LLS: Some edits for the LLS GUI

linetools/isgm/abssystem.py

@@ -172,6 +172,24 @@ def chk_component(self, component):
         """Additional checks on the component"""
         return True
 
+    def list_of_abslines(self):
+        """ Generate a list of the absorption lines in this system
+
+        Drawn from the components
+
+        Returns
+        -------
+        abslist : list
+
+        """
+        abslist = []
+        for component in self._components:
+            for iline in component._abslines:
+                abslist.append(iline)
+        # Return
+        return abslist
+
+
 class GenericAbsSystem(AbsSystem):
     """Class for Generic Absorption Line System
     """

linetools/isgm/lls.py

@@ -14,6 +14,7 @@
 from linetools.analysis import absline as ltaa
 from linetools.lists.linelist import LineList
 from linetools.isgm.abssystem import AbsSystem, AbsSubSystem
+from linetools.isgm.abscomponent import AbsComponent
 from linetools.isgm import utils as ltiu
 from linetools.isgm.abssurvey import AbslineSurvey
 from linetools.abund import ions as ltai
@@ -253,15 +254,20 @@ def get_ions(self, use_Nfile=False, idict=None, update_zvlim=True, linelist=None
         else:
             raise ValueError("Need an option in get_ions")
 
-    def fill_lls_lines(self, bval=20.*u.km/u.s):
+    def fill_lls_lines(self, bval=20.*u.km/u.s, do_analysis=1):
         """
         Generate an HI line list for an LLS.
         Goes into self.lls_lines 
 
+        Now generates a component too.
+        Should have it check for an existing HI component..
+
         Parameters
         ----------
         bval : float, optional
           Doppler parameter in km/s
+        do_analysis : int, optional
+          flag for analysis
         """
         from linetools.lists import linelist as lll
 
@@ -275,10 +281,12 @@ def fill_lls_lines(self, bval=20.*u.km/u.s):
             aline.attrib['N'] = 10**self.NHI / u.cm**2
             aline.attrib['b'] = bval
             aline.attrib['z'] = self.zabs
-            # Could set RA and DEC too
-            aline.attrib['RA'] = self.coord.ra
-            aline.attrib['DEC'] = self.coord.dec
+            aline.analy['vlim'] = self.vlim
+            aline.analy['do_analysis'] = do_analysis
+            aline.attrib['coord'] = self.coord
             self.lls_lines.append(aline)
+        # Generate a component (should remove any previous HI)
+        self.add_component(AbsComponent.from_abslines(self.lls_lines))
 
     def flux_model(self, spec, smooth=0):
         """ Generate a LLS model given an input spectrum

linetools/isgm/tests/test_use_abssys.py

@@ -0,0 +1,46 @@
+# Module to run tests on generating AbsSystem
+
+from __future__ import print_function, absolute_import, division, unicode_literals
+
+# TEST_UNICODE_LITERALS
+
+import pytest
+from astropy import units as u
+from astropy.coordinates import SkyCoord
+import numpy as np
+
+from linetools.isgm.abscomponent import AbsComponent
+from linetools.isgm.abssystem import GenericAbsSystem, LymanAbsSystem
+from linetools.spectralline import AbsLine
+
+import pdb
+
+def test_list_of_abslines():
+    radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
+    # HI Lya, Lyb
+    lya = AbsLine(1215.670*u.AA)
+    lya.analy['vlim'] = [-300.,300.]*u.km/u.s
+    lya.attrib['z'] = 2.92939
+    lyb = AbsLine(1025.7222*u.AA)
+    lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
+    lyb.attrib['z'] = lya.attrib['z']
+    abscomp = AbsComponent.from_abslines([lya,lyb])
+    abscomp.coord = radec
+    # SiII
+    SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
+    abslines = []
+    for trans in SiIItrans:
+        iline = AbsLine(trans)
+        iline.attrib['z'] = 2.92939
+        iline.analy['vlim'] = [-250.,80.]*u.km/u.s
+        abslines.append(iline)
+    #
+    SiII_comp = AbsComponent.from_abslines(abslines)
+    SiII_comp.coord = radec
+    # Instantiate
+    gensys = GenericAbsSystem.from_components([abscomp,SiII_comp])
+    # Now the list
+    abslines = gensys.list_of_abslines()
+    # Test
+    assert len(abslines) == 6
+