Add in ImageJ2 -> napari colormap conversion

environment.yml

@@ -18,6 +18,7 @@ dependencies:
   - labeling >= 0.1.12
   - magicgui >= 0.5.1
   - napari
+  - numpy
   - openjdk=8
   - pyimagej >= 1.2.0
   # Project from source

setup.cfg

@@ -40,6 +40,7 @@ install_requires =
     confuse
     labeling >= 0.1.12
     napari
+    numpy
     magicgui >= 0.5.1
     pyimagej >= 1.2.0
 

src/napari_imagej/java.py

@@ -442,6 +442,10 @@ def SuperEllipsoid(self):
     def Dataset(self):
         return "net.imagej.Dataset"
 
+    @blocking_import
+    def DatasetView(self):
+        return "net.imagej.display.DatasetView"
+
     @blocking_import
     def DefaultROITree(self):
         return "net.imagej.roi.DefaultROITree"
@@ -450,6 +454,10 @@ def DefaultROITree(self):
     def ImageDisplay(self):
         return "net.imagej.display.ImageDisplay"
 
+    @blocking_import
+    def ImgPlus(self):
+        return "net.imagej.ImgPlus"
+
     @blocking_import
     def Mesh(self):
         return "net.imagej.mesh.Mesh"

src/napari_imagej/types/converters/images.py

@@ -3,13 +3,48 @@
 and napari Images
 """
 
+from typing import Any
+
+from imagej.dims import _has_axis
 from jpype import JArray, JByte
 from napari.layers import Image
 from napari.utils.colormaps import Colormap
+from numpy import ones
 from scyjava import Priority
 
 from napari_imagej.java import ij, jc
-from napari_imagej.types.converters import py_to_java_converter
+from napari_imagej.types.converters import java_to_py_converter, py_to_java_converter
+
+
+@java_to_py_converter(
+    predicate=lambda obj: ij().convert().supports(obj, jc.DatasetView),
+    priority=Priority.VERY_HIGH + 1,
+)
+def _dataset_view_to_image(image: Any) -> Image:
+    view = ij().convert().convert(image, jc.DatasetView)
+    # Construct a dataset from the data
+    data = ij().py.from_java(view.getData().getImgPlus().getImg())
+    name = view.getData().getName()
+    if view.getColorTables().size() > 0:
+        cmap = _color_table_to_colormap(view.getColorTables().get(0))
+        return Image(data=data, name=name, colormap=cmap)
+    return Image(data=data, name=name)
+
+
+def _can_convert_img_plus(obj: Any):
+    can_convert = ij().convert().supports(obj, jc.ImgPlus)
+    has_axis = _has_axis(obj)
+    return can_convert and has_axis
+
+
+@java_to_py_converter(predicate=_can_convert_img_plus, priority=Priority.VERY_HIGH)
+def _dataset_to_image(image: Any) -> Image:
+    imp = ij().convert().convert(image, jc.ImgPlus)
+    # Construct a dataset from the data
+    data = ij().py.from_java(imp.getImg())
+    name = imp.getName()
+    cmap = imp.getColorTable(0)
+    return Image(data=data, name=name, colormap=cmap)
 
 
 @py_to_java_converter(
@@ -23,13 +58,13 @@ def _image_to_dataset(image: Image) -> "jc.Dataset":
     dataset.setName(image.name)
     # Add color table, if the image uses a custom colormap
     if image.colormap.name != "gray":
-        color_table = _colormap_to_colorTable(image.colormap)
+        color_table = _colormap_to_color_table(image.colormap)
         dataset.initializeColorTables(1)
         dataset.setColorTable(color_table, 0)
     return dataset
 
 
-def _colormap_to_colorTable(cmap: Colormap):
+def _colormap_to_color_table(cmap: Colormap):
     """
     Converts a napari Colormap into a SciJava ColorTable.
     :param cmap: The napari Colormap
@@ -47,3 +82,18 @@ def _colormap_to_colorTable(cmap: Colormap):
             j_values[i][j] = value if value < 128 else value - 256
 
     return jc.ColorTable8(j_values)
+
+
+def _color_table_to_colormap(ctable: "jc.ColorTable"):
+    """
+    Converts a SciJava ColorTable into a napari Colormap.
+    :param ctable: The SciJava ColorTable
+    :return: An "equivalent" napari Colormap
+    """
+    components = ctable.getComponentCount()
+    bins = ctable.getLength()
+    data = ones((bins, 4), dtype=float)
+    for component in range(components):
+        for bin in range(bins):
+            data[bin, component] = float(ctable.get(component, bin)) / 255.0
+    return Colormap(colors=data)

src/napari_imagej/widgets/menu.py

@@ -205,36 +205,30 @@ def get_chosen_layer(self) -> None:
             # grab the chosen name
             name = choices["data"]
             # grab the chosen image
-            i = names.index(name)
-            image = ij().py.from_java(images[i])
-            # if the conversion is already a layer, add it directly
-            if isinstance(image, Layer):
-                image.name = name
-                self.viewer.add_layer(image)
-            # otherwise, try to coerce it into an Image layer
-            elif ij().py._is_arraylike(image):
-                self.viewer.add_image(data=image, name=name)
-            # if we can't coerce it, give up
-            else:
-                raise ValueError(f"{image} cannot be displayed in napari!")
+            view = (
+                ij().get("org.scijava.display.DisplayService").getDisplay(name).get(0)
+            )
+            self._add_image_from_display_view(view)
 
     def get_active_layer(self) -> None:
-        # Choose the active Dataset
-        image = ij().get("net.imagej.display.ImageDisplayService").getActiveDataset()
-        if image is 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)
+
+    def _add_image_from_display_view(self, view: "jc.DatasetView"):
         # Get the stuff needed for a new layer
-        py_image = ij().py.from_java(image)
-        name = ij().object().getName(image)
+        py_image = ij().py.from_java(view)
         # Create and add the layer
         if isinstance(py_image, Layer):
-            py_image.name = name
             self.viewer.add_layer(py_image)
         elif ij().py._is_arraylike(py_image):
+            name = ij().object().getName(view)
             self.viewer.add_image(data=py_image, name=name)
         else:
-            raise ValueError(f"{image} cannot be displayed in napari!")
+            raise ValueError(f"{view} cannot be displayed in napari!")
 
 
 class GUIButton(QPushButton):