Merge branches 'abssys_speedup' and 'master' of https://github.com/li…

…netools/linetools into abssys_speedup
linetools · May 16, 2016 · 98eda3e · 98eda3e
2 parents f50f0c7 + ebcbf94
commit 98eda3e
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Showing 2 changed files with 18 additions and 4 deletions.
diff --git a/linetools/isgm/abscomponent.py b/linetools/isgm/abscomponent.py
@@ -409,6 +409,10 @@ def synthesize_colm(self, overwrite=False, redo_aodm=False, **kwargs):
         # Collate
         self.flag_N = 0
         for aline in self._abslines:
+            if aline.attrib['flag_N'] == 0:  # No value
+                warnings.warn("Absline {} has flag=0.  Hopefully you expected that".format(str(aline)))
+                continue
+            # Check N is filled
             if np.allclose(aline.attrib['N'].value, 0.):
                 raise ValueError("Need to set N in attrib.  \n Consider linear_clm in linetools.analysis.absline")
             if aline.attrib['flag_N'] == 1:  # Good value?
@@ -445,10 +449,13 @@ def synthesize_colm(self, overwrite=False, redo_aodm=False, **kwargs):
                     if aline.attrib['N'] < self.N:
                         self.N = aline.attrib['N']
                         self.sig_N = aline.attrib['sig_N']
+            elif aline.attrib['flag_N'] == 0:  # No value
+                warnings.warn("Absline {} has flag=0.  Hopefully you expected that")
             else:
                 raise ValueError("Bad flag_N value")
         # Log values
-        self.logN, self.sig_logN = ltaa.log_clm(self)
+        if self.flag_N > 0:
+            self.logN, self.sig_logN = ltaa.log_clm(self)
 
     def repr_vpfit(self, b=10.*u.km/u.s, tie_strs=('', '', ''), fix_strs=('', '', '')):
         """

diff --git a/linetools/isgm/tests/test_use_abscomp.py b/linetools/isgm/tests/test_use_abscomp.py
@@ -26,7 +26,8 @@
 #pdb.set_trace()
 # Set of Input lines
 
-def mk_comp(ctype,vlim=[-300.,300]*u.km/u.s,add_spec=False, use_rand=True):
+def mk_comp(ctype,vlim=[-300.,300]*u.km/u.s,add_spec=False, use_rand=True,
+            add_trans=False):
     # Read a spectrum Spec
     if add_spec:
         xspec = lsio.readspec(lt_path+'/spectra/tests/files/UM184_nF.fits')
@@ -37,6 +38,8 @@ def mk_comp(ctype,vlim=[-300.,300]*u.km/u.s,add_spec=False, use_rand=True):
         all_trans = ['HI 1215', 'HI 1025']
     elif ctype == 'SiII':
         all_trans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
+        if add_trans:
+            all_trans += ['SiII 1193']
     abslines = []
     for trans in all_trans:
         iline = AbsLine(trans)
@@ -75,18 +78,22 @@ def test_build_table():
     assert isinstance(comp_tbl,QTable)
 
 def test_synthesize_colm():
-    abscomp,_ = mk_comp('SiII', vlim=[-250,80.]*u.km/u.s, add_spec=True)
+    abscomp,_ = mk_comp('SiII', vlim=[-250,80.]*u.km/u.s, add_spec=True,
+                        add_trans=True)
     # Column
     abscomp.synthesize_colm(redo_aodm=True)
     # Test
     np.testing.assert_allclose(abscomp.logN, 13.594445560856554)
     # Reset flags (for testing)
-    abscomp2,_ = mk_comp('SiII', vlim=[-250,80.]*u.km/u.s, add_spec=True, use_rand=False)
+    abscomp2,_ = mk_comp('SiII', vlim=[-250,80.]*u.km/u.s, add_spec=True, use_rand=False,
+                         add_trans=True)
     for iline in abscomp2._abslines:
         if iline.data['name'] == 'SiII 1260':
             iline.attrib['flag_N'] = 2
         elif iline.data['name'] == 'SiII 1808':
             iline.attrib['flag_N'] = 3
+        elif iline.data['name'] == 'SiII 1193':
+            iline.attrib['flag_N'] = 0
         else:
             iline.attrib['flag_N'] = 1
     abscomp2.synthesize_colm()