diff --git a/imcal.py b/imcal.py
index cc4b5e61fb472c9629c0842633e82d97a8918ed1..7f57c3fe1fe814eba300b0ebf723098266e2cc20 100755
--- a/imcal.py
+++ b/imcal.py
@@ -39,11 +39,9 @@ _POOL_TIME = 300 # SECONDS
_MAX_TIME = 1 * 3600 # SECONDS
_MAX_POOL = _MAX_TIME // _POOL_TIME
-def execute_binary(binary, args, simg=None):
- if simg:
- command = [f'singularity exec {simg} {binary}'] + args
- else:
- command = [f'{binary}'] + args
+def execute_binary(binary, args, ):
+
+ command = [f'{binary}'] + args
logging.debug('executing %s', ','.join(command))
dppp_process = subprocess.Popen(command)
for i in range(_MAX_POOL):
@@ -125,10 +123,11 @@ def modify_filename(fname, string, ext=None):
return fbase + string + fext
-def wsclean(msin, wsclean_bin='wsclean', datacolumn='DATA', outname=None, pixelsize=3, imagesize=3072, mgain=0.8, multifreq=0, autothresh=0.3,
+def wsclean(msin, wsclean_bin='wsclean', datacolumn='DATA', outname=None, pixelsize=3, imagesize=3072, mgain=0.8,
+ multifreq=0, autothresh=0.3,
automask=3, niter=1000000, multiscale=False, save_source_list=True,
clearfiles=True, clip_model_level=None,
- fitsmask=None, simg=None, kwstring=''):
+ fitsmask=None, kwstring=''):
"""
wsclean
"""
@@ -153,8 +152,6 @@ def wsclean(msin, wsclean_bin='wsclean', datacolumn='DATA', outname=None, pixels
cmd = f'wsclean -name {outname} -data-column {datacolumn} -size {imagesize} {imagesize} -scale {pixelsize}asec -niter {niter} \
{kwstring} {msin}'
cmd = " ".join(cmd.split())
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
logging.debug("Running command: %s", cmd)
subprocess.call(cmd, shell=True)
@@ -181,15 +178,12 @@ def smoothImage(imgfits, psf=30, out=None) :
return fits_reconvolve_psf(imgfits, Beam(psf*u.arcsec), out=out)
-def create_mask(imgfits, residfits, clipval, outname='mask.fits', simg=None):
+def create_mask(imgfits, residfits, clipval, outname='mask.fits', ):
"""
Create mask using Tom's code (e-mail on 1 Jul 2021)
"""
cmd1 = f'makeNoiseMapFitsLow {imgfits} {residfits} noise.fits noiseMap.fits'
cmd2 = f'makeMaskFits noiseMap.fits {outname} {clipval}'
- if simg:
- cmd1 = f'singularity exec {simg} ' + cmd1
- cmd2 = f'singularity exec {simg} ' + cmd2
logging.debug("Running command: %s", cmd1)
subprocess.call(cmd1, shell=True)
logging.debug("Running command: %s", cmd2)
@@ -197,7 +191,7 @@ def create_mask(imgfits, residfits, clipval, outname='mask.fits', simg=None):
return outname
-def makeNoiseImage(imgfits, residfits, low=False, simg=None) :
+def makeNoiseImage(imgfits, residfits, low=False, ) :
"""
Create mask using Tom's code (e-mail on 1 Jul 2021)
"""
@@ -205,8 +199,6 @@ def makeNoiseImage(imgfits, residfits, low=False, simg=None) :
cmd = f'makeNoiseMapFitsLow {imgfits} {residfits} noiseLow.fits noiseMapLow.fits'
else :
cmd = f'makeNoiseMapFits {imgfits} {residfits} noise.fits noiseMap.fits'
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
logging.debug("Running command: %s", cmd)
subprocess.call(cmd, shell=True)
@@ -214,26 +206,22 @@ def makeNoiseImage(imgfits, residfits, low=False, simg=None) :
def makeCombMask(ima1='noiseMap.fits', ima2='noiseMapLow.fits',
- clip1=5, clip2=7, outname='mask.fits', simg=None) :
+ clip1=5, clip2=7, outname='mask.fits', ) :
"""
Create mask using Tom's code (e-mail on 1 Jul 2021)
"""
cmd = f'makeCombMaskFits {ima1} {ima2} {outname} {clip1} {clip2}'
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
logging.debug("Running command: %s", cmd)
subprocess.call(cmd, shell=True)
return
-def get_image_ra_dec_min_max(msin, simg=None):
+def get_image_ra_dec_min_max(msin, ):
"""
Determine image center coords, min and max values for msin
"""
cmd = f'wsclean -niter 0 -size 3072 3072 -scale 3arcsec -use-wgridder {msin}'
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
subprocess.call(cmd, shell=True)
data = fits.getdata('wsclean-image.fits')
header = fits.getheader('wsclean-image.fits')
@@ -241,45 +229,36 @@ def get_image_ra_dec_min_max(msin, simg=None):
return header['CRVAL1'], header['CRVAL2'], np.nanmin(data), np.nanmax(data)
-def makesourcedb(modelfile, out=None, simg=None):
+def makesourcedb(modelfile, out=None, ):
""" Make sourcedb file from a clustered model """
out = out or os.path.splitext(modelfile)[0] + '.sourcedb'
cmd = 'makesourcedb in={} out={}'.format(modelfile, out)
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
logging.debug("Running command: %s", cmd)
subprocess.call(cmd, shell=True)
return out
-def bbs2model(inp, out=None, simg=None):
+def bbs2model(inp, out=None, ):
