Merge branch '222-n-rendering-layers-in-overlay'

sksurgeryvtk/models/voxelise.py

@@ -606,7 +606,8 @@ def apply_displacement_to_mesh(mesh: Union[vtk.vtkDataObject, str],
         0,
         vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
         "preoperativeSurface")
-    threshold.ThresholdByLower(0)
+    threshold.SetLowerThreshold(0)
+    threshold.SetThresholdFunction(threshold.THRESHOLD_LOWER)
     threshold.SetInputData(field)
     threshold.Update()
     fieldInternal = threshold.GetOutput()

sksurgeryvtk/models/vtk_grid_model.py

@@ -125,5 +125,7 @@ def threshold_between(self, lower: float, upper: float):
         :param upper: Upper limit
         :type upper: float
         """
-        self.threshold.ThresholdBetween(lower, upper)
+        self.threshold.SetLowerThreshold(lower)
+        self.threshold.SetUpperThreshold(upper)
+        self.threshold.SetThresholdFunction(self.threshold.THRESHOLD_BETWEEN)
         self.threshold.Update()

tests/camera/test_liver_overlay.py

@@ -13,12 +13,15 @@
 
 skip_pytest_in_runner_macos = pytest.mark.skipif(
     platform.system() == "Darwin",
-    reason=f'for [{platform.system()} OSs with CI=[{os.environ.get("CI")}] with RUNNER_OS=[{os.environ.get("RUNNER_OS")}] '
-           f'{os.environ.get("SESSION_MANAGER")[0:20] if (platform.system() == "Darwin" and os.environ.get("GITHUB_ACTIONS") == None) else ""} '
-           f'with {os.environ.get("XDG_CURRENT_DESKTOP") if (platform.system() == "Darwin" and os.environ.get("GITHUB_ACTIONS") == None) else ""} '
+    reason=f'for [{platform.system()} OSs with '
+           f'CI=[{os.environ.get("CI")}] with '
+           f'RUNNER_OS=[{os.environ.get("RUNNER_OS")}] '
+           f'SESSION_MANAGER=[{os.environ.get("SESSION_MANAGER")[0:20] if (platform.system() == "Darwin" and os.environ.get("GITHUB_ACTIONS") is not None and os.environ.get("SESSION_MANAGER") is not None) else ""}] '
+           f'XDG_CURRENT_DESKTOP=[{os.environ.get("XDG_CURRENT_DESKTOP") if (platform.system() == "Darwin" and os.environ.get("GITHUB_ACTIONS") is not None) else ""}] '
            f'due to issues with Fatal Python error: Segmentation fault'
 )
 
+
 def _reproject_and_save_image(image,
                               model_to_camera,
                               point_cloud,
@@ -59,6 +62,7 @@ def _reproject_and_save_image(image,
 
     cv2.imwrite(output_file, output_image)
 
+
 @skip_pytest_in_runner_macos
 def test_overlay_liver_points(setup_vtk_overlay_window):
     """

tests/conftest.py

@@ -21,7 +21,6 @@ def setup_qt():
 @pytest.fixture(scope="session")
 def setup_vtk_err(setup_qt):
     """ Used to send VTK errors to file instead of screen. """
-
     err_out = vtk.vtkFileOutputWindow()
     err_out.SetFileName('tests/output/vtk.err.txt')
     vtk_std_err = vtk.vtkOutputWindow()
@@ -32,11 +31,9 @@ def setup_vtk_err(setup_qt):
 @pytest.fixture(scope="function")
 def setup_vtk_overlay_window(setup_vtk_err):
     """
-    This function so you can select offscreen or not, while debugging.
-
-    `init_widget_flag` is set to false `init_widget_flag` when testing in Linux OS machines.
-    Otherwise, `init_widget_flag = True`, calling `self.Initialize` and `self.Start` in the init function of
-        VTKOverlayWindow class
+    Sets `init_widget_flag` to False on Linux, and True on Windows and Mac.
+    When init_widget_flag==True, the VTKOverlayWindow constructor calls
+    `self.Initialize` and `self.Start` when creating the widget.
     """
 
     vtk_std_err, setup_qt = setup_vtk_err
@@ -52,22 +49,21 @@ def setup_vtk_overlay_window(setup_vtk_err):
 
