocation_parameters['contfile'] = self.__contfile( _invocation_parameters ) if contfile is None else contfile
_invocation_parameters['field'] = self.__field( _invocation_parameters ) if field is None else field
_invocation_parameters['intent'] = self.__intent( _invocation_parameters ) if intent is None else intent
_invocation_parameters['spw'] = self.__spw( _invocation_parameters ) if spw is None else spw
_invocation_parameters['combine'] = self.__combine( _invocation_parameters ) if combine is None else combine
_invocation_parameters['dryrun'] = self.__dryrun( _invocation_parameters ) if dryrun is None else dryrun
_invocation_parameters['acceptresults'] = self.__acceptresults( _invocation_parameters ) if acceptresults is None else acceptresults
else:
# invoke with inp/go semantics
_invocation_parameters['vis'] = self.__vis( self.__globals_( ) )
_invocation_parameters['caltable'] = self.__caltable( self.__globals_( ) )
_invocation_parameters['contfile'] = self.__contfile( self.__globals_( ) )
_invocation_parameters['field'] = self.__field( self.__globals_( ) )
_invocation_parameters['intent'] = self.__intent( self.__globals_( ) )
_invocation_parameters['spw'] = self.__spw( self.__globals_( ) )
_invocation_parameters['combine'] = self.__combine( self.__globals_( ) )
_invocation_parameters['solint'] = self.__solint( self.__globals_( ) )
_invocation_parameters['fitorder'] = self.__fitorder( self.__globals_( ) )
_invocation_parameters['pipelinemode'] = self.__pipelinemode( self.__globals_( ) )
_invocation_parameters['dryrun'] = self.__dryrun( self.__globals_( ) )
_invocation_parameters['acceptresults'] = self.__acceptresults( self.__globals_( ) )
try:
with open(_prefile,'w') as _f:
for _i in _invocation_parameters:
_f.write("%-13s = %s\n" % (_i,noobj(repr(_invocation_parameters[_i]))))
_f.write("#hif_uvcontfit( ")
count = 0
for _i in _invocation_parameters:
_f.write("%s=%s" % (_i,noobj(repr(_invocation_parameters[_i]))))
count += 1
if count < len(_invocation_parameters): _f.write(",")
_f.write(" )\n")
except: pass
try:
_return_result_ = _hif_uvcontfit_t( _invocation_parameters['vis'],_invocation_parameters['caltable'],_invocation_parameters['contfile'],_invocation_parameters['field'],_invocation_parameters['intent'],_invocation_parameters['spw'],_invocation_parameters['combine'],_invocation_parameters['solint'],_invocation_parameters['fitorder'],_invocation_parameters['pipelinemode'],_invocation_parameters['dryrun'],_invocation_parameters['acceptresults'] )
except Exception as e:
from traceback import format_exc
from casatasks import casalog
casalog.origin('hif_uvcontfit')
casalog.post("Exception Reported: Error in hif_uvcontfit: %s" % str(e),'SEVERE')
casalog.post(format_exc( ))
_return_result_ = False
try:
os.rename(_prefile,_postfile)
except: pass
return _return_result_
hif_uvcontfit = _hif_uvcontfit( )