SpectralCube to specutils transition in cubeviz

Concept of loading spectrum1d as cube in CubevizExample

Get slider working correctly

SpectralCube to specutils transition in cubeviz

Manga cube loaded using Spectrum1D, still some things to iron out

Add support for loading Spectrum1D cubes

Fix codestyle checks

Use correct axes without np swapaxes

Set correct RA and Dec to x y axes, respectively

Remove excess commits and get slider working

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -4,9 +4,11 @@
 import numpy as np
 from astropy.io import fits
 from spectral_cube import SpectralCube
-from spectral_cube.io.fits import FITSReadError
 from specutils import Spectrum1D
 
+from astropy.wcs import WCS
+from astropy import units as u
+
 from jdaviz.core.registries import data_parser_registry
 
 __all__ = ['parse_data']
@@ -56,6 +58,8 @@ def parse_data(app, file_obj, data_type=None, data_label=None):
     #  into something glue can understand.
     elif isinstance(file_obj, SpectralCube):
         _parse_spectral_cube(app, file_obj, data_type or 'flux', data_label)
+    elif isinstance(file_obj, Spectrum1D) and len(file_obj.shape) == 3:
+        _parse_spectrum1d_3d(app, file_obj)
     elif isinstance(file_obj, Spectrum1D):
         _parse_spectrum1d(app, file_obj)
 
@@ -67,48 +71,33 @@ def _parse_hdu(app, hdulist, file_name=None):
 
     file_name = file_name or "Unknown HDU object"
 
-    # WCS may only exist in a single extension (in this case, just the flux
-    #  flux extension), so first find and store then wcs information.
-    wcs = None
-
-    for hdu in hdulist:
-        if hdu.data is None or not hdu.is_image:
-            continue
-
-        try:
-            sc = SpectralCube.read(hdu, format='fits')
-        except (ValueError, FITSReadError):
-            continue
-        else:
-            wcs = sc.wcs
-
     # Now loop through and attempt to parse the fits extensions as spectral
     #  cube object. If the wcs fails to parse in any case, use the wcs
     #  information we scraped above.
     for hdu in hdulist:
         data_label = f"{file_name}[{hdu.name}]"
 
-        if hdu.data is None or not hdu.is_image:
+        if hdu.data is None or not hdu.is_image or len(hdu.data.shape) != 3:
             continue
 
-        # This is supposed to fail on attempting to load anything that
-        # isn't cube-shaped. But it's not terribly reliable
+        wcs = WCS(hdu.header)
+
         try:
-            sc = SpectralCube.read(hdu, format='fits')
-        except (ValueError, OSError):
-            # This will fail if the parsing of the wcs does not provide
-            # proper celestial axes
-            try:
-                hdu.header.update(wcs.to_header())
-                sc = SpectralCube.read(hdu)
-            except (ValueError, AttributeError) as e:
-                logging.warning(e)
-                continue
-        except FITSReadError as e:
-            logging.warning(e)
-            continue
+            flux_unit = u.Unit(hdu.header['BUNIT'])
+        except KeyError:
+            logging.warn("No flux units found in hdu, using u.count as a stand-in")
+            flux_unit = u.count
+        finally:
+            flux = hdu.data * flux_unit
+
+        # flux = np.moveaxis(flux, 1, 2)
 
-        app.add_data(sc, data_label)
+        try:
+            sc = Spectrum1D(flux=flux, wcs=wcs)
+            app.data_collection[data_label] = sc
+        except Exception as e:
+            logging.warn(e)
+            continue
 
         # If the data type is some kind of integer, assume it's the mask/dq
         if hdu.data.dtype in (int, np.uint, np.uint32) or \
@@ -123,6 +112,23 @@ def _parse_hdu(app, hdulist, file_name=None):
             app.add_data_to_viewer('flux-viewer', data_label)
             app.add_data_to_viewer('spectrum-viewer', data_label)
 
+    # _fix_axes(app)
+
+
+def _fix_axes(app):
+    # Calibrate viewers to work with the updated Spectrum1D that can handle
+    # cubes. This needs to be done because the shape is different from
+    # SpectralCube, which was used previously.
+    # Setting the y and x axes needs to happen in this order to avoid an
+    # error for setting both axes to the same value.
+    app.get_viewer("mask-viewer").viewer_options.y_att_world_selected = 1
+    app.get_viewer("mask-viewer").viewer_options.x_att_world_selected = 0
+    app.get_viewer("uncert-viewer").viewer_options.y_att_world_selected = 1
+    app.get_viewer("uncert-viewer").viewer_options.x_att_world_selected = 0
+    app.get_viewer("flux-viewer").viewer_options.y_att_world_selected = 1
+    app.get_viewer("flux-viewer").viewer_options.x_att_world_selected = 0
+    app.get_viewer("spectrum-viewer").viewer_options.x_att_selected = 5
+
 
 def _parse_spectral_cube(app, file_obj, data_type='flux', data_label=None):
     data_label = data_label or f"Unknown spectral cube[{data_type.upper()}]"
@@ -141,6 +147,36 @@ def _parse_spectral_cube(app, file_obj, data_type='flux', data_label=None):
     # TODO: SpectralCube does not store data quality information
 
 
+def _parse_spectrum1d_3d(app, file_obj):
+    # Load spectrum1d as a cube
+
+    for attr in ["flux", "mask", "uncertainty"]:
+        if attr == "mask":
+            flux = getattr(file_obj, attr) * file_obj.flux.unit
+        elif attr == "uncertainty":
+            flux = getattr(file_obj, attr)
+            flux = u.Quantity(flux.array) * file_obj.flux.unit
+        else:
+            flux = getattr(file_obj, attr)
+
+        flux = np.moveaxis(flux, 1, 0)
+
+        s1d = Spectrum1D(flux=flux, wcs=file_obj.wcs)
+
+        data_label = f"Unknown spectrum object[{attr}]"
+        app.data_collection[data_label] = s1d
+
+        if attr == 'flux':
+            app.add_data_to_viewer('flux-viewer', f"{data_label}")
+            app.add_data_to_viewer('spectrum-viewer', f"{data_label}")
+        elif attr == 'mask':
+            app.add_data_to_viewer('mask-viewer', f"{data_label}")
+        elif attr == 'uncertainty':
+            app.add_data_to_viewer('uncert-viewer', f"{data_label}")
+
+    # _fix_axes(app)
+
+
 def _parse_spectrum1d(app, file_obj):
     data_label = "Unknown spectrum object"