""" Convert model file to AO format """
out = out or os.path.splitext(inp)[0] + '.ao'
cmd = 'bbs2model {} {}'.format(inp, out)
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
logging.debug("Running command: %s", cmd)
subprocess.call(cmd, shell=True)
return out
-def render(bkgr, model, out=None, simg=None):
+def render(bkgr, model, out=None, ):
out = out or os.path.split(bkgr)[0] + '/restored.fits'
cmd = 'render -a -r -t {} -o {} {}'.format(bkgr, out, model)
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
logging.debug("Running command: %s", cmd)
subprocess.call(cmd, shell=True)
return out
-def execute_dppp(args, simg=None):
- if simg:
- command = ['singularity', 'exec', f'{simg}', 'DP3'] + args
- else:
- command = ['DP3'] + args
-
+def execute_dppp(args, ):
+
+ command = ['DP3'] + args
logging.debug('executing %s', ','.join(command))
dppp_process = subprocess.Popen(command)
for i in range(_MAX_POOL):
@@ -300,7 +279,7 @@ def check_return_code(return_code):
pass
-def split_ms(msin_path, startchan, nchan=0, msout_path='', simg=None):
+def split_ms(msin_path, startchan, nchan=0, msout_path='', ):
"""
use casacore.tables.msutil.msconcat() to concat the new MS files
"""
@@ -313,14 +292,14 @@ def split_ms(msin_path, startchan, nchan=0, msout_path='', simg=None):
f'msin.startchan={startchan}',
f'msin.nchan={nchan}',
f'msout={msout_path}']
- return_code = execute_dppp(command_args, simg=simg)
+ return_code = execute_dppp(command_args)
logging.debug('Split of %s returned status code %s', msin_path, return_code)
check_return_code(return_code)
return msout_path
def dical(msin, srcdb, msout=None, h5out=None, solint=1, startchan=0, split_nchan=0,
- mode='phaseonly', cal_nchan=0, uvlambdamin=500, simg=None):
+ mode='phaseonly', cal_nchan=0, uvlambdamin=500, ):
""" direction independent calibration with DPPP """
h5out = h5out or modify_filename(msin, f'_dical_dt{solint}_{mode}', ext='.h5')
msout = msout or modify_filename(msin, f'_dical_dt{solint}_{mode}')
@@ -338,14 +317,14 @@ def dical(msin, srcdb, msout=None, h5out=None, solint=1, startchan=0, split_ncha
if startchan or split_nchan:
logging.info('Calibrating MS channels: %d - %d', startchan, split_nchan)
command_args += [f'msin.startchan={startchan}', f'msin.nchan={split_nchan}']
- return_code = execute_dppp(command_args, simg=simg)
+ return_code = execute_dppp(command_args)
logging.debug('DICAL returned status code %s', return_code)
check_return_code(return_code)
return msout
def ddecal(msin, srcdb, msout=None, h5out=None, solint=120, nfreq=30,
- startchan=0, nchan=0, mode='diagonal', uvlambdamin=500, subtract=True, simg=None):
+ startchan=0, nchan=0, mode='diagonal', uvlambdamin=500, subtract=True, ):
""" Perform direction dependent calibration with DPPP """
h5out = h5out or os.path.split(msin)[0] + '/ddcal.h5'
msbase = os.path.basename(msin).split('.')[0]
@@ -368,22 +347,17 @@ def ddecal(msin, srcdb, msout=None, h5out=None, solint=120, nfreq=30,
'.format(msin=msin, msout=msout, startchan=startchan, nchan=nchan, mode=mode,
srcdb=srcdb, solint=solint, h5out=h5out, subtract=subtract, nfreq=nfreq,
uvlambdamin=uvlambdamin)
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
cmd = " ".join(cmd.split())
logging.debug("Running command: %s", cmd)
subprocess.call(cmd, shell=True)
return msout, h5out
-def phase_shift(msin, new_center, msout=None, simg=None):
+def phase_shift(msin, new_center, msout=None, ):
""" new_center examples: [12h31m34.5, 52d14m07.34] or [187.5deg, 52.45deg] """
msout = msout or '.'
cmd = "DP3 msin={msin} msout={msout} msout.overwrite=True steps=[phaseshift] \
phaseshift.phasecenter={new_center}".format(**locals())
- if simg:
- cmd = f'singularity exec {simg} ' + cmd
-
cmd = " ".join(cmd.split())
subprocess.call(cmd, shell=True)
@@ -490,7 +464,7 @@ def main(msin, steps='all', outbase=None, cfgfile='imcal.yml', force=False):
with open(cfgfile) as f:
cfg = yaml.safe_load(f)
- simg = cfg['global']['singularity_image_path']
+
if steps == 'all':
steps = ['nvss', 'mask', 'dical', 'ddcal']
@@ -553,7 +527,7 @@ def main(msin, steps='all', outbase=None, cfgfile='imcal.yml', force=False):
if (not os.path.exists(ms_split)) and (cfg['split']['startchan'] or cfg['split']['nchan']):
ms_split = split_ms(msin, msout_path=ms_split, **cfg['split'])
- makesourcedb(nvss_model, out=nvssMod, simg=simg)
+ makesourcedb(nvss_model, out=nvssMod)
dical(ms_split, nvssMod, msout=dical0, h5out=h5_0, **cfg['nvsscal'])
view_sols(h5_0, outname=msbase+'_sols_dical0')