From d9cdaed941c6603ba06617bb3ec2c90dd7f6b402 Mon Sep 17 00:00:00 2001
From: Griffin Foster <griffin.foster@gmail.com>
Date: Fri, 14 Feb 2014 15:41:34 +0200
Subject: [PATCH 1/2] lsm: added a verify function to assure sources are in
 real positions in the sky

---
 Pyxides/lsm.py | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/Pyxides/lsm.py b/Pyxides/lsm.py
index 2d76688..783e443 100644
--- a/Pyxides/lsm.py
+++ b/Pyxides/lsm.py
@@ -83,6 +83,7 @@ def pybdsm_search (image="${imager.RESTORED_IMAGE}",output="$PYBDSM_OUTPUT",pol=
     args = []
   if select:
     args += [ "--select",select ];
+  verifyGaulModel(gaul)
   tigger_convert(gaul,output,"-t","ASCII","--format",
       "name Isl_id Source_id Wave_id ra_d E_RA dec_d E_DEC i E_Total_flux Peak_flux E_Peak_flux Xposn E_Xposn Yposn E_Yposn Maj E_Maj Min E_Min PA E_PA emaj_d E_DC_Maj emin_d E_DC_Min pa_d E_DC_PA Isl_Total_flux E_Isl_Total_flux Isl_rms Isl_mean Resid_Isl_rms Resid_Isl_mean S_Code"
      +
@@ -97,6 +98,26 @@ def pybdsm_search (image="${imager.RESTORED_IMAGE}",output="$PYBDSM_OUTPUT",pol=
     
 document_globals(pybdsm_search,"PYBDSM_* imager.RESTORED_IMAGE");
 
+def verifyGaulModel(gaullsm):
+  """Check all sources in a gaul file are in valid locations before running tigger
+  convert. Useful when images are 'all-sky' and have undefined regions.
+  """
+  falseSources=0
+  olsm=''
+  fh=open(gaullsm,'r')
+  for ll in fh.readlines():
+    cll=' '.join(ll.split())
+    if cll=='' or cll.startswith('#'):
+      olsm+=ll
+      continue
+    lineArray=cll.split(' ')
+    if math.isnan(float(lineArray[4])): falseSources+=1
+    else: olsm+=ll
+  fh.close()
+
+  fh=open(gaullsm,'w')
+  fh.write(olsm)
+  fh.close()
 
 
 def transfer_tags (fromlsm="$LSMREF",lsm="$LSM",output="$LSM",tags="dE",tolerance=60*ARCSEC):
@@ -162,4 +183,4 @@ def pointify (lsm="$LSM",output="$LSM",name=""):
 document_globals(add_ccs,"MODEL_CC_*");  
 
   
-  
\ No newline at end of file
+  

From 27b4ae31edaf894fa7c1948a9a7a7936d6442d35 Mon Sep 17 00:00:00 2001
From: SpheMakh <sphemakh@gmail.com>
Date: Sun, 28 Sep 2014 17:13:09 +0200
Subject: [PATCH 2/2] imager.py: Fixed incorrect order of passing arguments to
 ms.copycol() on line 327

---
 Pyxides/imager.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Pyxides/imager.py b/Pyxides/imager.py
index 0cff3f5..850382b 100644
--- a/Pyxides/imager.py
+++ b/Pyxides/imager.py
@@ -324,7 +324,7 @@ def predict_vis (msname="$MS",image="$MODEL_IMAGE",column="MODEL_DATA",channeliz
   rm_fr(casaimage);
   
   if column != "MODEL_DATA":
-    ms.copycol(msname,"MODEL_DATA",column);
+    ms.copycol(msname=msname,fromcol="MODEL_DATA",tocol=column);
 
 document_globals(predict_vis,"MS MODEL_IMAGE COPY_IMAGE_TO ms.IFRS ms.DDID ms.FIELD ms.CHANRANGE");