Merge pull request #305 from bd-j/ref

update citation info, AGNSpecModel line indices
bd-j · Dec 6, 2023 · 9526327 · 9526327
2 parents f46ca4e + 0f93422
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diff --git a/doc/index.rst b/doc/index.rst
@@ -34,6 +34,7 @@ Prospector allows you to:
    sfhs
    nebular
    output
+   ref
 
 .. toctree::
    :maxdepth: 1
@@ -55,37 +56,6 @@ Prospector allows you to:
    api/plotting_api
    api/utils_api
 
-License and Attribution
-------------------------------
-
-*Copyright 2014-2022 Benjamin D. Johnson and contributors.*
-
-This code is available under the `MIT License
-<https://raw.github.com/bdj/prospector/blob/main/LICENSE>`_.
-
-If you use this code, please reference `this paper <https://ui.adsabs.harvard.edu/abs/2021ApJS..254...22J/abstract>`_:
-
-.. code-block:: none
-
-    @ARTICLE{2021ApJS..254...22J,
-        author = {{Johnson}, Benjamin D. and {Leja}, Joel and {Conroy}, Charlie and {Speagle}, Joshua S.},
-            title = "{Stellar Population Inference with Prospector}",
-        journal = {\apjs},
-        keywords = {Galaxy evolution, Spectral energy distribution, Astronomy data modeling, 594, 2129, 1859, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics},
-            year = 2021,
-            month = jun,
-        volume = {254},
-        number = {2},
-            eid = {22},
-            pages = {22},
-            doi = {10.3847/1538-4365/abef67},
-    archivePrefix = {arXiv},
-        eprint = {2012.01426},
-    primaryClass = {astro-ph.GA},
-        adsurl = {https://ui.adsabs.harvard.edu/abs/2021ApJS..254...22J},
-        adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-    }
-
 Changelog
 ---------
 

diff --git a/doc/nebular.rst b/doc/nebular.rst
@@ -75,7 +75,7 @@ photometry).  These parameters are:
 
 In all cases the line names to use in these lists are those given in the FSPS
 emission line line information table, ``$SPS_HOME/data/emlines_info.dat``, e.g.
-``"Ly alpha 1216"`` for the Lyman-alpha 1216 Angstrom line.
+``"Ly-alpha 1215"`` for the Lyman-alpha 1216 Angstrom line.
 
 Nebular Parameter Templates
 ---------------------------

diff --git a/doc/quickstart.rst b/doc/quickstart.rst
@@ -91,7 +91,7 @@ Get a 'Source'
 Now we need an object that will actually generate the galaxy spectrum using
 stellar population synthesis.  For this we will use an object that wraps FSPS
 allowing access to all the parameterized SFHs.  We will also just check which
-spectral and isochrone librariews are being used.
+spectral and isochrone libraries are being used.
 
 .. code:: python
 

diff --git a/doc/ref.rst b/doc/ref.rst
@@ -0,0 +1,41 @@
+
+License and Attribution
+=======================
+
+*Copyright 2014-2023 Benjamin D. Johnson and contributors.*
+
+This code is available under the `MIT License
+<https://raw.github.com/bdj/prospector/blob/main/LICENSE>`_.
+
+If you use this code, please reference `this paper <https://ui.adsabs.harvard.edu/abs/2021ApJS..254...22J/abstract>`_:
+
+.. code-block:: none
+
+    @ARTICLE{2021ApJS..254...22J,
+        author = {{Johnson}, Benjamin D. and {Leja}, Joel and {Conroy}, Charlie and {Speagle}, Joshua S.},
+            title = "{Stellar Population Inference with Prospector}",
+        journal = {\apjs},
+        keywords = {Galaxy evolution, Spectral energy distribution, Astronomy data modeling, 594, 2129, 1859, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics},
+            year = 2021,
+            month = jun,
+        volume = {254},
+        number = {2},
+            eid = {22},
+            pages = {22},
+            doi = {10.3847/1538-4365/abef67},
+    archivePrefix = {arXiv},
+        eprint = {2012.01426},
+    primaryClass = {astro-ph.GA},
+        adsurl = {https://ui.adsabs.harvard.edu/abs/2021ApJS..254...22J},
+        adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+    }
+
+and `Leja et al 2019 <https://ui.adsabs.harvard.edu/abs/2017ApJ...837..170L/abstract>`
+
+
+Please also see the reference requirements for dependencies
+
+* `FSPS <https://github.com/cconroy20/fsps#references>``
+* `python-fsps <https://python-fsps.readthedocs.io/en/latest/#license>`
+* `dynesty <https://dynesty.readthedocs.io/en/latest/references.html>`
+* `emcee <https://emcee.readthedocs.io/en/stable/#license-attribution>`
diff --git a/prospect/models/sedmodel.py b/prospect/models/sedmodel.py
@@ -908,15 +908,18 @@ def _available_parameters(self):
 
