added ddcal step

cluster.py

@@ -456,7 +456,7 @@ def main(img, resid, model, auto=True, add_manual=False, nclusters=5, boxsize=25
          nbright=80, cluster_radius=5, cluster_overlap=1.6):
 
     path = os.path.split(os.path.abspath(img))[0]
-    output = os.path.join(path, 'clustered.txt')
+    output = os.path.spitext(img)[0]+'-clustered.txt'
 
     df = pd.read_csv(model, skipinitialspace=True)
     df['ra'] = df.Ra.apply(ra2deg)
@@ -492,6 +492,7 @@ def main(img, resid, model, auto=True, add_manual=False, nclusters=5, boxsize=25
         write_df(df, clusters, output=output)
     fig.tight_layout()
     fig.savefig(path+'/clustering.png')
+    return output
 
 
 ### if __name__ == "__main__":

imcal.py

@@ -26,6 +26,8 @@ from astropy.time import Time
 import astropy.units as u
 from astropy.io import fits
 
+from cluster import main as cluster
+
 
 _POOL_TIME = 300 # SECONDS
 _MAX_TIME = 1 * 3600 # SECONDS
@@ -325,6 +327,8 @@ def main(msin, outbase=None, cfgfile='imcal.yml'):
     img2 = outbase + '_2'
     img3 = outbase + '_3'
     img_final = outbase
+    img_ddsub = outbase + '-ddsub'
+    img_ddcal = outbase + '-ddcal'
 
     mask0 = 'mask0.fits'
     mask1 = 'mask1.fits'
@@ -337,13 +341,15 @@ def main(msin, outbase=None, cfgfile='imcal.yml'):
     dical1 = outbase + '_dical1.MS'
     dical2 = outbase + '_dical2.MS'
     dical3 = outbase + '_dical3.MS'
+    ddsub = outbase + '_ddsub.MS'
 
     h5_1 = outbase + '_dical1.h5'
     h5_2 = outbase + '_dical2.h5'
     h5_3 = outbase + '_dical3.h5'
+    h5_dd = outbase + '_dd.h5'
 
 
-    if os.path.exists(img_final+'-image.fits'):
+    if os.path.exists(img_ddcal+'-image.fits'):
         logging.info('The final image exists. Exiting...')
         return 0
 
@@ -398,6 +404,31 @@ def main(msin, outbase=None, cfgfile='imcal.yml'):
     if (not os.path.exists(img_final +'-image.fits')) and (not os.path.exists(img_final +'-MFS-image.fits')):
         wsclean(dical3, outname=img_final, **cfg['clean4'])
 
+
+# Cluster
+    if (not os.path.exists(img_final +'-clustered.txt')):
+        clustered_model = cluster(img_final+'-image.fits', img_final+'-residual.fits', img_final+'-sources.txt', **cfg['cluster'])
+
+# Makesourcedb
+        clustered_sdb = makesourcedb(clustered_model, img_final+'-clustered.sourcedb')
+
+# DDE calibration + peeling everything
+    if (not os.path.exists(ddsub)):
+        ddsub, h5out = ddecal(dical3, clustered_sdb, msout=ddsub, h5out=h5_dd,
+                            solint=120, mode='diagonal')
+
+# view the solutions and save figure
+        view_sols(h5_dd)
+
+    if (not os.path.exists(img_ddsub+'-image.fits')):
+        wsclean(ddsub, outname=img_ddsub, **cfg['clean4'])
+
+    aomodel = bbs2model(img_final+'-sources.txt', img_final+'-model.ao')
+
+    render(img_ddsub+'-image.fits', aomodel, out=img_ddcal+'-image.fits')
+
+
+
     return 0
 
 

imcal.yml

@@ -64,7 +64,7 @@ dical3:
     solint: 800
     mode: 'diagonal'
     uvlambdamin: 500 # Ignore baselines / channels with UV < uvlambdamin wavelengths.
-    cal_nchan: 30 # number of chans with the same solutions
+    cal_nchan: 31 # number of chans with the same solutions
     
 clean4:
     imagesize: 3072
@@ -76,27 +76,38 @@ clean4:
     fitsmask: 'mask2.fits'
     kwstring: '-use-wgridder -parallel-deconvolution 1400 -parallel-gridding 8 -deconvolution-channels 3 -weight briggs 0.0'
 
-### END
-
 ####################### CLUSTERING #######################
-#cluster:
-#    nbright: 80 # number of brightest clean components (CC) to check for artefacts
-#    boxsize: 250 # the boxsize around CC in pixels where to check for artefacts
-#    nclusters: 10 # number of clusters ('auto' -- to set automatically)
-#    cluster_radius: 5 # arcmin
-#    cluster_overlap: 1.6 # if lower than 2 clusters can intersect
-#    auto: True
-#    add_manual: False
-#
+cluster:
+    nbright: 80 # number of brightest clean components (CC) to check for artefacts
+    boxsize: 250 # the boxsize around CC in pixels where to check for artefacts
+    nclusters: 10 # number of clusters ('auto' -- to set automatically)
+    cluster_radius: 5 # arcmin
+    cluster_overlap: 1.6 # if lower than 2 clusters can intersect
+    auto: True
+    add_manual: False
+
 ######################## DD CALIBRATION #######################
-#ddcal: # see DPPP/DDECal documentation
-#    solint: 120 # Solution interval in timesteps (1 ~ 30sec for Apertif).
-#    mode: 'diagonal' # Type of constraint to apply. 
-#    nchan: 15 # Number of channels in each channel block, for which the solution is assumed to be constant.
-#    startchan: 0
-#    nchan: 192
-#    uvlambdamin: 500 # Ignore baselines / channels with UV < uvlambdamin wavelengths.
-#
+ddcal: # see DPPP/DDECal documentation
+    solint: 120 # Solution interval in timesteps (1 ~ 30sec for Apertif).
+    mode: 'diagonal' # Type of constraint to apply. 
+    nfreq: 15 # Number of channels in each channel block, for which the solution is assumed to be constant.
+    startchan: 0
+    nchan: 0
+    uvlambdamin: 500 # Ignore baselines / channels with UV < uvlambdamin wavelengths.
+
+clean5:
+    imagesize: 3072
+    pixelsize: 3
+    multifreq: 8
+    automask: 4.5
+    autothresh: 0.5
+    multiscale: True
+    fitsmask: 'mask2.fits'
+    kwstring: '-use-wgridder -parallel-deconvolution 1400 -parallel-gridding 8 -deconvolution-channels 3 -weight briggs 0.0'    
+    
+### END
+
+
 ## TODO:    
 #plotsols:
 #