 @pytest.fixture(scope="function")
 def setup_vtk_overlay_window_no_init(setup_vtk_err):
-    """ This function so you can select offscreen or not, while debugging. """
+    """
+    Similar to the above function, except init_widget=False, so
+    `self.Initialize` and `self.Start` are not called in the VTKOverlayWindow constructor.
+    """
 
     vtk_std_err, setup_qt = setup_vtk_err
 
     vtk_overlay = VTKOverlayWindow(offscreen=False, init_widget=False)
     return vtk_overlay, vtk_std_err, setup_qt
 
 
-# Note: These windows will persist while all unit tests run.
-#       Don't waste time trying to debug why you see >1 windows.
-@pytest.fixture(scope="function")
-def vtk_overlay_with_gradient_image(setup_vtk_overlay_window):
-    """ Creates a VTKOverlayWindow with gradient image. """
-
-    vtk_overlay, vtk_std_err, setup_qt = setup_vtk_overlay_window
-
+def _create_gradient_image():
+    """
+    Creates a dummy gradient image for testing only.
+    """
     width = 512
     height = 256
     image = np.ones((height, width, 3), dtype=np.uint8)
@@ -76,6 +72,17 @@ def vtk_overlay_with_gradient_image(setup_vtk_overlay_window):
             image[y][x][0] = y
             image[y][x][1] = y
             image[y][x][2] = y
+    return image
+
+
+# Note: These windows will persist while all unit tests run.
+#       Don't waste time trying to debug why you see >1 windows.
+@pytest.fixture(scope="function")
+def vtk_overlay_with_gradient_image(setup_vtk_overlay_window):
+    """ Creates a VTKOverlayWindow with gradient image. """
+
+    vtk_overlay, vtk_std_err, setup_qt = setup_vtk_overlay_window
+    image = _create_gradient_image()
     vtk_overlay.set_video_image(image)
     return image, vtk_overlay, vtk_std_err, setup_qt
 
@@ -93,3 +100,59 @@ def vtk_interlaced_stereo_window(setup_vtk_err):
 
     vtk_interlaced = VTKStereoInterlacedWindow(offscreen=False, init_widget=init_widget_flag)
     return vtk_interlaced, vtk_std_err, setup_qt
+
+
+@pytest.fixture(scope="function")
+def setup_vtk_overlay_window_video_only_layer_2(setup_vtk_err):
+    """
+    Sets `init_widget_flag` to False on Linux, and True on Windows and Mac.
+    When init_widget_flag==True, the VTKOverlayWindow constructor calls
+    `self.Initialize` and `self.Start` when creating the widget.
+
+    As of Issue #222: And also sets video_in_layer_0=False and video_in_layer_2=True
+    in VTKOverlayWindow constructor. See VTKOverlayWindow docstring for explanation.
+    """
+
+    vtk_std_err, setup_qt = setup_vtk_err
+
+    if platform.system() == 'Linux':
+        init_widget_flag = False
+    else:
+        init_widget_flag = True
+
+    vtk_overlay = VTKOverlayWindow(offscreen=False,
+                                   init_widget=init_widget_flag,
+                                   video_in_layer_0=False,
+                                   video_in_layer_2=True
+                                   )
+    image = _create_gradient_image()
+    vtk_overlay.set_video_image(image)
+    return vtk_overlay, vtk_std_err, setup_qt
+
+
+@pytest.fixture(scope="function")
+def setup_vtk_overlay_window_video_both_layer_0_and_2(setup_vtk_err):
+    """
+    Sets `init_widget_flag` to False on Linux, and True on Windows and Mac.
+    When init_widget_flag==True, the VTKOverlayWindow constructor calls
+    `self.Initialize` and `self.Start` when creating the widget.
+
+    As of Issue #222: And also sets video_in_layer_0=True and video_in_layer_2=True
+    in VTKOverlayWindow constructor. See VTKOverlayWindow docstring for explanation.
+    """
+
+    vtk_std_err, setup_qt = setup_vtk_err
+
+    if platform.system() == 'Linux':
+        init_widget_flag = False
+    else:
+        init_widget_flag = True
+
+    vtk_overlay = VTKOverlayWindow(offscreen=False,
+                                   init_widget=init_widget_flag,
+                                   video_in_layer_0=True,
+                                   video_in_layer_2=True
+                                   )
+    image = _create_gradient_image()
+    vtk_overlay.set_video_image(image)
+    return vtk_overlay, vtk_std_err, setup_qt

tests/models/test_vtk_cylinder_model.py

@@ -50,6 +50,6 @@ def test_cylinder_model(setup_vtk_overlay_window):
 
