def sdfit(infile=None, datacolumn=None, antenna=None, field=None, spw=None,
timerange=None, scan=None, pol=None, intent=None,
timeaverage=None, timebin=None, timespan=None,
polaverage=None, polaveragemode=None,
fitfunc=None, fitmode=None, nfit=None, thresh=None, avg_limit=None,
minwidth=None, edge=None, outfile=None, overwrite=None):
casalog.origin('sdfit')
try:
if os.path.exists(outfile):
if overwrite:
os.system('rm -rf %s' % outfile)
else:
raise ValueError(outfile + ' exists.')
if (fitmode not in ['list', 'auto']):
raise ValueError, "fitmode='%s' is not supported yet" % fitmode
if (spw == ''): spw = '*'
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=antenna, time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection), field=field,
antenna=antenna, timerange=timerange,
scan=scan, polarization=pol, intent=intent)
tempfile = 'temp_sdfit_'+str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempfile):
tempfile += str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempfile):
raise Exception('temporary file ' + tempfile + ' exists...')
tempoutfile = tempfile + '_temp_output_ms'
if os.path.exists(tempoutfile):
tempoutfile += str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempoutfile):
raise Exception('temporary ms file ' + tempoutfile + ' exists...')
if fitmode=='auto': nfit = [-1]
num_fit_str = str(',').join(map(str, nfit))
sdms.fit_line(datacolumn=datacolumn, spw=spw, pol=pol,
timeaverage=timeaverage, timebin=timebin, timespan=timespan,
polaverage=polaverage, polaveragemode=polaveragemode,
fitfunc=fitfunc, nfit=num_fit_str,
linefinding=(fitmode=='auto'), threshold=thresh,
avg_limit=avg_limit, minwidth=minwidth, edge=edge,
tempfile=tempfile, tempoutfile=tempoutfile)
if os.path.exists(tempfile):
return get_results(tempfile, fitfunc, nfit, outfile)
else:
raise Exception('temporary file was unexpectedly not created.')
except Exception, instance:
raise Exception, instance
def sdfit(infile=None, datacolumn=None, antenna=None, field=None, spw=None,
timerange=None, scan=None, pol=None, intent=None,
timebin=None, timespan=None,
polaverage=None,
fitfunc=None, fitmode=None, nfit=None, thresh=None, avg_limit=None,
minwidth=None, edge=None, outfile=None, overwrite=None):
casalog.origin('sdfit')
try:
if os.path.exists(outfile):
if overwrite:
os.system('rm -rf %s' % outfile)
else:
raise ValueError(outfile + ' exists.')
if (fitmode not in ['list', 'auto']):
raise ValueError, "fitmode='%s' is not supported yet" % fitmode
if (spw == ''): spw = '*'
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=antenna, time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection), field=field,
antenna=antenna, timerange=timerange,
scan=scan, polarization=pol, intent=intent)
tempfile = 'temp_sdfit_'+str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempfile):
tempfile += str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempfile):
raise Exception('temporary file ' + tempfile + ' exists...')
tempoutfile = tempfile + '_temp_output_ms'
if os.path.exists(tempoutfile):
tempoutfile += str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempoutfile):
raise Exception('temporary ms file ' + tempoutfile + ' exists...')
if fitmode=='auto': nfit = [-1]
num_fit_str = str(',').join(map(str, nfit))
sdms.fit_line(datacolumn=datacolumn, spw=spw, pol=pol,
timebin=timebin, timespan=timespan,
polaverage=polaverage,
fitfunc=fitfunc, nfit=num_fit_str,
linefinding=(fitmode=='auto'), threshold=thresh,
avg_limit=avg_limit, minwidth=minwidth, edge=edge,
tempfile=tempfile, tempoutfile=tempoutfile)
if os.path.exists(tempfile):
return get_results(tempfile, fitfunc, nfit, outfile)
else:
raise Exception('temporary file was unexpectedly not created.')
except Exception, instance:
raise Exception, instance
def tsdfit(infile=None, datacolumn=None, antenna=None, field=None, spw=None, timerange=None, scan=None, pol=None,
fitfunc=None, fitmode=None, nfit=None, thresh=None, min_nchan=None, avg_limit=None, box_size=None,
edge=None, outfile=None, overwrite=None):
casalog.origin('tsdbaseline')
try:
if os.path.exists(outfile):
if overwrite:
os.system('rm -rf %s' % outfile)
else:
raise ValueError(outfile + ' exists.')
