fluxes, shapes fixed

Author: Sebokolodi

Sourcery/CHANGES.md

@@ -6,3 +6,4 @@
 #### Shapes are corrected: sourcery able to assign pnt and Gau appropriately, and uses DC_Maj/Min as a model and Maj/Min for reliability computation.
 #### The flux estimations are corrected. Uses masked image to create islands and the actual image for detection (model fitting)
 #### Takes the radius of sources to exclude inside the reliability script (previously it was done inside main-- had problems)
+#### Has an option to remove sources with correlation < 0.002 and reliability > 0.60

Sourcery/config.json

@@ -9,6 +9,7 @@
        "do_psf_corr": true,
        "do_local_var": true,
        "do_nearsources":false,
+       "reset_rel": false,
        "increase_beam_cluster": true,
        "psf_corr_region" : 5,
        "local_var_region" : 10,

Sourcery/main.py

@@ -67,8 +67,9 @@ def main():
         default=True, help="Make reliability density plot. Default is True."
         " To disable add -dmp on the command line.")
 
-    add("-rel", "--rel-thresh", dest="rel_thresh", default=None, type=float, 
-        help= "Sets a reliability threshold. Default is None.")
+    add("-drel", "--reset-rel", dest="reset_rel", action="store_true",
+        default=False, help=" Assigns R=0 for sources with cf < 0.002 and" 
+        "R > 0.60.")
 
     add("-beam", "--beam-cluster", dest="do_beam", default=False,
         action="store_true", help= "Increases the Gaussian groupings by 20 percent the"
@@ -268,7 +269,7 @@ def get_prefix(prefix, imagename, outdir):
                      neg_smooth=args.neg_smooth, loglevel=args.log_level, 
                      thresh_isl=args.thresh_isl, thresh_pix=args.thresh_pix,
                      neg_thresh_isl=args.neg_thresh_isl, neg_thresh_pix=
-                     args.neg_thresh_pix, prefix=prefix,  
+                     args.neg_thresh_pix, prefix=prefix, reset_rel=args.reset_rel, 
                      do_nearsources=args.do_nearsources, increase_beam_cluster=
                      args.do_beam, savemask_neg=args.savemask_neg,
                      savemask_pos=args.savemask_pos, **pybdsm_opts)

Sourcery/reliabilityestimates.py

@@ -25,9 +25,10 @@ def __init__(self, imagename, psfname=None, sourcefinder_name='pybdsm',
                  makeplots=True, do_psf_corr=True, do_local_var=True,
                  psf_corr_region=5, local_var_region=10, rel_excl_src=None, 
                  pos_smooth=2, neg_smooth=2, loglevel=0, thresh_pix=5,
-                 thresh_isl=3, neg_thresh_isl=3, neg_thresh_pix=5,
-                 prefix=None, do_nearsources=False, increase_beam_cluster=False,
-                 savemask_pos=False, savemask_neg=False, **kw):
+                 thresh_isl=3, neg_thresh_isl=3, neg_thresh_pix=5, reset_rel=None,
+                 prefix=None, do_nearsources=False, savefits=False,
+                 increase_beam_cluster=False, savemask_pos=False, savemask_neg=False,
+                 **kw):
 
         """ Takes in image and extracts sources and makes 
             reliability estimations..
@@ -89,6 +90,10 @@ def __init__(self, imagename, psfname=None, sourcefinder_name='pybdsm',
         savefits: boolean. Default is False.
             If True a negative image is saved.
 
+        reset_rel: boolean. Default is False. If true then
+            sources with correlation < 0.002 and rel >0.60
+            have their reliabilities set to 0.
+
         increase_beam_cluster: boolean, optional. If True, sources
             groupings will be increase by 20% the beam size. If False,
             the actual beam size will be used. Default is False.
@@ -137,7 +142,8 @@ def __init__(self, imagename, psfname=None, sourcefinder_name='pybdsm',
         self.do_psf_corr = do_psf_corr
         self.savemaskpos = savemask_pos
         self.savemaskneg = savemask_neg
-        self.savefits = False
+        self.savefits = savefits
+        self.derel = reset_rel
 
         if not self.psfname:
             self.log.info(" No psf provided, do_psf_corr is set to False.")
@@ -312,6 +318,9 @@ def params(self, modelfits, data_image):
                               cf =  (numpy.diag((numpy.rot90(c_region))**2)
                                            .sum())**0.5/2**0.5
                               srs.setAttribute("cf", cf)
+                              #srs.setAttribute("ex", emaj)
+                              #srs.setAttribute("ey", emin)
+                              #srs.setAttribute("I_err", data["E_Total_flux"][i])
                               corr.append(cf)
                               model.sources.append(srs) 
                               peak.append(peak_flux)
@@ -320,6 +329,9 @@ def params(self, modelfits, data_image):
                               loc.append(local)
                       else:
                           model.sources.append(srs) 
+                          #srs.setAttribute("ex", emaj)
+                          #srs.setAttribute("ey", emin)
+                          #srs.setAttribute("I_err", data["E_Total_flux"][i])
                           peak.append(peak_flux)
                           total.append(flux)
                           area.append(srcarea)
@@ -451,10 +463,10 @@ def get_reliability(self):
 
         # remove sources with poor correlation and high reliability,
         # the values are currently arbitrary
-        if self.do_psf_corr:
+        if self.do_psf_corr and self.derel:
             for s in pmodel.sources:
                 cf, r = s.cf, s.rel
-                if cf < 0.01 and r > 0.70:
+                if cf < 0.002 and r > 0.60:
                     s.rel = 0.0    
 
         if self.makeplots: