Merge f5bc7a9 into f9c14d5

linetools · Feb 4, 2019 · a4fd523 · a4fd523
2 parents f9c14d5 + f5bc7a9
commit a4fd523
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/linetools/isgm/abscomponent.py b/linetools/isgm/abscomponent.py
@@ -287,15 +287,16 @@ def from_dict(cls, idict, coord=None, skip_abslines=False, **kwargs):
                         slf.attrib[ak] = np.array(slf.attrib[ak])
 
         # Deprecated column (again)
-        if Ntup is not None:
+        if (Ntup is not None):
             warnings.warn('Overwriting column density attributes (if they existed).', DeprecationWarning)
             slf.attrib['flag_N'] = Ntup[0]
             slf.attrib['logN'] = Ntup[1]
             if isiterable(Ntup[2]):
                 slf.attrib['sig_logN'] = np.array(Ntup[2])
             else:
                 slf.attrib['sig_logN'] = np.array([Ntup[2]]*2)
-            _, _ = ltaa.linear_clm(slf.attrib)  # Set linear quantities
+        # set linear quantities in column density
+        _, _ = ltaa.linear_clm(slf.attrib)
 
         # Add AbsLine objects
         if not skip_abslines:
@@ -1009,6 +1010,9 @@ def to_dict(self):
         cdict['lines'] = {}
         for iline in self._abslines:
             cdict['lines'][iline.wrest.value] = iline.to_dict()
+        # set linear quantities in column density
+        _, _ = ltaa.linear_clm(cdict['attrib'])
+
         # Polish
         cdict = ltu.jsonify(cdict)
         # Return

diff --git a/linetools/isgm/utils.py b/linetools/isgm/utils.py
@@ -402,8 +402,7 @@ def table_from_complist(complist, summed_ion=False, NHI_obj=None, vrange=None,
     tab['ion'] = [icomp.Zion[1] for icomp in complist]
 
     # . attributes (required ones)
-    for attrib in ['zcomp', 'Ej', 'flag_N', 'logN', 'sig_logN',
-                   'b','sig_b','vel','sig_vel']:
+    for attrib in ['zcomp', 'Ej']:
         values = [getattr(icomp,attrib) for icomp in complist]
         if isinstance(values[0], u.Quantity):
             values = u.Quantity(values)
@@ -422,8 +421,9 @@ def table_from_complist(complist, summed_ion=False, NHI_obj=None, vrange=None,
             ion_names[-1] += '*'
     tab['ion_name'] = ion_names
 
-    # attrib dict
-    for attrib in ['sig_z', 'b', 'sig_b', 'vel', 'sig_vel', 'specfile']:
+    # attrib dict containing logN, b, etc
+    for attrib in ['flag_N', 'logN', 'sig_logN', 'sig_z',
+                   'b', 'sig_b', 'vel', 'sig_vel', 'specfile']:
         try:
             values = [icomp.attrib[attrib] for icomp in complist]
         except KeyError: