Merge pull request #365 from nasa-fornax/raen/spectra_generator/cleanup

Minor bug fixes for spectra_generator

spectroscopy/code_src/plot_functions.py

@@ -96,6 +96,10 @@ def create_figures(df_spec, bin_factor, show_nbr_figures, save_output):
         Whether to save the figures. If saved, they will be in the "output" directory.
     """
 
+    output_dir = 'output'
+    if save_output and not os.path.exists(output_dir):
+        os.mkdir(output_dir)
+
     for cc, (objectid, singleobj_df) in enumerate(df_spec.data.groupby('objectid')):
 
         fig = plt.figure(figsize=(9, 6))
@@ -151,7 +155,7 @@ def create_figures(df_spec, bin_factor, show_nbr_figures, save_output):
         ax1.legend(bbox_to_anchor=(1.27, 1), fontsize=11)
 
         if save_output:
-            savename = os.path.join("output", "spectra_{}.pdf".format(objectid))
+            savename = os.path.join(output_dir, "spectra_{}.pdf".format(objectid))
             plt.savefig(savename, bbox_inches="tight")
 
         if cc < show_nbr_figures:

spectroscopy/data/README.md

@@ -0,0 +1,8 @@
+# Data - Spectroscopy
+
+This directory is used for data that is downloaded or otherwise retrieved for the spectroscopy use case. Users may
+also store additional data here. Note that there is a separate directory for output generated by the notebooks or
+its users.
+
+Data should not be committed to the code repository. This directory is included in the .gitignore file to prevent
+accidental commits.

spectroscopy/output/README.md

@@ -0,0 +1,7 @@
+# Output - Spectroscopy
+
+This directory is used for output generated by the spectroscopy use case. This includes results, figures, logs,
+etc. Users may also store their own output here.
+
+Output should not be committed to the code repository. This directory is included in the .gitignore file to
+prevent accidental commits.

spectroscopy/spectra_generator.md

@@ -168,6 +168,9 @@ labels.append("JADESGS-z7-01-QU")
 coords.append(SkyCoord("{} {}".format("+53.15398", "-27.80095"), unit=(u.deg, u.deg)))
 labels.append("TestJWST")
 
+coords.append(SkyCoord("{} {}".format("+150.33622", "+55.89878"), unit=(u.deg, u.deg)))
+labels.append("Twin Quasar")
+
 sample_table = clean_sample(coords, labels, precision=2.0 * u.arcsecond, verbose=1)
 ```