if (fitmode != 'list'):
raise ValueError, "fitmode='%s' is not supported yet" % fitmode
if (spw == ''): spw = '*'
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=str(antenna), time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection), field=field,
antenna=str(antenna), timerange=timerange,
scan=scan)
tempfile = 'temp_tsdfit_'+str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempfile):
tempfile += str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempfile):
raise Exception('temporary file ' + tempfile + ' exists...')
tempoutfile = tempfile + '_temp_output_ms'
if os.path.exists(tempoutfile):
tempoutfile += str(datetime.datetime.fromtimestamp(time.time())).replace('-','').replace(' ','').replace(':','')
if os.path.exists(tempoutfile):
raise Exception('temporary ms file ' + tempoutfile + ' exists...')
sdms.fit_line(datacolumn=datacolumn, spw=spw, pol=pol, fitfunc=fitfunc,
nfit=str(nfit)[1:-1].replace(' ', ''),
tempfile=tempfile, tempoutfile=tempoutfile)
if os.path.exists(tempfile):
return get_results(tempfile, fitfunc, nfit, outfile)
else:
raise Exception('temporary file was unexpectedly not created.')
except Exception, instance:
raise Exception, instance
def sdbaseline(infile=None,
datacolumn=None,
antenna=None,
field=None,
spw=None,
timerange=None,
scan=None,
pol=None,
intent=None,
maskmode=None,
thresh=None,
avg_limit=None,
minwidth=None,
edge=None,
blmode=None,
dosubtract=None,
blformat=None,
bloutput=None,
bltable=None,
blfunc=None,
order=None,
npiece=None,
applyfft=None,
fftmethod=None,
fftthresh=None,
addwn=None,
rejwn=None,
clipthresh=None,
clipniter=None,
blparam=None,
verbose=None,
showprogress=None,
minnrow=None,
outfile=None,
overwrite=None):
casalog.origin('sdbaseline')
try:
if (outfile == '') or not isinstance(outfile, str):
print("type=%s, value=%s" % (type(outfile), str(outfile)))
raise ValueError, "outfile name is empty."
if os.path.exists(outfile) and not overwrite:
raise Exception(outfile + ' exists.')
if (maskmode == 'interact'):
raise ValueError, "maskmode='%s' is not supported yet" % maskmode
if (blfunc == 'variable' and not os.path.exists(blparam)):
raise ValueError, "input file '%s' does not exists" % blparam
if (spw == ''): spw = '*'
if (blmode == 'apply'):
if not os.path.exists(bltable):
raise ValueError, "file specified in bltable '%s' does not exist." % bltable
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile) and (infile != outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile,
spw=spw,
field=field,
baseline=antenna,
time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection),
field=field,
antenna=antenna,
timerange=timerange,
scan=scan,
polarization=pol,
intent=intent)
sdms.apply_baseline_table(bltable=bltable,
datacolumn=datacolumn,
spw=spw,
outfile=outfile)
sdms.close()
restore_sorted_table_keyword(infile, sorttab_info)
elif (blmode == 'fit'):
if (blfunc == 'sinusoid'):
addwn = sdutil.parse_wavenumber_param(addwn)
rejwn = sdutil.parse_wavenumber_param(rejwn)
check_fftthresh(fftthresh)
blformat, bloutput = prepare_for_blformat_bloutput(
infile, blformat, bloutput, overwrite)
output_bloutput_text_header(blformat, bloutput, blfunc, maskmode,
infile, outfile)
if (blfunc == 'variable'):
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile) and (infile != outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile,
spw=spw,
field=field,
baseline=antenna,
time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection),
field=field,
antenna=antenna,
timerange=timerange,
scan=scan,
polarization=pol,
intent=intent)
params, func = prepare_for_baselining(
blfunc=blfunc,
datacolumn=datacolumn,
outfile=outfile,
bloutput=','.join(bloutput),
dosubtract=dosubtract,
spw=spw,
pol=pol,
linefinding=(maskmode == 'auto'),
threshold=thresh,
avg_limit=avg_limit,
minwidth=minwidth,
edge=edge,
order=order,
npiece=npiece,
applyfft=applyfft,
fftmethod=fftmethod,
fftthresh=fftthresh,
addwn=addwn,
rejwn=rejwn,
clip_threshold_sigma=clipthresh,
num_fitting_max=clipniter + 1,
blparam=blparam)
func(**params)
sdms.close()
if (blfunc == 'variable'):
restore_sorted_table_keyword(infile, sorttab_info)
except Exception, instance:
raise Exception, instance
def tsdbaseline(infile=None, datacolumn=None, antenna=None, field=None, spw=None, timerange=None, scan=None, pol=None, maskmode=None, thresh=None, avg_limit=None, minwidth=None, edge=None, blmode=None, dosubtract=None, blformat=None, bloutput=None, bltable=None, blfunc=None, order=None, npiece=None, applyfft=None, fftmethod=None, fftthresh=None, addwn=None, rejwn=None, clipthresh=None, clipniter=None, blparam=None, verify=None, verbose=None, showprogress=None, minnrow=None, outfile=None, overwrite=None):
casalog.origin('tsdbaseline')
try:
if (outfile == '') or not isinstance(outfile, str):
print("type=%s, value=%s" % (type(outfile), str(outfile)))
raise ValueError, "outfile name is empty."
