def deconv(dirty_image,
psf_image,
model_image='${im.MODEL_IMAGE}',
residual_image='${im.RESIDUAL_IMAGE}',
restored_image='${im.RESTORED_IMAGE}',
image_prefix='${im.BASENAME_IMAGE}',
path='$MORESANE_PATH',
**kw):
""" Runs PyMORESANE """
# Check if PyMORESANE is where it is said to be
model_image, residual_image, restored_image, path = interpolate_locals(
'model_image residual_image restored_image path')
found_path = argo.findImager(path, imager_name='PyMORESANE')
if not found_path:
abort('could not find PyMORESANE at $path')
kw['modelname'] = model_image
kw['residualname'] = residual_image
kw['restoredname'] = restored_image
# make dict of imager arguments that have been specified globally or locally
args = dict([(arg, globals()[arg]) for arg in _moresane_args
if arg in globals() and globals()[arg] is not None])
args.update([(arg, kw[arg]) for arg in _moresane_args if arg in kw])
x.sh(
argo.gen_run_cmd(path,
args,
suf='--',
assign='=',
pos_args=[dirty_image, psf_image, image_prefix]))
def _run(msname='$MS',clean=False,path='${im.WSCLEAN_PATH}',**kw):
""" Run WSCLEAN """
msname,path = interpolate_locals('msname path')
path = argo.findImager(path,imager_name='WSCLEAN')
if path is False:
abort('Could not find WSCLEAN in system path, alises or at $path')
# make dict of imager arguments that have been specified globally or locally
args = dict([ (arg,globals()[arg.replace("-","_")]) for arg in _wsclean_args
if arg.replace("-","_") in globals() and globals()[arg.replace("-","_")] is not None ]);
args.update([ (arg,kw[arg]) for arg in _wsclean_args if arg in kw ])
# map image size/resolution parameters
csz = kw.get('cellsize',cellsize)
np = kw.get('npix',npix)
args['scale'] = csz if isinstance(csz,(int,float)) else argo.toDeg(csz)
args['size']= '%d %d'%(np,np)
# map weight parameters
wgt = args['weight'];
if wgt == "robust" or wgt == "briggs":
args['weight'] = 'briggs %.2f'%(kw.get('robust',robust))
# map threshold
if isinstance(args['threshold'],str):
args['threshold'] = im.argo.toJy(args['threshold'])
# map clean parameter
if not clean:
args['niter'] = 0
ms.FIELD is not None and args.setdefault('field',ms.FIELD)
x.sh(argo.gen_run_cmd(path,args,suf='-',assign=' ',pos_args=[msname] if not isinstance(msname,(list,tuple)) else msname))
def _run (convert_output_to_fits=True,lwimager_path="$LWIMAGER_PATH",**kw):
# look up lwimager
lwimager_path = interpolate_locals("lwimager_path");
lwimager_path = argo.findImager(lwimager_path)
# make dict of imager arguments that have been specified globally or locally
args = dict([ (arg,globals()[arg]) for arg in _lwimager_args if arg in globals() and globals()[arg] is not None ]);
args.update([ (arg,kw[arg]) for arg in _lwimager_args if arg in kw ]);
if no_weight_fov:
args.pop('weight_fov',0);
# add ifrs, spwid and field arguments
ms.IFRS is not None and args.setdefault('ifrs',ms.IFRS);
ms.DDID is not None and args.setdefault('spwid',ms.DDID);
ms.FIELD is not None and args.setdefault('field',ms.FIELD);
# have an IFR subset? Parse that too
msname,ifrs = kw['ms'],args.pop('ifrs',None);
if ifrs and ifrs.lower() != "all":
import Meow.IfrSet
subset = Meow.IfrSet.from_ms(msname).subset(ifrs).taql_string();
