working towards support for L2 files, linking corrections

CHANGES.rst

@@ -21,7 +21,7 @@ New Features
 
 - The standalone version of jdaviz now uses solara instead of voila, resulting in faster load times. [#2909]
 
-- New configuration for ramp/Level 1 data products from Roman WFI and JWST [#3120, #3148, #3167, #3171]
+- New configuration for ramp/Level 1 data products from Roman WFI and JWST [#3120, #3148, #3167, #3171, #3194]
 
 Cubeviz
 ^^^^^^^

jdaviz/configs/default/plugins/data_quality/data_quality.py

@@ -106,8 +106,9 @@ def _update_available_viewers(self):
         def is_image_viewer(viewer):
             from jdaviz.configs.imviz.plugins.viewers import ImvizImageView
             from jdaviz.configs.cubeviz.plugins.viewers import CubevizImageView
+            from jdaviz.configs.rampviz.plugins.viewers import RampvizImageView
 
-            return isinstance(viewer, (ImvizImageView, CubevizImageView))
+            return isinstance(viewer, (ImvizImageView, CubevizImageView, RampvizImageView))
 
         viewer_filter_names = [filt.__name__ for filt in self.viewer.filters]
         if 'is_image_viewer' not in viewer_filter_names:
@@ -151,6 +152,9 @@ def load_default_flag_maps(self):
 
     @property
     def dq_layer_selected_flattened(self):
+        if not hasattr(self, 'dq_layer'):
+            return []
+
         selected_dq = self.dq_layer.selected_obj
         if not len(selected_dq):
             return []
@@ -170,6 +174,7 @@ def unique_flags(self):
             return []
 
         dq = selected_dq[0].get_image_data()
+
         return np.unique(dq[~np.isnan(dq)])
 
     @property
@@ -210,11 +215,15 @@ def init_decoding(self, event={}, viewers=None):
 
             # for cubeviz, also change uncert-viewer defaults to
             # map the out-of-bounds regions to the cmap's `bad` color:
-            if self.app.config == 'cubeviz':
-                uncert_viewer = self.app.get_viewer(
-                    self.app._jdaviz_helper._default_uncert_viewer_reference_name
+            if self.app.config in ('cubeviz', 'rampviz'):
+                viewer = self.app.get_viewer(
+                    getattr(
+                        self.app._jdaviz_helper,
+                        '_default_uncert_viewer_reference_name', 'level-2'
+                    )
                 )
-                for layer in uncert_viewer.layers:
+
+                for layer in viewer.layers:
                     # allow bad alpha for image layers, not subsets:
                     if not hasattr(layer, 'subset_array'):
                         layer.composite._allow_bad_alpha = True

jdaviz/configs/default/plugins/plot_options/plot_options.py

@@ -1164,10 +1164,12 @@ def _viewer_is_image_viewer(self):
         from jdaviz.configs.imviz.plugins.viewers import ImvizImageView
         from jdaviz.configs.cubeviz.plugins.viewers import CubevizImageView
         from jdaviz.configs.mosviz.plugins.viewers import MosvizImageView, MosvizProfile2DView
+        from jdaviz.configs.rampviz.plugins.viewers import RampvizImageView
 
         def _is_image_viewer(viewer):
             return isinstance(viewer, (ImvizImageView, CubevizImageView,
-                                       MosvizImageView, MosvizProfile2DView))
+                                       MosvizImageView, MosvizProfile2DView,
+                                       RampvizImageView))
 
         viewers = self.viewer.selected_obj
         if not isinstance(viewers, list):

jdaviz/configs/rampviz/helper.py

@@ -1,4 +1,4 @@
-from jdaviz.core.events import SliceSelectSliceMessage
+from jdaviz.core.events import SliceSelectSliceMessage, NewViewerMessage
 from jdaviz.core.helpers import CubeConfigHelper
 from jdaviz.configs.rampviz.plugins.viewers import RampvizImageView
 
@@ -98,3 +98,27 @@ def get_data(self, data_label=None, spatial_subset=None,
         return self._get_data(data_label=data_label, spatial_subset=spatial_subset,
                               temporal_subset=temporal_subset,
                               cls=cls, use_display_units=use_display_units)
+
+    def create_image_viewer(self, viewer_name=None, data=None):
+        """
+        Create a new image viewer.
+
+        Parameters
+        ----------
+        viewer_name : str or `None`
+            Viewer name/ID to use. If `None`, it is auto-generated.
+
+        Returns
+        -------
+        viewer : `~jdaviz.configs.imviz.plugins.viewers.ImvizImageView`
+            Image viewer instance.
+
+        """
+        from jdaviz.configs.imviz.plugins.viewers import ImvizImageView
+
+        # Cannot assign data to real Data because it loads but it will
+        # not update checkbox in Data menu.
+
+        return self.app._on_new_viewer(
+            NewViewerMessage(ImvizImageView, data=None, sender=self.app),
+            vid=viewer_name, name=viewer_name)

jdaviz/configs/rampviz/plugins/parsers.py

@@ -195,7 +195,6 @@ def _roman_3d_to_glue_data(
 
     data_reshaped = move_group_axis_last(data)
     diff_data_reshaped = move_group_axis_last(diff_data)
-    data_reshaped = data_reshaped - data_reshaped[..., 0]
 