if os.path.exists(outfile) and not overwrite:
raise Exception(outfile + ' exists.')
if (maskmode == 'interact'):
raise ValueError, "maskmode='%s' is not supported yet" % maskmode
if (blfunc == 'variable' and not os.path.exists(blparam)):
raise ValueError, "input file '%s' does not exists" % blparam
if (spw == ''): spw = '*'
if blmode == 'apply':
if not os.path.exists(bltable):
raise ValueError, "file specified in bltable '%s' does not exist." % bltable
with sdutil.tbmanager(infile + '/DATA_DESCRIPTION') as tb:
spw_ids = tb.getcol('SPECTRAL_WINDOW_ID')
with sdutil.tbmanager(infile + '/ANTENNA') as tb:
ant_ids = range(tb.nrows())
with sdutil.tbmanager(infile + '/FEED') as tb:
feed_ids = numpy.unique(tb.getcol('FEED_ID'))
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=str(antenna), time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection), field=field,
antenna=str(antenna), timerange=timerange,
scan=scan)
sdms.apply_baseline_table(bltable=bltable,
datacolumn=datacolumn,
spw=spw,
outfile=outfile)
sdms.close()
restore_sorted_table_keyword(infile, sorttab_info)
elif blmode == 'fit':
blout_exists = False
if (isinstance(bloutput, str) and os.path.exists(bloutput)):
blout_exists = True
elif isinstance(bloutput, list):
for blout in bloutput:
if os.path.exists(blout):
blout_exists = True
break
if blout_exists and not overwrite:
raise ValueError, "file(s) specified in bloutput exists."
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=str(antenna), time=timerange,
scan=scan)
if blfunc == 'variable':
sorttab_info = remove_sorted_table_keyword(infile)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection), field=field,
antenna=str(antenna), timerange=timerange,
scan=scan)
#if(outfile==''):
# outfile=infile
# if isinstance(blformat, str):
# if('' == blformat):
# #blformat=',,'
# bloutput=',,'
# print 'blformat'
# if('text' == blformat):
# bloutput_tmp = infile + '_blparam.txt'
# bloutput = ',' + bloutput_tmp + ','
# if os.path.exists(bloutput):
# raise Exception(fname + ' exists.')
new_bloutput=[]
if isinstance(blformat, str):
blformat = [blformat]
if isinstance(bloutput, str):
bloutput = [bloutput]
if isinstance(blformat, list):
if('' in blformat):
blformat = ',,'
#elif(len(blformat) > 3 ):
# raise ValueError, "The maximum size of blformat must be three."
elif(len(blformat) != len(bloutput)):
raise ValueError, "The size of blfomat must be the same as that of bloutput."
elif [key for key, val in Counter(blformat).items() if val>1]:
raise ValueError, "Same multiple blformats are not allowed."
else:
if('csv' in blformat):
if(''!= bloutput[blformat.index('csv')]):
fname=bloutput[blformat.index('csv')]
if not overwrite and os.path.exists(fname):
raise Exception(fname + ' exists.')
new_bloutput.append(bloutput[blformat.index('csv')])
else:
fname= infile + '_blparam.csv'
if not overwrite and os.path.exists(fname):
raise Exception(fname + ' exists. ')######################################################
new_bloutput.append(infile + '_blparam.csv')
else:
new_bloutput.append('')
if('text' in blformat):
if(''!= bloutput[blformat.index('text')]):
new_bloutput.append(bloutput[blformat.index('text')])
fname = bloutput[blformat.index('text')]
if not overwrite and os.path.exists(fname):
raise Exception(fname + ' exists.')
