Test conversion behavior

src/napari_imagej/java.py

@@ -322,6 +322,10 @@ def ColorTable(self):
     def ColorTable8(self):
         return "net.imglib2.display.ColorTable8"
 
+    @blocking_import
+    def ColorTables(self):
+        return "net.imagej.display.ColorTables"
+
     @blocking_import
     def ComplexType(self):
         return "net.imglib2.type.numeric.ComplexType"

src/napari_imagej/types/converters/images.py

@@ -28,7 +28,8 @@ def _dataset_view_to_image(image: Any) -> Image:
         name=view.getData().getName(),
     )
     if view.getColorTables().size() > 0:
-        kwargs["colormap"] = _color_table_to_colormap(view.getColorTables().get(0))
+        if not jc.ColorTables.isGrayColorTable(view.getColorTables().get(0)):
+            kwargs["colormap"] = _color_table_to_colormap(view.getColorTables().get(0))
     return Image(**kwargs)
 
 
@@ -47,7 +48,7 @@ def _dataset_to_image(image: Any) -> Image:
         name=imp.getName(),
     )
     if imp.getColorTableCount():
-        kwargs["colormap"] = imp.getColorTable(0)
+        kwargs["colormap"] = _color_table_to_colormap(imp.getColorTable(0))
     return Image(**kwargs)
 
 

src/napari_imagej/widgets/menu.py

@@ -4,7 +4,7 @@
 from enum import Enum
 from pathlib import Path
 from threading import Thread
-from typing import Any, Dict, Optional
+from typing import Any, Dict, Optional, Union
 
 from jpype import JImplements, JOverride
 from magicgui.widgets import request_values
@@ -202,21 +202,24 @@ def get_chosen_layer(self) -> None:
         if choices is not None:
             # grab the chosen name
             name = choices["data"]
-            # grab the chosen image
-            view = (
-                ij().get("org.scijava.display.DisplayService").getDisplay(name).get(0)
-            )
-            self._add_image_from_display_view(view)
+            display = ij().display().getDisplay(name)
+            # if the image is displayed, convert the DatasetView
+            if display:
+                self._add_image(display.get(0))
+            # Otherwise, just convert the object
+            else:
+                image = images[names.index(name)]
+                self._add_image(image)
 
     def get_active_layer(self) -> None:
         # Choose the active DatasetView
         view = ij().get("net.imagej.display.ImageDisplayService").getActiveDatasetView()
         if view is None:
             log_debug("There is no active window to export to napari")
             return
-        self._add_image_from_display_view(view)
+        self._add_image(view)
 
-    def _add_image_from_display_view(self, view: "jc.DatasetView"):
+    def _add_image(self, view: Union["jc.Dataset", "jc.DatasetView"]):
         # Get the stuff needed for a new layer
         py_image = ij().py.from_java(view)
         # Create and add the layer

tests/types/test_converters.py

@@ -760,7 +760,87 @@ def test_OutOfBoundsFactory_conversion(ij):
 # -- Images -- #
 
 
-def test_image_layer_to_img(ij):
-    image = Image(data=np.ones((10, 10)))
+@pytest.fixture
+def test_dataset(ij) -> "jc.Dataset":
+    name = "test.foo"
+    dataset: jc.Dataset = ij.dataset().create(ij.py.to_java(np.ones((10, 10))))
+    dataset.setName(name)
+    return dataset
+
+
+@pytest.fixture
+def test_dataset_view(ij, test_dataset) -> "jc.DatasetView":
+    view: jc.DatasetView = ij.get(
+        "net.imagej.display.ImageDisplayService"
+    ).createDataView(test_dataset)
+    view.rebuild()
+    view.resetColorTables(True)
+    yield view
+    # dispose of the view so it does not affect later tests
+    view.dispose()
+
+
+def _assert_equal_color_maps(j_map: "jc.ColorTable", p_map):
+    p_color = p_map.map([x / 255 for x in range(256)])
+    # Assert color table "equality"
+    for i in range(j_map.getLength()):
+        for j in range(j_map.getComponentCount()):
+            assert j_map.get(j, i) == int(round(p_color[i, j] * 255))
+
+
+def test_image_layer_to_dataset(ij):
+    """Test conversion of an Image layer with a default colormap"""
+    name = "test_foo"
+    image = Image(data=np.ones((10, 10)), name=name)
+    j_img = ij.py.to_java(image)
+    assert isinstance(j_img, jc.Dataset)
+    assert name == j_img.getName()
+    assert 0 == j_img.getColorTableCount()
+
+
+def test_colormap_image_layer_to_dataset(ij):
+    """Test conversion of an Image layer with a chosen colormap"""
+    name = "test_foo"
+    image = Image(data=np.ones((10, 10)), name=name, colormap="red")
     j_img = ij.py.to_java(image)
     assert isinstance(j_img, jc.Dataset)
+    assert name == j_img.getName()
+    assert 1 == j_img.getColorTableCount()
+    _assert_equal_color_maps(j_img.getColorTable(0), image.colormap)
+
+
+def test_dataset_to_image_layer(ij, test_dataset):
+    """Test conversion of a Dataset with no colormap"""
+    p_img = ij.py.from_java(test_dataset)
+    assert isinstance(p_img, Image)
+    assert test_dataset.getName() == p_img.name
+    assert "gray" == p_img.colormap.name
+
+
+def test_colormap_dataset_to_image_layer(ij, test_dataset):
+    """Test conversion of a Dataset with a colormap"""
+    test_dataset.initializeColorTables(1)
+    test_dataset.setColorTable(jc.ColorTables.CYAN, 0)
+    p_img = ij.py.from_java(test_dataset)
+    assert isinstance(p_img, Image)
+    assert test_dataset.getName() == p_img.name
+    assert "gray" != p_img.colormap.name
+    _assert_equal_color_maps(test_dataset.getColorTable(0), p_img.colormap)
+
+
+def test_dataset_view_to_image_layer(ij, test_dataset_view):
+    """Test conversion of a Dataset with no colormap"""
+    p_img = ij.py.from_java(test_dataset_view)
+    assert isinstance(p_img, Image)
+    assert test_dataset_view.getData().getName() == p_img.name
+    assert "gray" == p_img.colormap.name
+
+
+def test_colormap_dataset_view_to_image_layer(ij, test_dataset_view):
+    """Test conversion of a Dataset with a colormap"""
+    test_dataset_view.setColorTable(jc.ColorTables.CYAN, 0)
+    p_img = ij.py.from_java(test_dataset_view)
+    assert isinstance(p_img, Image)
+    assert test_dataset_view.getData().getName() == p_img.name
+    assert "gray" != p_img.colormap.name
+    _assert_equal_color_maps(test_dataset_view.getColorTables().get(0), p_img.colormap)

tests/widgets/test_menu.py

@@ -271,8 +271,7 @@ def test_data_choosers(asserter, qtbot, ij, gui_widget_chooser):
     button_to.clicked.emit()
 
     # Assert that the data is now in ImageJ2
-    asserter(lambda: isinstance(ij.display().getActiveDisplay(), jc.ImageDisplay))
-    assert "test_to" == ij.display().getActiveDisplay().getName()
+    asserter(lambda: isinstance(ij.display().getDisplay("test_to"), jc.ImageDisplay))
 
     # Use the chooser to transfer that data back
     button_from.clicked.emit()