     # load these cubes into the cache:
     app._jdaviz_helper.cube_cache[ramp_cube_data_label] = NDDataArray(
@@ -246,7 +245,18 @@ def _parse_hdulist(
     hdu = hdulist[1]  # extension containing the ramp
 
     if hdu.header['NAXIS'] == 2:
+        # this may be a calibrated Level 2 image:
         _parse_image_imviz(app, hdulist, data_label=file_name, ext=ext, parent=parent)
+        new_viewer_name = 'level-2'
+
+        # create a level-2 viewer if none exists:
+        if new_viewer_name not in app.get_viewer_reference_names():
+            app._jdaviz_helper.create_image_viewer(viewer_name=new_viewer_name)
+
+        # add the SCI extension to the level-2 viewer:
+        if 'SCI' in ext:
+            idx = len(ext) - ext.index('SCI')
+            app.add_data_to_viewer(new_viewer_name, app.data_collection[-idx].label)
         return
 
     elif hdu.header['NAXIS'] != 4:
@@ -283,27 +293,6 @@ def _parse_hdulist(
 def _parse_ramp_cube(app, ramp_cube_data, flux_unit, file_name,
                      group_viewer_reference_name, diff_viewer_reference_name,
                      meta=None):
-
-    # Identify NIRSpec IRS2 detector mode, which needs special treatment.
-    # jdox: https://jwst-docs.stsci.edu/jwst-near-infrared-spectrograph/nirspec-instrumentation/
-    # nirspec-detectors/nirspec-detector-readout-modes-and-patterns/nirspec-irs2-detector-readout-mode
-    if 'meta.model_type' in meta:
-        # this is a Level1bModel, which has metadata in a Node rather
-        # than a dictionary:
-        from_jwst_nirspec_irs2 = (
-            meta.get('meta._primary_header.TELESCOP') == 'JWST' and
-            meta.get('meta._primary_header.INSTRUME') == 'NIRSPEC' and
-            'IRS2' in meta.get('meta._primary_header.READPATT', '')
-        )
-    else:
-        # assume this was parsed from FITS:
-        header = meta.get('_primary_header', {})
-        from_jwst_nirspec_irs2 = (
-            header.get('TELESCOP') == 'JWST' and
-            header.get('INSTRUME') == 'NIRSPEC' and
-            'IRS2' in header.get('READPATT', '')
-        )
-
     # last axis is the group axis, first two are spatial axes:
     diff_data = np.vstack([
         # begin with a group of zeros, so
@@ -312,12 +301,9 @@ def _parse_ramp_cube(app, ramp_cube_data, flux_unit, file_name,
         np.diff(ramp_cube_data, axis=0)
     ])
 
-    def move_axes(x):
-        return np.swapaxes(move_group_axis_last(x), 0, 1)
-
-    ramp_cube = NDDataArray(move_axes(ramp_cube_data), unit=flux_unit, meta=meta)
-    ramp_cube = ramp_cube.subtract(ramp_cube[..., :1])
-    diff_cube = NDDataArray(move_axes(diff_data), unit=flux_unit, meta=meta)
+    ramp_data = move_group_axis_last(ramp_cube_data)
+    ramp_cube = NDDataArray(ramp_data, unit=flux_unit, meta=meta)
+    diff_cube = NDDataArray(move_group_axis_last(diff_data), unit=flux_unit, meta=meta)
 
     group_data_label = app.return_data_label(file_name, ext="DATA")
     diff_data_label = app.return_data_label(file_name, ext="DIFF")

jdaviz/configs/rampviz/plugins/ramp_extraction/ramp_extraction.py

@@ -138,7 +138,7 @@ def integration_viewer(self):
 
     def _on_data_added(self, msg={}):
         # only perform the default collapse after the first data load:
-        if len(self.app.data_collection) == 2 and len(self.app._jdaviz_helper.cube_cache):
+        if len(self.app._jdaviz_helper.cube_cache) and not self.extraction_available:
             self.extract(add_data=True)
             self.integration_viewer._initialize_x_axis()
 

jdaviz/configs/rampviz/plugins/viewers.py

@@ -129,7 +129,8 @@ def _default_integration_viewer_reference_name(self):
     def _initial_x_axis(self, *args):
         # Make sure that the x_att is correct on data load
         ref_data = self.state.reference_data
-        if ref_data and ref_data.ndim == 3:
+
+        if ref_data:
             self.state.x_att = ref_data.id["Pixel Axis 0 [z]"]
 
     def set_plot_axes(self):

jdaviz/configs/rampviz/tests/test_parser.py

@@ -41,5 +41,5 @@ def test_load_nirspec_irs2(rampviz_helper, jwst_level_1b_rectangular_ramp):
 
     parsed_cube_shape = rampviz_helper.app.data_collection[0].shape
     assert parsed_cube_shape == (
-        original_cube_shape[1], original_cube_shape[2], original_cube_shape[0]
+        original_cube_shape[2], original_cube_shape[1], original_cube_shape[0]
     )

jdaviz/core/tools.py

@@ -105,7 +105,7 @@ def on_limits_change(self, *args):
             to_lims = self._map_limits(self.viewer, viewer, from_lims)
             matched_refdata = viewer.state.reference_data
 
-            if hasattr(viewer, '_get_fov'):
+            if hasattr(viewer, '_get_fov') and matched_refdata is not None:
                 to_fov_sky = viewer._get_fov(wcs=matched_refdata.coords)
             else:
                 to_fov_sky = None