f = open(fname, "w")
blf = blfunc.lower()
mm = maskmode.lower()
if blf == 'poly':
ftitles = ['Fit order']
elif blf == 'chebyshev':
ftitles = ['Fit order']
elif blf == 'cspline':
ftitles = ['nPiece']
#print 'task 2'
else: # sinusoid
ftitles = ['applyFFT', 'fftMethod', 'fftThresh', 'addWaveN', 'rejWaveN']
if mm == 'auto':
mtitles = ['Threshold', 'avg_limit', 'Edge']
elif mm == 'list':
mtitles = []
else: # interact
mtitles = []
ctitles = ['clipThresh', 'clipNIter']
#fkeys = getattr(self, '%s_keys'%(blfunc))
#mkeys = getattr(self, '%s_keys'%(maskmode))
outfile2=''
if(outfile==''):
outfile2 = infile
else:
outfile2 = outfile
info = [['Source Table', infile],
['Output File', outfile2]]
#['Function', blfunc],
#['Fit order', order]]
#for i in xrange(len(ftitles)):
# info.append([ftitles[i],getattr(self,fkeys[i])])
#if blf != 'poly':
# for i in xrange(len(ctitles)):
# info.append([ctitles[i],clip_keys[i]])
info.append(['Mask mode', maskmode])
#for i in xrange(len(mtitles)):
# info.append([mtitles[i],getattr(mkeys[i])])
separator = "#"*60 + "\n"
f.write(separator)
for i in xrange(len(info)):
f.write('%12s: %s\n'%tuple(info[i]))
f.write(separator)
f.close()
else:
#new_bloutput.append(infile + '_blparam.txt')
new_bloutput.append(infile + '_blparam.txt')
fname2 = infile + '_blparam.txt'
if not overwrite and os.path.exists(fname2):
raise Exception(fname2 + ' exists.')
f = open(fname2, "w")
blf = blfunc.lower()
mm = maskmode.lower()
if blf == 'poly':
ftitles = ['Fit order']
elif blf == 'chebyshev':
ftitles = ['Fit order']
elif blf == 'cspline':
ftitles = ['nPiece']
else: # sinusoid
ftitles = ['applyFFT', 'fftMethod', 'fftThresh', 'addWaveN', 'rejWaveN']
if mm == 'auto':
mtitles = ['Threshold', 'avg_limit', 'Edge']
elif mm == 'list':
mtitles = []
else: # interact
mtitles = []
ctitles = ['clipThresh', 'clipNIter']
#fkeys = getattr(self, '%s_keys'%(blfunc))
#mkeys = getattr(self, '%s_keys'%(maskmode))
outfile2=''
if(outfile==''):
outfile2 = infile
info = [['Source Table', infile],
['Output File', outfile]]
#['Function', blfunc],
#['Fit order', order]]
#for i in xrange(len(ftitles)):
# info.append([ftitles[i],getattr(self,fkeys[i])])
#if blf != 'poly':
# for i in xrange(len(ctitles)):
# info.append([ctitles[i],clip_keys[i]])
info.append(['Mask mode', maskmode])
#for i in xrange(len(mtitles)):
# info.append([mtitles[i],getattr(mkeys[i])])
separator = "#"*60 + "\n"
f.write(separator)
for i in xrange(len(info)):
f.write('%12s: %s\n'%tuple(info[i]))
f.write(separator)
f.close()
else:
new_bloutput.append('')
if('table' in blformat):
#print 'blformat->',type(blformat), blformat
#print "blformat.index('table')", blformat.index('table')
#print "bloutput[blformat.index('table')])", bloutput[blformat.index('table')]
if(''!= bloutput[blformat.index('table')]):
fname = bloutput[blformat.index('table')]
if not overwrite and os.path.exists(fname):
raise Exception(fname + ' exists.')#############################################
new_bloutput.append(bloutput[blformat.index('table')])
else:
fname = infile + '_blparam.bltable'
if not overwrite and os.path.exists(fname):
raise Exception(fname + ' exists.')#############################################
print ''
new_bloutput.append(fname)
else:
new_bloutput.append('')
blformat = ",".join(blformat)
bloutput = ",".join(new_bloutput)
#print 'task blformat',type(blformat), blformat
#print 'task bloutput',type(bloutput), bloutput
params, func = prepare_for_baselining(blfunc=blfunc,
datacolumn=datacolumn,
outfile=outfile,
bltable=bloutput, # remove this line once text/csv output becomes available (2015/7/1 WK)
blformat=blformat,
bloutput=bloutput,
dosubtract=dosubtract,
spw=spw,
pol=pol,
order=order,
npiece=npiece,
blparam=blparam,
clip_threshold_sigma=clipthresh,
num_fitting_max=clipniter+1,
linefinding=(maskmode=='auto'),
threshold=thresh,
avg_limit=avg_limit,
minwidth=minwidth,
edge=edge)
if overwrite:
if os.path.exists(outfile):
os.system('rm -rf %s' % outfile)
for bloutfile in new_bloutput:
if os.path.exists(bloutfile):
os.system('rm -rf %s' % bloutfile)
#print params
if(blformat != ',,'):
func(**params)
if (blfunc == 'variable'):
restore_sorted_table_keyword(infile, sorttab_info)
except Exception, instance:
raise Exception, instance
def tsdbaseline(infile=None,
datacolumn=None,
antenna=None,
field=None,
spw=None,
timerange=None,
scan=None,
pol=None,
maskmode=None,
thresh=None,
avg_limit=None,
minwidth=None,
edge=None,
blmode=None,
dosubtract=None,
blformat=None,
bloutput=None,
bltable=None,
blfunc=None,
order=None,
npiece=None,
applyfft=None,
fftmethod=None,
fftthresh=None,
addwn=None,
rejwn=None,
clipthresh=None,
clipniter=None,
blparam=None,
verify=None,
verbose=None,
showprogress=None,
minnrow=None,
outfile=None,
overwrite=None):
casalog.origin('tsdbaseline')
try:
if (outfile == '') or not isinstance(outfile, str):
print("type=%s, value=%s" % (type(outfile), str(outfile)))
raise ValueError, "outfile name is empty."
