Improve labels transfer to ImageJ

dev-environment.yml

@@ -29,7 +29,7 @@ dependencies:
   - numpy
   - openjdk=11
   - pandas
-  - pyimagej >= 1.4.1
+  - pyimagej >= 1.5.0
   - scyjava >= 1.9.1
   - superqt >= 0.7.0
   - xarray < 2024.10.0

environment.yml

@@ -29,7 +29,7 @@ dependencies:
   - numpy
   - openjdk=11
   - pandas
-  - pyimagej >= 1.4.1
+  - pyimagej >= 1.5.0
   - scyjava >= 1.9.1
   - superqt >= 0.7.0
   - xarray < 2024.10.0

pyproject.toml

@@ -42,7 +42,7 @@ dependencies = [
     "napari >= 0.4.17",
     "numpy",
     "pandas",
-    "pyimagej >= 1.4.1",
+    "pyimagej >= 1.5.0",
     "scyjava >= 1.9.1",
     "superqt >= 0.7.0",
     "xarray < 2024.10.0",

src/napari_imagej/widgets/widget_utils.py

@@ -2,6 +2,7 @@
 from logging import getLogger
 from typing import List
 
+from imagej.convert import index_img_to_roi_tree
 from jpype import JArray, JByte
 from scyjava import jvm_started
 from magicgui import magicgui
@@ -156,7 +157,7 @@ def __init__(self, title: str, error_message: str, *args, **kwargs):
 
 
 _IMAGE_LAYER_TYPES = (Image, Labels)
-_ROI_LAYER_TYPES = (Points, Shapes)
+_ROI_LAYER_TYPES = (Labels, Points, Shapes)
 
 
 class LayerComboBox(QWidget):
@@ -261,7 +262,7 @@ def __init__(self, viewer: Viewer):
         for layer in viewer.layers:
             if isinstance(layer, _IMAGE_LAYER_TYPES):
                 self.imgs.append(layer)
-            elif isinstance(layer, _ROI_LAYER_TYPES):
+            if isinstance(layer, _ROI_LAYER_TYPES):
                 self.rois.append(layer)
 
         # Add combo boxes
@@ -298,11 +299,18 @@ def pass_to_ij():
             j_img = nij.ij.py.to_java(
                 img, dim_order=self.dims_container.provided_labels()
             )
+            # Labels layers should display the index image
+            if isinstance(j_img, jc.ImgLabeling):
+                j_img = nij.ij.py.to_dataset(j_img.getIndexImg())
+                j_img.setName(img.name)
             if roi:
                 if isinstance(roi, Points):
                     j_point = nij.ij.py.to_java(roi)
                     j_roi = jc.DefaultROITree()
                     j_roi.addROIs(jc.ArrayList([j_point]))
+                elif isinstance(roi, Labels):
+                    j_label = nij.ij.py.to_java(roi)
+                    j_roi = index_img_to_roi_tree(nij.ij, j_label.getIndexImg())
                 else:
                     j_roi = nij.ij.py.to_java(roi)
                 j_img.getProperties().put("rois", j_roi)

tests/widgets/test_menu.py

@@ -7,7 +7,7 @@
 import numpy
 import pytest
 from napari import Viewer
-from napari.layers import Image, Layer, Shapes
+from napari.layers import Image, Labels, Layer, Shapes
 from napari.viewer import current_viewer
 from qtpy.QtCore import QRunnable, Qt, QThreadPool
 from qtpy.QtGui import QPixmap
@@ -395,6 +395,120 @@ def check_active_display():
     asserter(check_active_display)
 
