some changes

imcal.py

@@ -28,11 +28,11 @@ import astropy.units as u
 from astropy.io import fits
 
 # the executables:
-dppp_bin = distutils.spawn.find_executable('DPPP') or '/home/offringa/Software/DP3/build/DP3'
-wsclean_bin = distutils.spawn.find_executable('wsclean') or '/home/offringa/Software/wsclean/build/wsclean'
-makesourcedb_bin = distutils.spawn.find_executable('makesourcedb') or '/home/offringa/Software/DP3/build/makesourcedb'
-bbs2model_bin = distutils.spawn.find_executable('bbs2model') or '/home/offringa/Software/lofartools/build/bbs2model'
-render_bin = distutils.spawn.find_executable('render') or '/home/offringa/Software/lofartools/build/render'
+dppp_bin = distutils.spawn.find_executable('DPPP')
+wsclean_bin = distutils.spawn.find_executable('wsclean')
+makesourcedb_bin = distutils.spawn.find_executable('makesourcedb')
+bbs2model_bin = distutils.spawn.find_executable('bbs2model')
+render_bin = distutils.spawn.find_executable('render')
 
 # Tom's masking code
 makeMaskFits = '/home/kutkin/rapthor/makeMaskFits'
@@ -53,10 +53,10 @@ def modify_filename(fname, string, ext=None):
     return fbase + string + fext
 
 
-def wsclean(msin, outname=None, pixelsize=3, mgain=0.8, imagesize=3072, multifreq=8, autothresh=0.3,
-            automask=3, niter=1000000, multiscale=False, save_source_list=True,
-            usefitsmask=False, fitsmaskname='mask.fits',
-            kwstring=''):
+def wsclean(msin, outname=None, pixelsize=3, imagesize=3072, mgain=0.8, multifreq=0, autothresh=0.3,
+            automask=3, niter=1000000, multiscale=False, save_source_list=False,
+            clearfiles=True,
+            fitsmask=None, kwstring=''):
     """
     wsclean
     """
@@ -69,14 +69,14 @@ def wsclean(msin, outname=None, pixelsize=3, mgain=0.8, imagesize=3072, multifre
         kwstring += f' -auto-threshold {autothresh}'
     if automask is not None:
         kwstring += f' -auto-mask {automask}'
-    if mgain is not None:
+    if mgain:
         kwstring += f' -mgain {mgain}'
     if save_source_list:
         kwstring += ' -save-source-list'
     if multifreq:
         kwstring += f' -join-channels -channels-out {multifreq} -fit-spectral-pol 2'
-    if usefitsmask:
-        kwstring += f' -fits-mask {fitsmaskname}'
+    if fitsmask:
+        kwstring += f' -fits-mask {fitsmask}'
 
     cmd = f'{wsclean_bin} -name {outname} -size {imagesize} {imagesize} -scale {pixelsize}asec -niter {niter} \
             {kwstring} {msin}'
@@ -87,6 +87,11 @@ def wsclean(msin, outname=None, pixelsize=3, mgain=0.8, imagesize=3072, multifre
     for fname in glob.glob(outname+'*.fits'):
         newname = fname.replace('MFS-', '')
         os.rename(fname, newname)
+    if clearfiles:
+        todelete = glob.glob(f'{outname}-000[0-9]-*.fits') # multifreq images
+        for f in todelete:
+            os.remove(f)
+
     return 0
 
 

imcal.yml

 #:===========================================================================
 # Settings for imcal
 #:===========================================================================
-####################### DICAL IMAGING #######################
+####################### IMAGING #######################
 
 #global:
 #    dppp_bin: 'DPPP' # on blizzard
@@ -22,10 +22,10 @@ clean1: # wsclean setup
     imagesize: 3072
     pixelsize: 3 
     multifreq: 0
+    mgain: 0
     automask: 20
     autothresh: 5
-    usefitsmask: True
-    fitsmaskname: 'mask0.fits'
+    fitsmask: 'mask0.fits'
     multiscale: False
     kwstring: '-use-wgridder -parallel-deconvolution 1400' # use this for additional wsclean options, e.g. '-weight uniform -use-idg' 
 
@@ -41,8 +41,7 @@ clean2:
     multifreq: 8  
     automask: 10
     autothresh: 5
-    usefitsmask: True
-    fitsmaskname: 'mask0.fits'
+    fitsmask: 'mask0.fits'
     multiscale: True
     kwstring: '-use-wgridder -parallel-deconvolution 1400 -parallel-gridding 8 -deconvolution-channels 3'
     
@@ -58,8 +57,7 @@ clean3:
     multifreq: 8  
     automask: 7
     autothresh: 3.5
-    usefitsmask: True
-    fitsmaskname: 'mask1.fits'
+    fitsmask: 'mask1.fits'
     multiscale: True
     kwstring: '-use-wgridder -parallel-deconvolution 1400 -parallel-gridding 8 -deconvolution-channels 3'
     
@@ -67,7 +65,7 @@ dical3:
     solint: 800
     mode: 'diagonal'
     uvlambdamin: 500 # Ignore baselines / channels with UV < uvlambdamin wavelengths.
-    cal_nchan: 31 # number of chans with the same solutions
+    cal_nchan: 30 # number of chans with the same solutions
     
 clean4:
     imagesize: 3072
@@ -76,9 +74,8 @@ clean4:
     automask: 4.5
     autothresh: 0.5
     multiscale: True
-    usefitsmask: True
-    fitsmaskname: 'mask2.fits'
-    kwstring: '-use-wgridder -parallel-deconvolution 1400 -parallel-gridding 8 -deconvolution-channels 3 -weight briggs -1.0'
+    fitsmask: 'mask2.fits'
+    kwstring: '-use-wgridder -parallel-deconvolution 1400 -parallel-gridding 8 -deconvolution-channels 3 -weight briggs 0.0'
 
 ### END