if os.path.exists(outfile) and not overwrite:
raise Exception(outfile + ' exists.')
if (maskmode == 'interact'):
raise ValueError, "maskmode='%s' is not supported yet" % maskmode
if (blfunc == 'variable' and not os.path.exists(blparam)):
raise ValueError, "input file '%s' does not exists" % blparam
if (spw == ''): spw = '*'
if blmode == 'apply':
if not os.path.exists(bltable):
raise ValueError, "file specified in bltable '%s' does not exist." % bltable
with sdutil.tbmanager(infile + '/DATA_DESCRIPTION') as tb:
spw_ids = tb.getcol('SPECTRAL_WINDOW_ID')
with sdutil.tbmanager(infile + '/ANTENNA') as tb:
ant_ids = range(tb.nrows())
with sdutil.tbmanager(infile + '/FEED') as tb:
feed_ids = numpy.unique(tb.getcol('FEED_ID'))
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile,
spw=spw,
field=field,
baseline=str(antenna),
time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection),
field=field,
antenna=str(antenna),
timerange=timerange,
scan=scan)
sdms.apply_baseline_table(bltable=bltable,
datacolumn=datacolumn,
spw=spw,
outfile=outfile)
sdms.close()
restore_sorted_table_keyword(infile, sorttab_info)
elif blmode == 'fit':
blout_exists = False
if (isinstance(bloutput, str) and os.path.exists(bloutput)):
blout_exists = True
elif isinstance(bloutput, list):
for blout in bloutput:
if os.path.exists(blout):
blout_exists = True
break
if blout_exists and not overwrite:
raise ValueError, "file(s) specified in bloutput exists."
selection = ms.msseltoindex(vis=infile,
spw=spw,
field=field,
baseline=str(antenna),
time=timerange,
scan=scan)
if blfunc == 'variable':
sorttab_info = remove_sorted_table_keyword(infile)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection),
field=field,
antenna=str(antenna),
timerange=timerange,
scan=scan)
#if(outfile==''):
# outfile=infile
# if isinstance(blformat, str):
# if('' == blformat):
# #blformat=',,'
# bloutput=',,'
# print 'blformat'
# if('text' == blformat):
# bloutput_tmp = infile + '_blparam.txt'
# bloutput = ',' + bloutput_tmp + ','
# if os.path.exists(bloutput):
# raise Exception(fname + ' exists.')
new_bloutput = []
if isinstance(blformat, str):
blformat = [blformat]
if isinstance(bloutput, str):
bloutput = [bloutput]
if isinstance(blformat, list):
if ('' in blformat):
blformat = ',,'
#elif(len(blformat) > 3 ):
# raise ValueError, "The maximum size of blformat must be three."
elif (len(blformat) != len(bloutput)):
raise ValueError, "The size of blfomat must be the same as that of bloutput."
elif [
key for key, val in Counter(blformat).items()
if val > 1
]:
raise ValueError, "Same multiple blformats are not allowed."
else:
if ('csv' in blformat):
if ('' != bloutput[blformat.index('csv')]):
fname = bloutput[blformat.index('csv')]
if not overwrite and os.path.exists(fname):
raise Exception(fname + ' exists.')
new_bloutput.append(
bloutput[blformat.index('csv')])
else:
fname = infile + '_blparam.csv'
if not overwrite and os.path.exists(fname):
raise Exception(
fname + ' exists. '
) ######################################################
new_bloutput.append(infile + '_blparam.csv')
else:
new_bloutput.append('')
if ('text' in blformat):
if ('' != bloutput[blformat.index('text')]):
new_bloutput.append(
bloutput[blformat.index('text')])
fname = bloutput[blformat.index('text')]
if not overwrite and os.path.exists(fname):
raise Exception(fname + ' exists.')
