get aegean to work

aimfast/aimfast.py

@@ -885,9 +885,14 @@ def tigger_src_wsclean(src, idx):
  model = Tigger.load(catalog)
  if ext in ['.tab', '.csv']:
  data = Table.read(catalog, format='ascii')
+ if ext == '.tab':
+ fits_file = catalog.replace('_comp.tab', '.fits')
+ else:
+ fits_file = catalog.replace('_comp.csv', '.fits')
+ fitsinfo = fitsInfo(fits_file)
  for i, src in enumerate(data):
  model.sources.append(tigger_src_ascii(src, i))
- centre = fitsInfo['centre'] or _get_phase_centre(model)
+ centre = fitsinfo['centre'] or _get_phase_centre(model)
  model.ra0, model.dec0 = map(np.deg2rad, centre)
  model.save(catalog[:-4]+".lsm.html")
  if ext in ['.fits']:
@@ -1404,7 +1409,6 @@ def _source_flux_plotter(results, all_models, inline=False, units='milli',
  z = np.array(phase_centre_dist)
  axis_labels = ['Model 1 log (flux)', 'Model 2 log (flux)']
  elif plot_type == 'snr':
- print(flux_in_data)
  x = np.log(np.array(flux_in_data) * FLUX_UNIT_SCALER[units][0])
  y = ((np.array(flux_in_data) * FLUX_UNIT_SCALER[units][0])/
  (np.array(flux_out_data) * FLUX_UNIT_SCALER[units][0]))

aimfast/auxiliary.py

@@ -201,18 +201,25 @@ def get_online_catalog(catalog='NVSS', width='1d', thresh=1.0,
 
 def aegean(image, kwargs, log):
  args = ['aegean']
+ outfile = ''
  for name, value in kwargs.items():
  if value is None:
  continue
  elif value is False:
  continue
  if name == 'filename': # positional argument
  args += ['{0}'.format(value)]
+ elif name == 'table':
+ outfile = "{}.tab".format(kwargs['filename'][:-5])
+ args += ['{0}{1} {2}'.format('--', name, outfile)]
+ # Aegean add '_comp' to the file name e.g. im_comp.tab
+ outfile = "{}_comp.tab".format(kwargs['filename'][:-5])
  else:
  args += ['{0}{1} {2}'.format('--', name, value)]
  log.info("Running: {}".format(" ".join(args)))
  run = subprocess.run(" ".join(args), shell=True)
  log.info("The exit code was: {}".format(run.returncode))
+ return outfile
 
 
 def bdsf(image, kwargs, log):

aimfast/source_finder.yml

@@ -41,7 +41,7 @@ pybdsf:
  psf_snrtop: 0.15
  psf_stype_only: true
  psf_smooth:
- psf_high_snr: 
+ psf_high_snr:
  indir:
  opdir_overwrite:
  output_all:
@@ -71,7 +71,7 @@ aegean:
  enable: false
  filename: # Image to extract radio sources
  table: ascii # Additional table outputs, format inferred from extension (database: .db, votable: .vot, and ascii: .csv/.tab)
- slice: # If the input data is a cube, then this slice will determine the array index of the image which will be processed by aegean
+ slice: 0  # If the input data is a cube, then this slice will determine the array index of the image which will be processed by aegean
  psf: # A .fits file that represents the local psf
  noise: # A .fits file that represents the image noise
  region: # Use this regions file to restrict source finding in this image. Use MIMAS region (.mim) files