     def init_aline_info(self):
         """AGN line spectrum. Based on data as reported in Richardson et al.
-        2014 (Table 3, the 'a42' dataset) and normalized to Hbeta.index=48 is Hbeta
+        2014 (Table 3, the 'a42' dataset) and normalized to Hbeta.
+
+        index=59 is Hbeta
         """
-        ainds = np.array([31, 33, 34, 35, 37, 42, 43, 44, 48,
-                          49, 50, 52, 56, 57, 58, 60, 61, 62,
-                          63, 64, 65, 66, 68])
+        ainds = np.array([38, 40, 41, 43, 45, 50, 51, 52, 59,
+                          61, 62, 64, 68, 69, 70, 72, 73, 74,
+                          75, 76, 77, 78, 80])
         afluxes = np.array([2.96, 0.06, 0.1 , 1.  , 0.2 , 0.25, 0.48, 0.13, 1.,
                             2.87, 8.53, 0.07, 0.02, 0.1 , 0.33, 0.09, 0.79, 2.86,
                             2.13, 0.03, 0.77, 0.65, 0.19])
-        self._aline_lum = np.zeros(128)
+        self._aline_lum = np.zeros(len(self.emline_info))
+        assert np.abs(self.emline_info["wave"][59] - 4863) < 2
         self._aline_lum[ainds] = afluxes
 
     def predict_spec(self, obs, sigma_spec=None, **extras):

diff --git a/tests/test_eline.py b/tests/test_eline.py
@@ -19,12 +19,12 @@ def test_eline_parsing():
     model_pars.update(TemplateLibrary["nebular"])
 
     # test ignoring a line
-    lya = "Ly alpha 1216"
+    lya = "Ly-alpha 1215"
     model_pars["elines_to_ignore"] = dict(init=lya, isfree=False)
     model = SpecModel(model_pars)
     model.parse_elines()
     assert not np.isin(lya, model.emline_info["name"][model._use_eline])
-    assert np.isin("H alpha 6563", model.emline_info["name"][model._use_eline])
+    assert np.isin("Ba-alpha 6563", model.emline_info["name"][model._use_eline])
     assert np.all(model._fix_eline)
     assert model._use_eline.sum() == len(model._use_eline) - 1
     assert len(model._use_eline) == len(model.emline_info)
@@ -36,7 +36,7 @@ def test_eline_parsing():
     assert model._fit_eline.sum() == len(model._use_eline)
 
     # test fitting just a line or two
-    fit_lines = ["[OIII]5007"]
+    fit_lines = ["[O III] 5007"]
     model_pars["elines_to_fit"] = dict(init=fit_lines)
     model = SpecModel(model_pars)
     model.parse_elines()
@@ -173,7 +173,7 @@ def test_eline_implementation():
     spec, phot, mfrac = model.predict(model.theta, obs=obs, sps=sps)
 
     # test ignoring a line
-    lya = "Ly alpha 1216"
+    lya = "Ly-alpha 1215"
     model_pars["elines_to_ignore"] = dict(init=lya, isfree=False)
     model = SpecModel(model_pars)
     spec_nolya, phot_nolya, mfrac = model.predict(model.theta, obs=obs, sps=sps)