Avoid FlatLaf crashing the GUI

.github/workflows/build.yml

@@ -96,8 +96,8 @@ jobs:
         with:
           configuration: --check-only
 
-  test-imagej-legacy:
-    name: Test legacy inclusion
+  test-ij2:
+    name: Test pure IJ2
     runs-on: ubuntu-latest
     defaults:
       # Steps that rely on the activated environment must be run with this shell setup.
@@ -124,7 +124,7 @@ jobs:
 
       - name: Setup Testing Environment Variables
         run: |
-          echo "NAPARI_IMAGEJ_INCLUDE_IMAGEJ_LEGACY=true" >> $GITHUB_ENV
+          echo "NAPARI_IMAGEJ_INCLUDE_IMAGEJ_LEGACY=false" >> $GITHUB_ENV
 
       - name: Test napari-imagej
         uses: GabrielBB/xvfb-action@v1

dev-environment.yml

@@ -25,7 +25,7 @@ dependencies:
   - magicgui >= 0.5.1
   - napari
   - openjdk=8
-  - pyimagej >= 1.2.0
+  - pyimagej >= 1.3.0
   - scyjava >= 1.7.0
   # Test dependencies
   - numpy

environment.yml

@@ -26,7 +26,7 @@ dependencies:
   - napari
   - numpy
   - openjdk=8
-  - pyimagej >= 1.2.0
+  - pyimagej >= 1.3.0
   - scyjava >= 1.7.0
   # Project from source
   - pip

setup.cfg

@@ -44,7 +44,7 @@ install_requires =
     napari
     numpy
     magicgui >= 0.5.1
-    pyimagej >= 1.2.0
+    pyimagej >= 1.3.0
     scyjava >= 1.7.0
 
 [options.packages.find]

src/napari_imagej/config_default.yaml

@@ -18,8 +18,9 @@ imagej_base_directory: '.'
 
 # This can be used to include original ImageJ functionality.
 # Iff true, original ImageJ functionality (ij.* packages) will be available.
-# Defaults to false.
-include_imagej_legacy: false
+# Iff false, many ImageJ2 rewrites of original ImageJ functionality are available.
+# Defaults to true as the ImageJ legacy UI is most popular and familiar.
+include_imagej_legacy: true
 
 # Designates the mode of execution for ImageJ2.
 # Allowed options are 'headless' and 'interactive'.

src/napari_imagej/java.py

@@ -14,7 +14,7 @@
         - object whose fields are lazily-loaded Java Class instances.
 """
 from threading import Lock
-from typing import Callable, List, Tuple
+from typing import Any, Callable, Dict, List, Tuple
 
 import imagej
 from jpype import JClass
@@ -89,11 +89,95 @@ def initialize(self):
         """
         Creates the ImageJ instance
         """
-        # Initialize ImageJ
         log_debug("Initializing ImageJ2")
 
-        # -- IMAGEJ CONFIG -- #
+        # determine whether imagej is already running
+        imagej_already_initialized: bool = hasattr(imagej, "gateway") and imagej.gateway
 
