From fe40115396c23658a8a931cf3d484eeed1c60674 Mon Sep 17 00:00:00 2001
From: "Brett M. Morris" <bmmorris@stsci.edu>
Date: Tue, 19 Mar 2024 15:10:15 -0400
Subject: [PATCH] support for Imviz blinking, glue 'bad' masks

---
 jdaviz/configs/imviz/plugins/parsers.py | 10 ++++++++++
 jdaviz/configs/imviz/plugins/viewers.py | 18 +++++++++++++++---
 jdaviz/tests/test_app.py                |  1 -
 3 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/jdaviz/configs/imviz/plugins/parsers.py b/jdaviz/configs/imviz/plugins/parsers.py
index 97558ed568..06cbb44263 100644
--- a/jdaviz/configs/imviz/plugins/parsers.py
+++ b/jdaviz/configs/imviz/plugins/parsers.py
@@ -186,6 +186,16 @@ def _parse_image(app, file_obj, data_label, ext=None, parent=None):
             data.coords.bounding_box = None
         if not data.meta.get(_wcs_only_label, False):
             data_label = app.return_data_label(data_label, alt_name="image_data")
+
+        # TODO: generalize/centralize this for use in other configs too
+        if parent is not None and ext == 'DQ':
+            print('data', data.main_components)
+            # nans are used to mark "good" flags in the DQ colormap, so
+            # convert DQ array to float to support nans:
+            cid = data.get_component("DQ")
+            data_arr = np.float32(cid.data)
+            data_arr[data_arr == 0] = np.nan
+            data.update_components({cid: data_arr})
         app.add_data(data, data_label, parent=parent)
 
     # Do not link image data here. We do it at the end in Imviz.load_data()
diff --git a/jdaviz/configs/imviz/plugins/viewers.py b/jdaviz/configs/imviz/plugins/viewers.py
index 285d801b77..788ae57fef 100644
--- a/jdaviz/configs/imviz/plugins/viewers.py
+++ b/jdaviz/configs/imviz/plugins/viewers.py
@@ -86,9 +86,16 @@ def blink_once(self, reversed=False):
         # Simple blinking of images - this will make it so that only one
         # layer is visible at a time and cycles through the layers.
 
-        # Exclude Subsets: They are global
+        # Exclude Subsets (they are global) and children via associated data
+
+        def is_parent(data):
+            return self.session.jdaviz_app._get_assoc_data_parent(data.label) is None
+
         valid = [ilayer for ilayer, layer in enumerate(self.state.layers)
-                 if layer_is_image_data(layer.layer)]
+                 if layer_is_image_data(layer.layer) and is_parent(layer.layer)]
+        children = [ilayer for ilayer, layer in enumerate(self.state.layers)
+                    if layer_is_image_data(layer.layer) and not is_parent(layer.layer)]
+
         n_layers = len(valid)
 
         if n_layers == 1:
@@ -116,7 +123,12 @@ def blink_once(self, reversed=False):
                 next_layer = valid[(valid.index(visible[-1]) + delta) % n_layers]
                 self.state.layers[next_layer].visible = True
 
-                for ilayer in (set(valid) - set([next_layer])):
+                # make invisible all parent layers other than the next layer:
+                layers_to_set_not_visible = set(valid) - set([next_layer])
+                # no child layers are visible by default:
+                layers_to_set_not_visible.update(set(children))
+
+                for ilayer in layers_to_set_not_visible:
                     self.state.layers[ilayer].visible = False
 
                 # We can display the active data label in Compass plugin.
diff --git a/jdaviz/tests/test_app.py b/jdaviz/tests/test_app.py
index 2658568d35..9179af4350 100644
--- a/jdaviz/tests/test_app.py
+++ b/jdaviz/tests/test_app.py
@@ -184,4 +184,3 @@ def test_data_associations(imviz_helper):
 
     assert imviz_helper.app._get_assoc_data_children('parent_data') == ['child_data']
     assert imviz_helper.app._get_assoc_data_parent('child_data') == 'parent_data'
-