 
+def test_labels_transfer_as_data(
+    popup_handler, asserter, ij, gui_widget: NapariImageJMenu
+):
+    """Tests the detailed image exporter"""
+    if settings.headless():
+        pytest.skip("Only applies when not running headlessly")
+
+    button: ToIJDetailedButton = gui_widget.to_ij_detail
+    assert not button.isEnabled()
+
+    # Add some labels to the viewer
+    sample_data = numpy.ones((50, 100), dtype=numpy.uint8)
+    labels = Labels(data=sample_data, name="test_labels")
+    current_viewer().add_layer(labels)
+    asserter(lambda: button.isEnabled())
+
+    def handle_transfer(widget: QDialog) -> bool:
+        if not isinstance(widget, DetailExportDialog):
+            print("Not an AdvancedExportDialog")
+            return False
+        if not widget.img_container.combo.currentText() == "test_labels":
+            print(widget.img_container.combo.currentText())
+            print("Unexpected starting image text")
+            return False
+        if not widget.roi_container.combo.currentText() == "--------":
+            print("Unexpected starting roi text")
+            return False
+        if labels not in widget.roi_container.choices:
+            print("Labels layer not available")
+            return False
+
+        ok_button = widget.buttons.button(QDialogButtonBox.Ok)
+        ok_button.clicked.emit()
+        return True
+
+    popup_handler(button.clicked.emit, handle_transfer)
+
+    # Assert that the data is now in Fiji
+    def check_active_display():
+        if not ij.display().getActiveDisplay():
+            return False
+        dataset = ij.display().getActiveDisplay().getActiveView().getData()
+        if not dataset.getName() == "test_labels":
+            return False
+
+        return True
+
+    asserter(check_active_display)
+
+
+def test_labels_transfer_as_rois(
+    popup_handler, asserter, ij, gui_widget: NapariImageJMenu
+):
+    """Tests the detailed image exporter"""
+    if settings.headless():
+        pytest.skip("Only applies when not running headlessly")
+
+    button: ToIJDetailedButton = gui_widget.to_ij_detail
+    assert not button.isEnabled()
+
+    # Add an image to the viewer
+    sample_data = numpy.ones((50, 100, 3), dtype=numpy.uint8)
+    # NB: Unnatural data order used for testing in handler
+    dims = ("X", "Y", "Z")
+    sample_data = DataArray(data=sample_data, dims=dims)
+    image: Image = Image(data=sample_data, name="test_to")
+    current_viewer().add_layer(image)
+    asserter(lambda: button.isEnabled())
+
+    # Add some labels to the viewer
+    sample_data = numpy.ones((50, 100), dtype=numpy.uint8)
+    labels = Labels(data=sample_data, name="test_labels")
+    current_viewer().add_layer(labels)
+
+    def handle_transfer(widget: QDialog) -> bool:
+        if not isinstance(widget, DetailExportDialog):
+            print("Not an AdvancedExportDialog")
+            return False
+        # Note test_labels is the active layer - it will be the current text
+        if not widget.img_container.combo.currentText() == "test_labels":
+            print(widget.img_container.combo.currentText())
+            print("Unexpected starting image text")
+            return False
+        if not widget.roi_container.combo.currentText() == "--------":
+            print("Unexpected starting roi text")
+            return False
+        if labels not in widget.roi_container.choices:
+            print("Labels layer not available")
+            return False
+
+        widget.img_container.combo.setCurrentText("test_to")
+        widget.roi_container.combo.setCurrentText("test_labels")
+
+        ok_button = widget.buttons.button(QDialogButtonBox.Ok)
+        ok_button.clicked.emit()
+        return True
+
+    popup_handler(button.clicked.emit, handle_transfer)
+
+    # Assert that the data is now in Fiji
+    def check_active_display():
+        if not ij.display().getActiveDisplay():
+            return False
+        dataset = ij.display().getActiveDisplay().getActiveView().getData()
+        if not dataset.getName() == "test_to":
+            return False
+        if dataset.getProperties().get("rois") is None:
+            return False
+
+        return True
+
+    asserter(check_active_display)
+
+
 def test_settings_no_change(gui_widget: NapariImageJMenu):
     """Ensure that no changes are made when there is no change from the defaults"""
     button: SettingsButton = gui_widget.settings_button