     # You don't really want this in a unit test, otherwise you can't exit.
     # If you want to do interactive testing, please uncomment the following line
-    # _pyside_qt_app.exec()
+    #_pyside_qt_app.exec()
     widget.close()
 

tests/models/test_vtk_surface_model.py

@@ -186,10 +186,10 @@ def test_flat_shaded_on_coloured_background(setup_vtk_overlay_window):
     widget, _, app = setup_vtk_overlay_window
     widget.add_vtk_actor(model.actor)
     model.set_no_shading(True)
-    widget.background_renderer.SetBackground(0, 0, 1)
+    widget.get_background_renderer().SetBackground(0, 0, 1)
     widget.show()
     model.set_no_shading(False)
-    widget.background_renderer.SetBackground(0, 1, 0)
+    widget.get_background_renderer().SetBackground(0, 1, 0)
     widget.show()
     # app.exec()
 

tests/widgets/test_vtk_overlay_window.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
-import platform
 import pytest
 from vtkmodules.vtkCommonColor import vtkNamedColors
 from vtkmodules.vtkFiltersSources import vtkConeSource
@@ -12,8 +11,6 @@
 )
 from PySide6.QtWidgets import QApplication, QWidget, QVBoxLayout
 from vtkmodules.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
-from sksurgeryvtk.widgets.vtk_overlay_window import VTKOverlayWindow
-
 import sksurgeryvtk.models.vtk_point_model as pm
 import sksurgeryvtk.models.vtk_surface_model as sm
 
@@ -23,7 +20,7 @@ def test_vtk_render_window_settings(setup_vtk_overlay_window):
 
     assert not widget.GetRenderWindow().GetStereoRender()
     assert not widget.GetRenderWindow().GetStereoCapableWindow()
-    # assert widget.GetRenderWindow().GetAlphaBitPlanes()
+    assert widget.GetRenderWindow().GetAlphaBitPlanes()
     assert widget.GetRenderWindow().GetMultiSamples() == 0
     widget.close()
 
@@ -33,36 +30,38 @@ def test_vtk_render_window_settings_no_init(setup_vtk_overlay_window_no_init):
 
     assert not widget.GetRenderWindow().GetStereoRender()
     assert not widget.GetRenderWindow().GetStereoCapableWindow()
-    # assert widget.GetRenderWindow().GetAlphaBitPlanes()
+    assert widget.GetRenderWindow().GetAlphaBitPlanes()
     assert widget.GetRenderWindow().GetMultiSamples() == 0
     widget.close()
 
 
 def test_vtk_foreground_render_settings(setup_vtk_overlay_window):
     widget, _vtk_std_err, _pyside_qt_app = setup_vtk_overlay_window
 
-    assert widget.foreground_renderer.GetLayer() == 1
-    assert widget.foreground_renderer.GetUseDepthPeeling()
+    layer = widget.get_foreground_renderer().GetLayer()
+    assert widget.get_foreground_renderer().GetLayer() == 1
+    assert widget.get_foreground_renderer().GetUseDepthPeeling()
     widget.close()
 
 
 def test_vtk_background_render_settings(setup_vtk_overlay_window):
     widget, _vtk_std_err, _pyside_qt_app = setup_vtk_overlay_window
 
-    assert widget.background_renderer.GetLayer() == 0
-    assert not widget.background_renderer.GetInteractive()
+    assert widget.get_background_renderer().GetLayer() == 0
+    assert not widget.get_background_renderer().GetInteractive()
     widget.close()
 
 
 def test_image_importer(setup_vtk_overlay_window):
     widget, _vtk_std_err, _pyside_qt_app = setup_vtk_overlay_window
 
-    width, height, _number_of_scalar_components = widget.input.shape
-    expected_extent = (0, height - 1, 0, width - 1, 0, 0)
+    width, height, _number_of_scalar_components = widget.rgb_input.shape
+    expected_extent = (0, height - 1, 0, width - 1, 0, 2)
+    actual_extent = widget.rgb_image_importer.GetDataExtent()
 
-    assert widget.image_importer.GetDataExtent() == expected_extent
-    assert widget.image_importer.GetDataScalarTypeAsString() == "unsigned char"
-    assert widget.image_importer.GetNumberOfScalarComponents() == 3
+    assert actual_extent == expected_extent
+    assert widget.rgb_image_importer.GetDataScalarTypeAsString() == "unsigned char"
+    assert widget.rgb_image_importer.GetNumberOfScalarComponents() == 3
     widget.close()
 