args['select'] = "(%s)&&(%s)"%(args['select'],subset) if 'select' in args else subset;
# make image names
fitsfiles = {};
for arg in _fileargs:
if arg in args:
if not args[arg].endswith(".img"):
fitsfiles[arg] = args[arg];
args[arg] = args[arg]+".img";
# run the imager
x.time("$lwimager_path",**args);
# convert CASA images to FITS
if convert_output_to_fits:
fs = kw.get('flux_rescale') or flux_rescale;
velo = kw.get('velocity') or velocity;
for arg in _fileargs:
if arg in fitsfiles:
_im = pyrap.images.image(args[arg]);
if fs and fs != 1:
_im.putdata(fs*_im.getdata());
_im.tofits(fitsfiles[arg],overwrite=True,velocity=velo);
subprocess.call("rm -fr "+args[arg],shell=True);
def deconv(dirty_image,psf_image,
model_image='${im.MODEL_IMAGE}',
residual_image='${im.RESIDUAL_IMAGE}',
restored_image='${im.RESTORED_IMAGE}',
image_prefix='${im.BASENAME_IMAGE}',
path='$MORESANE_PATH',**kw):
""" Runs PyMORESANE """
# Check if PyMORESANE is where it is said to be
model_image,residual_image,restored_image,path = interpolate_locals('model_image residual_image restored_image path')
found_path = argo.findImager(path,imager_name='PyMORESANE')
if not found_path:
abort('could not find PyMORESANE at $path')
kw['modelname'] = model_image
kw['residualname'] = residual_image
kw['restoredname'] = restored_image
# make dict of imager arguments that have been specified globally or locally
args = dict([ (arg,globals()[arg]) for arg in _moresane_args if arg in globals() and globals()[arg] is not None ]);
args.update([ (arg,kw[arg]) for arg in _moresane_args if arg in kw ])
x.sh(argo.gen_run_cmd(path,args,suf='--',assign='=',pos_args=[dirty_image,psf_image,image_prefix]))
def make_image(msname='$MS',image_prefix='${im.BASENAME_IMAGE}',column='${im.COLUMN}',
mslist=None, # if given, overrieds msname
path='${WSCLEAN_PATH}',
imager='$IMAGER',
restore=False,
dirty=True,
psf=False,
restore_lsm=False,
lsm='$LSM',
algorithm='${im.CLEAN_ALGORITHM}',
channelize=None,
psf_image='${im.PSF_IMAGE}',
dirty_image='${im.DIRTY_IMAGE}',
model_image='${im.MODEL_IMAGE}',
residual_image='${im.RESIDUAL_IMAGE}',
restored_image='${im.RESTORED_IMAGE}',
fullrest_image='${im.FULLREST_IMAGE}',
restoring_options='${im.RESTORING_OPTIONS}',
keep_component_images=False,
**kw):
""" run WSCLEAN """
makedir('$DESTDIR')
_imager = im.IMAGER
im.IMAGER = II(imager)
#Add algorithm label if required
if im.DECONV_LABEL and restore:
if isinstance(im.DECONV_LABEL,bool):
if im.DECONV_LABEL:
im.DECONV_LABEL = algorithm
elif im.DECONV_LABEL is False:
im.DECONV_LABEL = None
path,msname,image_prefix,column,dirty_image,model_image,residual_image,restored_image,psf_image,channelize,\
fullrest_image,restoring_options = \
interpolate_locals('path msname image_prefix column dirty_image model_image residual_image '
'restored_image psf_image channelize fullrest_image restoring_options')
# Check if WSCLEAN is where it is said to be
path = argo.findImager(path,imager_name='WSCLEAN')
# wsclean requires a WEIGHT_SPECTRUM column in the MS
if wsclean_version()[0]<1.6:
argo.addcol(msname,colname='WEIGHT_SPECTRUM',valuetype='float',init_with=1)
if 'datacolumn' not in kw.keys():
kw['datacolumn'] = column