+        # -- CONFIGURATION -- #
+
+        # Configure pyimagej
+        if imagej_already_initialized:
+            self._update_imagej_settings()
+        else:
+            ij_settings = self._configure_imagej()
+
+        # Configure napari-imagej
+        from napari_imagej.types.converters import install_converters
+
+        install_converters()
+
+        log_debug("Completed JVM Configuration")
+
+        # -- INITIALIZATION -- #
+
+        # Launch ImageJ
+        if imagej_already_initialized:
+            self.ij = imagej.gateway
+        else:
+            self.ij = imagej.init(**ij_settings)
+
+        # Log initialization
+        log_debug(f"Initialized at version {self.ij.getVersion()}")
+
+        # -- VALIDATION -- #
+
+        # Validate PyImageJ
+        self._validate_imagej()
+
+        # HACK: Avoid FlatLaf with ImageJ2 Swing UI;
+        # it doesn't work for reasons unknown.
+        # NB this SHOULD NOT be moved.
+        # This code must be in place before ANY swing components get created.
+        # Swing components could be created by any Java functionality (e.g. Commands).
+        # Therefore, we can't move it to e.g. the menu file
+        try:
+            ui = self.ij.ui().getDefaultUI().getInfo().getName()
+            log_debug(f"Default SciJava UI is {ui}.")
+            if ui == "swing":
+                SwingLookAndFeelService = jimport(
+                    "org.scijava.ui.swing.laf.SwingLookAndFeelService"
+                )
+                laf = self.ij.prefs().get(SwingLookAndFeelService, "lookAndFeel")
+                log_debug(f"Preferred Look+Feel is {laf}.")
+                if laf is None or laf.startsWith("FlatLaf"):
+                    UIManager = jimport("javax.swing.UIManager")
+                    fallback_laf = UIManager.getSystemLookAndFeelClassName()
+                    log_debug(
+                        f"Detected FlatLaf. Falling back to {fallback_laf} "
+                        "instead to avoid problems."
+                    )
+                    self.ij.prefs().put(
+                        SwingLookAndFeelService, "lookAndFeel", fallback_laf
+                    )
+        except Exception as exc:
+            from scyjava import jstacktrace
+
+            # NB: The hack failed, but no worries, just try to keep going.
+            print(jstacktrace(exc))
+
+    def _update_imagej_settings(self) -> None:
+        """
+        Updates napari-imagej's settings to reflect an active ImageJ instance.
+        """
+        # Scrape the JVM mode off of the active ImageJ instance
+        settings["jvm_mode"] = (
+            "headless" if imagej.gateway.ui().isHeadless() else "interactive"
+        )
+        # Determine if legacy is active on the active ImageJ instance
+        # NB bool is needed to coerce Nones into booleans.
+        settings["add_legacy"] = bool(
+            imagej.gateway.legacy and imagej.gateway.legacy.isActive()
+        )
+
+    def _configure_imagej(self) -> Dict[str, Any]:
+        """
+        Configures scyjava and pyimagej.
+        This function returns the settings that must be passed in the
+        actual initialization call.
+
+        :return: kwargs that should be passed to imagej.init()
+        """
         # ScyJava configuration
         # TEMP: Avoid issues caused by
         # https://github.com/imagej/pyimagej/issues/160
@@ -103,26 +187,14 @@ def initialize(self):
         config.add_option(f"-Dimagej2.dir={settings['imagej_base_directory'].get(str)}")
 
         # PyImageJ configuration
-        ij_settings = {}
-        ij_settings["ij_dir_or_version_or_endpoint"] = settings[
+        init_settings = {}
+        init_settings["ij_dir_or_version_or_endpoint"] = settings[
             "imagej_directory_or_endpoint"
         ].get(str)
-        ij_settings["mode"] = settings["jvm_mode"].get(str)
-        ij_settings["add_legacy"] = settings["include_imagej_legacy"].get(bool)
+        init_settings["mode"] = settings["jvm_mode"].get(str)
+        init_settings["add_legacy"] = settings["include_imagej_legacy"].get(bool)
 
-        # napari-imagej configuration
-        from napari_imagej.types.converters import install_converters
-
-        install_converters()
-
-        log_debug("Completed JVM Configuration")
-
-        # Launch PyImageJ
-        self.ij = imagej.init(**ij_settings)
-        # Validate PyImageJ
-        self._validate_imagej()
-        # Log initialization
-        log_debug(f"Initialized at version {self.ij.getVersion()}")
+        return init_settings
 
     def _validate_imagej(self):
         """

src/napari_imagej/types/converters/images.py

@@ -27,7 +27,7 @@ def _dataset_view_to_image(image: Any) -> Image:
         data=ij().py.from_java(view.getData().getImgPlus().getImg()),
         name=view.getData().getName(),
     )
-    if view.getColorTables().size() > 0:
+    if view.getColorTables() and view.getColorTables().size() > 0:
         if not jc.ColorTables.isGrayColorTable(view.getColorTables().get(0)):
             kwargs["colormap"] = _color_table_to_colormap(view.getColorTables().get(0))
     return Image(**kwargs)
@@ -58,7 +58,7 @@ def _dataset_to_image(image: Any) -> Image:
 def _image_to_dataset(image: Image) -> "jc.Dataset":
     # Construct a dataset from the data
     data = image.data
-    dataset: "jc.Dataset" = ij().py._numpy_to_dataset(data)
+    dataset: "jc.Dataset" = ij().py.to_dataset(data)
     # Add name
     dataset.setName(image.name)
     # Add color table, if the image uses a custom colormap

