Merge branch 'develop' into reidarxiv_err_msg

pypeit · Nov 1, 2023 · 75c14bc · 75c14bc
2 parents 23b369f + f0ec8e0
commit 75c14bc
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/pypeit/specutils/pypeit_loaders.py b/pypeit/specutils/pypeit_loaders.py
@@ -195,7 +195,13 @@ def pypeit_spec1d_loader(filename, extract=None, fluxed=True, strict=True, **kwa
         _ext, _cal = sobj.best_ext_match(extract=extract, fluxed=fluxed)
         _wave, _flux, _ivar, _gpm = sobj.get_box_ext(fluxed=_cal) if _ext == 'BOX' \
                                         else sobj.get_opt_ext(fluxed=_cal)
-        _wave, _flux, _ivar = _enforce_monotonic_wavelengths(_wave, _flux, _ivar, strict=strict)
+        if not np.all(_gpm):
+            msgs.warn(f'Ignoring {np.sum(np.logical_not(_gpm))} masked pixels.')
+        if not np.any(_gpm):
+            msgs.warn(f'Spectrum {sobj.NAME} is fully masked and will be ignored!')
+            continue
+        _wave, _flux, _ivar = _enforce_monotonic_wavelengths(_wave[_gpm], _flux[_gpm], _ivar[_gpm],
+                                                             strict=strict)
         flux_unit = astropy.units.Unit("1e-17 erg/(s cm^2 Angstrom)" if _cal else "electron")
         spec += \
             [Spectrum1D(flux=astropy.units.Quantity(_flux * flux_unit),