# Cater for moresane
do_moresane = False
if restore and algorithm.lower() in ['moresane','pymoresane']:
kw['niter'] = 0
kw['makepsf'] = True
psf = True
dirty = True
if isinstance(restore,dict):
kw0 = restore.copy()
else:
kw0 = {}
restore = False
do_moresane = True
from im import moresane
else:
if isinstance(restore,dict):
kw.update(restore)
restore = True
elif not isinstance(restore,bool):
restore = False
kw['name'] = image_prefix
# Check channel selection options in kw
if 'channelrange' in kw.keys():
if isinstance(kw['channelrange'],str):
start,end = map(int,kw['channelrange'].split())
else:
start,end = kw['channelrange']
else:
start,end = ms.CHANSTART,ms.CHANSTART+ms.NUMCHANS;
# if multiple MSs are specified, adjust channel range
if mslist:
end = ms.TOTAL_CHANNELS*(len(mslist)-1) + end
kw['channelrange'] = "%d %d"%(start,end);
nr = 1
if not channelize:
channelize = im.IMAGE_CHANNELIZE
if channelize:
nr = (end-start)//channelize
kw['channelsout'] = nr
if nr ==1:
channelize=False
if dirty: info("im.wsclean.make_image: making dirty image $dirty_image")
if restore: info(" making restored image $restored_image\
(model is $model_image, residual is $residual_image)")
if psf and not restore:
kw['makepsf'] = True
if 'pol' in kw.keys():
pol = kw['pol']
elif 'stokes' in kw.keys():
pol = kw['pol'] = kw.pop('stokes')
else:
pol = stokes
kw['pol'] = pol
if ',' in pol:
pol = pol.split(',')
kw['clean'] = restore
# also accepts list of MSs
_run(mslist or msname,**kw)
# delete gridding image unless user wants it
if not KEEP_GRIDDING_IMAGE:
rm_fr('$image_prefix-gridding.fits')
# delete first-residual images
first_residual_images = glob.glob(II("$image_prefix-*-first-residual.fits"))
if first_residual_images:
rm_fr(" ".join(first_residual_images))
#TODO(sphe): always keep wsclean MFS images?
# Combine images if needed
# mfs = mode if 'mode' not in kw.keys() else kw['mode']
# mfs = mode=='mfs'
# abort(mfs,mode)
def eval_list(vals):
l = []
for val in vals:
l.append(II(val))
return l
def combine_pol(pol,image_prefix=None,mfs=False):
dirtys = eval_list(['$image_prefix-%s-dirty.fits'%d for d in pol])
if dirty:
argo.combine_fits(dirtys,outname=dirty_image,ctype='STOKES',keep_old=keep_component_images)
else:
for item in dirtys:
rm_fr(item)
if restore:
model = eval_list(['$image_prefix-%s-model.fits'%d for d in pol])
argo.combine_fits(model,outname=model_image,ctype='STOKES',keep_old=keep_component_images)
residual = eval_list(['$image_prefix-%s-residual.fits'%d for d in pol])
argo.combine_fits(residual,outname=residual_image,ctype='STOKES',keep_old=keep_component_images)
restored = eval_list(['$image_prefix-%s-image.fits'%d for d in pol])
argo.combine_fits(restored,outname=restored_image,ctype='STOKES',keep_old=keep_component_images)
if mfs:
model_mfs = eval_list(['$image_prefix-MFS-%s-model.fits'%d for d in pol])
argo.combine_fits(model_mfs,
outname=model_image.replace('.model.fits','-MFS.model.fits'),
ctype='STOKES',keep_old=keep_component_images)
residual_mfs = eval_list(['$image_prefix-MFS-%s-residual.fits'%d for d in pol])
argo.combine_fits(residual_mfs,
outname=residual_image.replace('.residual.fits','-MFS.residual.fits'),
ctype='STOKES',keep_old=keep_component_images)
