Merge pull request #22 from NolanKoblischke/fix-continuum-fit-nan-issue

Handle NaNs in polynomial fitting of continuum
henrysky · Oct 25, 2023 · f825a5c · f825a5c
2 parents 97e799c + 8aed649
commit f825a5c
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -151,3 +151,7 @@ dmypy.json
 # Ignore all local history of files
 .history
 .ionide
+
+# Mac 
+.DS_Store
+
diff --git a/astroNN/apogee/chips.py b/astroNN/apogee/chips.py
@@ -243,10 +243,11 @@ def continuum(spectra, spectra_err, cont_mask, deg=2):
     for counter, (spectrum, spectrum_err, flux_ivar) in enumerate(
         zip(spectra, spectra_err, flux_ivars)
     ):
+        no_nan_mask = ~np.isnan(spectrum[cont_mask])
         fit = np.polynomial.chebyshev.Chebyshev.fit(
-            x=np.arange(spectrum.shape[0])[cont_mask],
-            y=spectrum[cont_mask],
-            w=flux_ivar[cont_mask],
+            x=np.arange(spectrum.shape[0])[cont_mask][no_nan_mask],
+            y=spectrum[cont_mask][no_nan_mask],
+            w=flux_ivar[cont_mask][no_nan_mask],
             deg=deg,
         )
         spectra[counter] = spectrum / fit(pix_element)