f = open(fname, "w")
blf = blfunc.lower()
mm = maskmode.lower()
if blf == 'poly':
ftitles = ['Fit order']
elif blf == 'chebyshev':
ftitles = ['Fit order']
elif blf == 'cspline':
ftitles = ['nPiece']
#print 'task 2'
else: # sinusoid
ftitles = [
'applyFFT', 'fftMethod', 'fftThresh',
'addWaveN', 'rejWaveN'
]
if mm == 'auto':
mtitles = ['Threshold', 'avg_limit', 'Edge']
elif mm == 'list':
mtitles = []
else: # interact
mtitles = []
ctitles = ['clipThresh', 'clipNIter']
#fkeys = getattr(self, '%s_keys'%(blfunc))
#mkeys = getattr(self, '%s_keys'%(maskmode))
outfile2 = ''
if (outfile == ''):
outfile2 = infile
else:
outfile2 = outfile
info = [['Source Table', infile],
['Output File', outfile2]]
#['Function', blfunc],
#['Fit order', order]]
#for i in xrange(len(ftitles)):
# info.append([ftitles[i],getattr(self,fkeys[i])])
#if blf != 'poly':
# for i in xrange(len(ctitles)):
# info.append([ctitles[i],clip_keys[i]])
info.append(['Mask mode', maskmode])
#for i in xrange(len(mtitles)):
# info.append([mtitles[i],getattr(mkeys[i])])
separator = "#" * 60 + "\n"
f.write(separator)
for i in xrange(len(info)):
f.write('%12s: %s\n' % tuple(info[i]))
f.write(separator)
f.close()
else:
#new_bloutput.append(infile + '_blparam.txt')
new_bloutput.append(infile + '_blparam.txt')
fname2 = infile + '_blparam.txt'
if not overwrite and os.path.exists(fname2):
raise Exception(fname2 + ' exists.')
f = open(fname2, "w")
blf = blfunc.lower()
mm = maskmode.lower()
if blf == 'poly':
ftitles = ['Fit order']
elif blf == 'chebyshev':
ftitles = ['Fit order']
elif blf == 'cspline':
ftitles = ['nPiece']
else: # sinusoid
ftitles = [
'applyFFT', 'fftMethod', 'fftThresh',
'addWaveN', 'rejWaveN'
]
if mm == 'auto':
mtitles = ['Threshold', 'avg_limit', 'Edge']
elif mm == 'list':
mtitles = []
else: # interact
mtitles = []
ctitles = ['clipThresh', 'clipNIter']
#fkeys = getattr(self, '%s_keys'%(blfunc))
#mkeys = getattr(self, '%s_keys'%(maskmode))
outfile2 = ''
if (outfile == ''):
outfile2 = infile
info = [['Source Table', infile],
['Output File', outfile]]
#['Function', blfunc],
#['Fit order', order]]
#for i in xrange(len(ftitles)):
# info.append([ftitles[i],getattr(self,fkeys[i])])
#if blf != 'poly':
# for i in xrange(len(ctitles)):
# info.append([ctitles[i],clip_keys[i]])
info.append(['Mask mode', maskmode])
#for i in xrange(len(mtitles)):
# info.append([mtitles[i],getattr(mkeys[i])])
separator = "#" * 60 + "\n"
f.write(separator)
for i in xrange(len(info)):
f.write('%12s: %s\n' % tuple(info[i]))
f.write(separator)
f.close()
else:
new_bloutput.append('')
if ('table' in blformat):
#print 'blformat->',type(blformat), blformat
#print "blformat.index('table')", blformat.index('table')
#print "bloutput[blformat.index('table')])", bloutput[blformat.index('table')]
if ('' != bloutput[blformat.index('table')]):
fname = bloutput[blformat.index('table')]
if not overwrite and os.path.exists(fname):
raise Exception(
fname + ' exists.'
) #############################################
new_bloutput.append(
bloutput[blformat.index('table')])
else:
fname = infile + '_blparam.bltable'
if not overwrite and os.path.exists(fname):
raise Exception(
fname + ' exists.'