restored_mfs = eval_list(['$image_prefix-MFS-%s-image.fits'%d for d in pol])
argo.combine_fits(restored_mfs,
outname=restored_image.replace('.restored.fits','-MFS.restored.fits'),
ctype='STOKES',keep_old=False)
else:
for fits in ['$image_prefix-%s-image.fits'%d for d in pol]:
rm_fr(fits)
if not channelize:
if psf:
x.mv('${image_prefix}-psf.fits $psf_image')
elif restore:
rm_fr('${image_prefix}-psf.fits')
if len(pol)>1:
combine_pol(pol,image_prefix)
else:
if dirty:
x.mv('${image_prefix}-dirty.fits $dirty_image')
else:
rm_fr('${image_prefix}-dirty.fits')
if restore:
x.mv('${image_prefix}-model.fits $model_image')
x.mv('${image_prefix}-residual.fits $residual_image')
x.mv('${image_prefix}-image.fits $restored_image')
# x.mv('${image_prefix}-psf.fits $psf_image')
else:
rm_fr('${image_prefix}-image.fits')
else:
# Combine component images from wsclean
labels = ['%04d'%d for d in range(nr)]
psfs = eval_list(['$image_prefix-%s-psf.fits'%d for d in labels])
if psf:
argo.combine_fits(psfs,outname=II('$image_prefix.psf.fits'),ctype='FREQ',keep_old=keep_component_images)
elif restore:
for fits in psfs:
rm_fr(fits)
for i in pol:
if len(pol) == 1:
i = ''
if i :
i = '-%s'%i
dirtys = eval_list(['$image_prefix-%s$i-dirty.fits'%d for d in labels])
if dirty:
argo.combine_fits(dirtys,
outname=II('$image_prefix$i-dirty.fits') if i else dirty_image,
ctype='FREQ',keep_old=keep_component_images)
if not restore:
xo.sh('rm -fr ${image_prefix}*image*.fits')
else:
for fits in dirtys:
rm_fr(fits)
if restore:
model = eval_list(['$image_prefix-%s$i-model.fits'%d for d in labels])
argo.combine_fits(model,outname=II('$image_prefix$i-model.fits') if i else model_image,
ctype='FREQ',keep_old=keep_component_images)
residual = eval_list(['$image_prefix-%s$i-residual.fits'%d for d in labels])
argo.combine_fits(residual,outname=II('$image_prefix$i-residual.fits') if i else residual_image,
ctype='FREQ',keep_old=keep_component_images)
restored = eval_list(['$image_prefix-%s$i-image.fits'%d for d in labels])
argo.combine_fits(restored,outname=II('$image_prefix$i-image.fits') if i else restored_image ,
ctype='FREQ',keep_old=keep_component_images)
if len(pol)==1:
for old,new in zip([image_prefix+'-MFS-%s.fits'%img for img in 'model residual image'.split()],
[model_image.replace('.model.fits','-MFS.model.fits'),
residual_image.replace('.residual.fits','-MFS.residual.fits'),
restored_image.replace('.restored.fits','-MFS.restored.fits')]):
#TODO(sphe) Should we always keep wsclean MFS images?
#if mfs:
x.mv('$old $new')
#else:
# rm_fr(old)
if len(pol)>1:
combine_pol(pol,image_prefix,mfs=True)
if do_moresane:
info(" im.moresane.deconv: making estored image $restored_image \
model is $model_image, residual is $residual_image)")
moresane.deconv(dirty_image,psf_image,model_image=model_image,
residual_image=residual_image,
restored_image=restored_image,**kw0)
if restore or do_moresane:
if lsm and restore_lsm:
info("Restoring LSM into FULLREST_IMAGE=$fullrest_image");
opts = restore_lsm if isinstance(restore_lsm,dict) else {};
tigger_restore(restoring_options,"-f",
restored_image,lsm,
fullrest_image,
kwopt_to_command_line(**opts));
im.IMAGER = _imager
