BUG: Fix parsing of MANGA cube (try 2)

CHANGES.rst

@@ -71,6 +71,9 @@ Cubeviz
 
 - Spectral Extraction: renamed ``collapse_to_spectrum(...)`` to ``extract(...)``. [#2859]
 
+- Generic FITS parsing now goes through ``specutils`` loaders first, if possible.
+  If a ``specutils`` loader is used, uncertainty is converted to standard deviation type. [#3119]
+
 - Custom Spectrum1D writer format ``jdaviz-cube`` is removed. Use ``wcs1d-fits`` from
   ``specutils`` instead. [#2094]
 
@@ -112,6 +115,11 @@ Cubeviz
 
 - Mouse over coordinates now responds to the selected surface brightness unit. [#2931]
 
+- Fixed MaNGA cube loading. Uncertainty type is also handled properly now. [#3119]
+
+- Fixed spectral axis value display in Markers plugin. Previously, it failed to display
+  very small values, resulting in zeroes. [#3119]
+
 Imviz
 ^^^^^
 

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -5,7 +5,7 @@
 import numpy as np
 from astropy import units as u
 from astropy.io import fits
-
+from astropy.nddata import StdDevUncertainty
 from astropy.time import Time
 from astropy.wcs import WCS
 from specutils import Spectrum1D
@@ -68,11 +68,18 @@ def parse_data(app, file_obj, data_type=None, data_label=None,
     #  generic enough to work with other file types (e.g. ASDF). For now, this
     #  supports MaNGA and JWST data.
     if isinstance(file_obj, fits.hdu.hdulist.HDUList):
-        _parse_hdulist(
-            app, file_obj, file_name=data_label,
-            flux_viewer_reference_name=flux_viewer_reference_name,
-            uncert_viewer_reference_name=uncert_viewer_reference_name
-        )
+        try:
+            _parse_spectrum1d_3d(
+                app, Spectrum1D.read(file_obj), data_label=data_label,
+                flux_viewer_reference_name=flux_viewer_reference_name,
+                uncert_viewer_reference_name=uncert_viewer_reference_name
+            )
+        except Exception:  # nosec
+            _parse_hdulist(
+                app, file_obj, file_name=data_label,
+                flux_viewer_reference_name=flux_viewer_reference_name,
+                uncert_viewer_reference_name=uncert_viewer_reference_name
+            )
     elif isinstance(file_obj, str):
         if file_obj.lower().endswith('.gif'):  # pragma: no cover
             _parse_gif(app, file_obj, data_label,
@@ -129,11 +136,18 @@ def parse_data(app, file_obj, data_type=None, data_label=None,
                         flux_viewer_reference_name=flux_viewer_reference_name,
                     )
             else:
-                _parse_hdulist(
-                    app, hdulist, file_name=data_label or file_name,
-                    flux_viewer_reference_name=flux_viewer_reference_name,
-                    uncert_viewer_reference_name=uncert_viewer_reference_name
-                )
+                try:
+                    _parse_spectrum1d_3d(
+                        app, Spectrum1D.read(hdulist), data_label=data_label or file_name,
+                        flux_viewer_reference_name=flux_viewer_reference_name,
+                        uncert_viewer_reference_name=uncert_viewer_reference_name
+                    )
+                except Exception:  # nosec
+                    _parse_hdulist(
+                        app, hdulist, file_name=data_label or file_name,
+                        flux_viewer_reference_name=flux_viewer_reference_name,
+                        uncert_viewer_reference_name=uncert_viewer_reference_name
+                    )
 
     # If the data types are custom data objects, use explicit parsers. Note
     #  that this relies on the glue-astronomy machinery to turn the data object
@@ -412,10 +426,7 @@ def _parse_spectrum1d_3d(app, file_obj, data_label=None,
         if attr == "mask":
             flux = val << u.dimensionless_unscaled  # DQ flags have no unit
         elif attr == "uncertainty":
-            if hasattr(val, "array"):
-                flux = u.Quantity(val.array, file_obj.flux.unit)
-            else:
-                continue
+            flux = val.represent_as(StdDevUncertainty).quantity
         else:
             flux = val
 

jdaviz/core/template_mixin.py

@@ -4546,24 +4546,24 @@ def float_precision(column, item):
                     return f"{item:0.3f}"
                 elif column in ('xcenter', 'ycenter'):
                     return f"{item:0.1f}"
-                elif column in ('sum', ):
+                elif column in ('sum', 'spectral_axis'):
                     return f"{item:.3e}"
                 else:
                     return f"{item:0.5f}"
 
             if isinstance(item, SkyCoord):
                 return item.to_string('hmsdms', precision=4)
-            if isinstance(item, u.Quantity) and not np.isnan(item):
+            elif isinstance(item, u.Quantity) and not np.isnan(item):
                 return f"{float_precision(column, item.value)} {item.unit.to_string()}"
 
-            if hasattr(item, 'to_string'):
+            elif hasattr(item, 'to_string'):
                 return item.to_string()
-            if isinstance(item, float) and np.isnan(item):
+            elif isinstance(item, float) and np.isnan(item):
                 return ''
-            if isinstance(item, tuple) and np.all([np.isnan(i) for i in item]):
+            elif isinstance(item, tuple) and np.all([np.isnan(i) for i in item]):
                 return ''
 
-            if isinstance(item, float):
+            elif isinstance(item, float):
                 return float_precision(column, item)
             elif isinstance(item, (list, tuple)):
                 return [float_precision(column, i) if isinstance(i, float) else i for i in item]