 
@@ -116,22 +115,21 @@ def test_basic_pyside_vtk_pipeline():
     ren = vtkRenderer()
     ren.AddActor(coneActor)
 
-    qvtk_render_window_iterator = QVTKRenderWindowInteractor()
-    qvtk_render_window_iterator.GetRenderWindow().AddRenderer(ren)
-    qvtk_render_window_iterator.resize(100, 100)
+    qvtk_render_window_interactor = QVTKRenderWindowInteractor()
+    qvtk_render_window_interactor.GetRenderWindow().AddRenderer(ren)
+    qvtk_render_window_interactor.resize(100, 100)
 
-    layout.addWidget(qvtk_render_window_iterator)
+    layout.addWidget(qvtk_render_window_interactor)
 
     # To exit window using 'q' or 'e' key
-    qvtk_render_window_iterator.AddObserver("ExitEvent", lambda o, e, a=_pyside_qt_app: a.quit())
-
-    qvtk_render_window_iterator.Initialize()
-    qvtk_render_window_iterator.Start()
+    qvtk_render_window_interactor.AddObserver("ExitEvent", lambda o, e, a=_pyside_qt_app: a.quit())
+    qvtk_render_window_interactor.Initialize()
+    qvtk_render_window_interactor.Start()
 
     # You don't really want this in a unit test, otherwise you can't exit.
     # If you want to do interactive testing, please uncomment the following line
     # _pyside_qt_app.exec()
-    qvtk_render_window_iterator.close()
+    qvtk_render_window_interactor.close()
 
 
 def test_basic_cone_overlay(vtk_overlay_with_gradient_image):
@@ -227,6 +225,10 @@ def test_add_model_to_background_renderer_raises_error(vtk_overlay_with_gradient
 
     with pytest.raises(ValueError):
         widget.add_vtk_models(surface, layer=0)
+
+    with pytest.raises(ValueError):
+        widget.add_vtk_models(surface, layer=2)
+
     widget.close()
 
 
@@ -238,17 +240,17 @@ def test_add_models_to_foreground_renderer(vtk_overlay_with_gradient_image):
     # If no layer is specified, default is 0
     widget.add_vtk_models(liver)
 
-    foreground_actors = widget.foreground_renderer.GetActors()
+    foreground_actors = widget.get_foreground_renderer().GetActors()
     assert foreground_actors.GetNumberOfItems() == 1
 
     # Explicitly specify use of foreground renderer
     widget.add_vtk_models(tumors, 1)
 
-    foreground_actors = widget.foreground_renderer.GetActors()
+    foreground_actors = widget.get_foreground_renderer().GetActors()
     assert foreground_actors.GetNumberOfItems() == 2
 
     # Check overlay renderer is empty
-    overlay_renderer_actors = widget.generic_overlay_renderer.GetActors()
+    overlay_renderer_actors = widget.get_overlay_renderer().GetActors()
     assert overlay_renderer_actors.GetNumberOfItems() == 0
     widget.close()
 
@@ -258,17 +260,17 @@ def test_add_models_to_overlay_renderer(vtk_overlay_with_gradient_image):
     tumors = [sm.VTKSurfaceModel('tests/data/models/Liver/liver_tumours.vtk', (1.0, 1.0, 1.0))]
     _image, widget, _vtk_std_err, _pyside_qt_app = vtk_overlay_with_gradient_image
 
-    widget.add_vtk_models(liver, 2)
+    widget.add_vtk_models(liver, 4)
 
-    overlay_actors = widget.generic_overlay_renderer.GetActors()
+    overlay_actors = widget.get_overlay_renderer().GetActors()
     assert overlay_actors.GetNumberOfItems() == 1
 
-    widget.add_vtk_models(tumors, 2)
+    widget.add_vtk_models(tumors, 4)
 
-    overlay_actors = widget.generic_overlay_renderer.GetActors()
+    overlay_actors = widget.get_overlay_renderer().GetActors()
     assert overlay_actors.GetNumberOfItems() == 2
 
     # Check foreground is empty
-    foreground_actors = widget.foreground_renderer.GetActors()
+    foreground_actors = widget.get_foreground_renderer().GetActors()
     assert foreground_actors.GetNumberOfItems() == 0
     widget.close()