) #############################################
print ''
new_bloutput.append(fname)
else:
new_bloutput.append('')
blformat = ",".join(blformat)
bloutput = ",".join(new_bloutput)
#print 'task blformat',type(blformat), blformat
#print 'task bloutput',type(bloutput), bloutput
params, func = prepare_for_baselining(
blfunc=blfunc,
datacolumn=datacolumn,
outfile=outfile,
bltable=
bloutput, # remove this line once text/csv output becomes available (2015/7/1 WK)
blformat=blformat,
bloutput=bloutput,
dosubtract=dosubtract,
spw=spw,
pol=pol,
order=order,
npiece=npiece,
blparam=blparam,
clip_threshold_sigma=clipthresh,
num_fitting_max=clipniter + 1,
linefinding=(maskmode == 'auto'),
threshold=thresh,
avg_limit=avg_limit,
minwidth=minwidth,
edge=edge)
if overwrite:
if os.path.exists(outfile):
os.system('rm -rf %s' % outfile)
for bloutfile in new_bloutput:
if os.path.exists(bloutfile):
os.system('rm -rf %s' % bloutfile)
#print params
if (blformat != ',,'):
func(**params)
if (blfunc == 'variable'):
restore_sorted_table_keyword(infile, sorttab_info)
except Exception, instance:
raise Exception, instance
def tsdbaseline(infile=None, datacolumn=None, antenna=None, field=None, spw=None, timerange=None, scan=None, pol=None, intent=None, maskmode=None, thresh=None, avg_limit=None, minwidth=None, edge=None, blmode=None, dosubtract=None, blformat=None, bloutput=None, bltable=None, blfunc=None, order=None, npiece=None,
applyfft=None, fftmethod=None, fftthresh=None,
addwn=None, rejwn=None, clipthresh=None, clipniter=None, blparam=None, verbose=None, showprogress=None, minnrow=None, outfile=None, overwrite=None):
casalog.origin('tsdbaseline')
try:
if (outfile == '') or not isinstance(outfile, str):
print("type=%s, value=%s" % (type(outfile), str(outfile)))
raise ValueError, "outfile name is empty."
if os.path.exists(outfile) and not overwrite:
raise Exception(outfile + ' exists.')
if (maskmode == 'interact'):
raise ValueError, "maskmode='%s' is not supported yet" % maskmode
if (blfunc == 'variable' and not os.path.exists(blparam)):
raise ValueError, "input file '%s' does not exists" % blparam
if (spw == ''): spw = '*'
if (blmode == 'apply'):
if not os.path.exists(bltable):
raise ValueError, "file specified in bltable '%s' does not exist." % bltable
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile) and (infile != outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=antenna, time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection), field=field,
antenna=antenna, timerange=timerange,
scan=scan, polarization=pol, intent=intent)
sdms.apply_baseline_table(bltable=bltable,
datacolumn=datacolumn,
spw=spw,
outfile=outfile)
sdms.close()
restore_sorted_table_keyword(infile, sorttab_info)
elif (blmode == 'fit'):
#if(blfunc=='sinusoid'):
# addwn=sdutil._parse_wn(addwn)
# rejwn=sdutil._parse_wn(rejwn)
sep=['-','<=','<','>=','>']
addwn_tmp=[]
if(blfunc=='sinusoid'):
if(type(addwn)==str):
for isep in sep:
if(addwn.find(isep) != -1 and isep=='-'):
for i in range(int(addwn.split('-')[1].strip())+1):
addwn_tmp.append(i)
for i in range(int(addwn.split('-')[0].strip())):
addwn_tmp.remove(i)
if(addwn.find(isep) != -1 and isep=='<'):
if(addwn.split('<')[0].strip()=='' and type(int(addwn.split('<')[1].strip()))==int):
for i in range(int(addwn.split('<')[1].strip())):
addwn_tmp.append(i)
break
elif(addwn.split('<')[1].strip()=='' and type(int(addwn.split('<')[0].strip()))==int):
addwn_tmp=addwn_string_greaterthan(infile, addwn, spw, inequality='<')
break
elif(addwn.split('<=')[1].strip()=='' and type(int(addwn.split('<=')[0].strip()))==int):
addwn_tmp=addwn_string_greaterthan(infile, addwn, spw, inequality='<=')
break
if(addwn.find(isep) != -1 and isep=='>'):
if(addwn.split('>=')[0].strip()=='' and type(int(addwn.split('>=')[1].strip()))==int):
addwn_tmp=addwn_string_greaterthan(infile, addwn, spw, inequality='>=')
break
elif(addwn.split('>')[1].strip()=='' and type(int(addwn.split('>')[0].strip()))==int):
for i in range(int(addwn.split('>')[0].strip())):
addwn_tmp.append(i)
break
elif(addwn.split('>')[0].strip()=='' and type(int(addwn.split('>')[1].strip()))==int):
addwn_tmp=addwn_string_greaterthan(infile, addwn, spw, inequality='>')
break
#print addwn_tmp
addwn=addwn_tmp
