Fix slice with different spectral_axis_index, add specutils_format kw…

…arg to cubeviz parser

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -22,7 +22,7 @@
 
 
 @data_parser_registry("cubeviz-data-parser")
-def parse_data(app, file_obj, data_type=None, data_label=None):
+def parse_data(app, file_obj, data_type=None, data_label=None, specutils_format=None):
     """
     Attempts to parse a data file and auto-populate available viewers in
     cubeviz.
@@ -37,6 +37,11 @@ def parse_data(app, file_obj, data_type=None, data_label=None):
         The data type used to explicitly differentiate parsed data.
     data_label : str, optional
         The label to be applied to the Glue data component.
+    specutils_format : str, optional
+        Optional format string to pass to Spectrum1D.read(), see
+        https://specutils.readthedocs.io/en/stable/spectrum1d.html#list-of-loaders
+        for valid format strings. Useful for processed files that may not include
+        the original headers with information used to auto-identify.
     """
 
     flux_viewer_reference_name = app._jdaviz_helper._default_flux_viewer_reference_name
@@ -67,6 +72,17 @@ def parse_data(app, file_obj, data_type=None, data_label=None):
                        spectrum_viewer_reference_name=spectrum_viewer_reference_name)
             return
 
+        elif specutils_format is not None:
+            sc = Spectrum1D.read(file_obj, format=specutils_format)
+            _parse_spectrum1d_3d(
+                app, sc, data_label=data_label,
+                flux_viewer_reference_name=flux_viewer_reference_name,
+                spectrum_viewer_reference_name=spectrum_viewer_reference_name,
+                uncert_viewer_reference_name=uncert_viewer_reference_name
+            )
+            app.get_tray_item_from_name("Spectral Extraction").disabled_msg = ""
+            return
+
         file_name = os.path.basename(file_obj)
 
         with fits.open(file_obj) as hdulist:

jdaviz/configs/cubeviz/plugins/slice/slice.py

@@ -100,7 +100,6 @@ def _initialize_location(self, *args):
         # initialize value_unit (this has to wait until data is loaded to an existing
         # slice_indicator_viewer, so we'll keep trying until it is set - after that, changes
         # will be handled by a change to global display units)
-        print("Initializing slice location")
         if not self.value_unit:
             for viewer in self.slice_indicator_viewers:
                 # ignore while x_display_unit is unset or still degrees (before data transpose)
@@ -311,7 +310,6 @@ def _on_snap_to_slice_changed(self, event):
     @observe('show_indicator', 'show_value')
     def _on_setting_changed(self, event):
         msg = SliceToolStateMessage({event['name']: event['new']}, viewer=None, sender=self)
-        print(msg)
         self.session.hub.broadcast(msg)
 
     def vue_goto_first(self, *args):

jdaviz/configs/cubeviz/plugins/viewers.py

@@ -55,10 +55,19 @@ def _set_slice_indicator_value(self, value):
 
 
 class WithSliceSelection:
-    @property
+    @cached_property
     def slice_index(self):
         # index in state.slices corresponding to the slice axis
-        return 2
+        for layer in self.layers:
+            try:
+                data_obj = layer.layer.data
+                return data_obj.meta['spectral_axis_index']
+            except (AttributeError, KeyError):
+                raise
+            else:
+                break
+        else:
+            return 2
 
     @property
     def slice_component_label(self):