src/napari_imagej/types/converters/labels.py

@@ -2,6 +2,7 @@
 scyjava Converters for converting between ImgLib2 ImgLabelings
 and napari Labels
 """
+from imagej.convert import imglabeling_to_labeling
 from labeling.Labeling import Labeling
 from napari.layers import Labels
 from scyjava import Priority
@@ -39,7 +40,7 @@ def _imglabeling_to_layer(imgLabeling: "jc.ImgLabeling") -> Labels:
     :param imgLabeling: the Java ImgLabeling
     :return: a Labels layer
     """
-    labeling: Labeling = ij().py._imglabeling_to_labeling(imgLabeling)
+    labeling: Labeling = imglabeling_to_labeling(ij(), imgLabeling)
     return _labeling_to_layer(labeling)
 
 

src/napari_imagej/utilities/_module_utils.py

@@ -13,6 +13,7 @@
 from inspect import Parameter, Signature, _empty, isclass, signature
 from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
+from imagej.images import is_arraylike
 from jpype import JException
 from magicgui.widgets import Container, Label, LineEdit, Widget, request_values
 from magicgui.widgets._bases import CategoricalWidget
@@ -306,7 +307,7 @@ def _pure_module_outputs(
             continue
         output = ij().py.from_java(output_entry.getValue())
         # Add arraylike outputs as images
-        if ij().py._is_arraylike(output):
+        if is_arraylike(output):
             layer = Layer.create(data=output, meta={"name": name}, layer_type="image")
             layer_outputs.append(layer)
         # Add Layers directly

src/napari_imagej/widgets/menu.py

@@ -61,16 +61,24 @@ def _showUI(self):
         """
         # First time showing
         if not self.gui.isVisible():
-            # First things first, show the GUI
-            ij().ui().showUI(self.gui)
-            # Then, add our custom settings to the User Interface
-            if ij().legacy and ij().legacy.isActive():
-                self._ij1_UI_setup()
-            else:
-                self._ij2_UI_setup()
+
+            def ui_setup():
+                # First things first, show the GUI
+                ij().ui().showUI(self.gui)
+                # Then, add our custom settings to the User Interface
+                if ij().legacy and ij().legacy.isActive():
+                    self._ij1_UI_setup()
+                else:
+                    self._ij2_UI_setup()
+
+            # Queue UI call on the EDT
+            # TODO: Use EventQueue.invokeLater scyjava wrapper, once it exists
+            ij().thread().queue(ui_setup)
         # Later shows - the GUI is "visible", but the appFrame probably isn't
         else:
-            self.gui.getApplicationFrame().setVisible(True)
+            # Queue UI call on the EDT
+            # TODO: Use EventQueue.invokeLater scyjava wrapper, once it exists
+            ij().thread().queue(lambda: self.gui.getApplicationFrame().setVisible(True))
 
     def _ij1_UI_setup(self):
         """Configures the ImageJ Legacy GUI"""
@@ -148,7 +156,7 @@ def _set_icon(self, path: str):
     def send_active_layer(self):
         active_layer: Optional[Layer] = self.viewer.layers.selection.active
         if active_layer:
-            ij().ui().show(ij().py.to_java(active_layer))
+            self._show(active_layer)
         else:
             log_debug("There is no active layer to export to ImageJ2")
 
@@ -165,7 +173,12 @@ def send_chosen_layer(self):
             layer = choices["layer"]
             if isinstance(layer, Layer):
                 # Pass the relevant data to ImageJ2
-                ij().ui().show(ij().py.to_java(layer))
+                self._show(layer)
+
+    def _show(self, layer):
+        # Queue UI call on the EDT
+        # TODO: Use EventQueue.invokeLater scyjava wrapper, once it exists
+        ij().thread().queue(lambda: ij().ui().show(ij().py.to_java(layer)))
 
 
 class FromIJButton(QPushButton):