blformat, bloutput = prepare_for_blformat_bloutput(infile, blformat, bloutput, overwrite)
output_bloutput_text_header(blformat, bloutput,
blfunc, maskmode,
infile, outfile)
if (blfunc == 'variable'):
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile) and (infile != outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=antenna, time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection),
field=field, antenna=antenna,
timerange=timerange, scan=scan,
polarization=pol, intent=intent)
params, func = prepare_for_baselining(blfunc=blfunc,
datacolumn=datacolumn,
outfile=outfile,
bloutput=','.join(bloutput),
dosubtract=dosubtract,
spw=spw,
pol=pol,
order=order,
npiece=npiece,
blparam=blparam,
clip_threshold_sigma=clipthresh,
num_fitting_max=clipniter+1,
linefinding=(maskmode=='auto'),
threshold=thresh,
avg_limit=avg_limit,
minwidth=minwidth,
edge=edge,
applyfft=applyfft,###############
fftmethod=fftmethod,############
fftthresh=fftthresh,############
addwn=addwn,###################
rejwn=rejwn)####################
func(**params)
sdms.close()
if (blfunc == 'variable'):
restore_sorted_table_keyword(infile, sorttab_info)
except Exception, instance:
raise Exception, instance
def sdbaseline(infile=None, datacolumn=None, antenna=None, field=None, spw=None, timerange=None, scan=None, pol=None, intent=None, maskmode=None, thresh=None, avg_limit=None, minwidth=None, edge=None, blmode=None, dosubtract=None, blformat=None, bloutput=None, bltable=None, blfunc=None, order=None, npiece=None, applyfft=None, fftmethod=None, fftthresh=None, addwn=None, rejwn=None, clipthresh=None, clipniter=None, blparam=None, verbose=None, showprogress=None, minnrow=None, outfile=None, overwrite=None):
casalog.origin('sdbaseline')
try:
if (outfile == '') or not isinstance(outfile, str):
print("type=%s, value=%s" % (type(outfile), str(outfile)))
raise ValueError, "outfile name is empty."
if os.path.exists(outfile) and not overwrite:
raise Exception(outfile + ' exists.')
if (maskmode == 'interact'):
raise ValueError, "maskmode='%s' is not supported yet" % maskmode
if (blfunc == 'variable' and not os.path.exists(blparam)):
raise ValueError, "input file '%s' does not exists" % blparam
if (spw == ''): spw = '*'
if (blmode == 'apply'):
if not os.path.exists(bltable):
raise ValueError, "file specified in bltable '%s' does not exist." % bltable
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile) and (infile != outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=antenna, time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection), field=field,
antenna=antenna, timerange=timerange,
scan=scan, polarization=pol, intent=intent)
sdms.apply_baseline_table(bltable=bltable,
datacolumn=datacolumn,
spw=spw,
outfile=outfile)
sdms.close()
restore_sorted_table_keyword(infile, sorttab_info)
elif (blmode == 'fit'):
if(blfunc == 'sinusoid'):
addwn = sdutil.parse_wavenumber_param(addwn)
rejwn = sdutil.parse_wavenumber_param(rejwn)
check_fftthresh(fftthresh)
blformat, bloutput = prepare_for_blformat_bloutput(infile, blformat, bloutput, overwrite)
output_bloutput_text_header(blformat, bloutput,
blfunc, maskmode,
infile, outfile)
if (blfunc == 'variable'):
sorttab_info = remove_sorted_table_keyword(infile)
if overwrite and os.path.exists(outfile) and (infile != outfile):
os.system('rm -rf %s' % outfile)
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
baseline=antenna, time=timerange,
scan=scan)
sdms.open(infile)
sdms.set_selection(spw=sdutil.get_spwids(selection),
field=field, antenna=antenna,
timerange=timerange, scan=scan,
polarization=pol, intent=intent)
params, func = prepare_for_baselining(blfunc=blfunc,
datacolumn=datacolumn,
outfile=outfile,
bloutput=','.join(bloutput),
dosubtract=dosubtract,
spw=spw,
pol=pol,
linefinding=(maskmode=='auto'),
threshold=thresh,
avg_limit=avg_limit,
minwidth=minwidth,
edge=edge,
order=order,
npiece=npiece,
applyfft=applyfft,
fftmethod=fftmethod,
fftthresh=fftthresh,
addwn=addwn,
rejwn=rejwn,
clip_threshold_sigma=clipthresh,
num_fitting_max=clipniter+1,
blparam=blparam)
func(**params)
sdms.close()
if (blfunc == 'variable'):
restore_sorted_table_keyword(infile, sorttab_info)
except Exception, instance:
raise Exception, instance
