feat: Meshes

.github/workflows/ci.yml

@@ -22,28 +22,52 @@ jobs:
       - run: pipx run check-manifest
 
   lint:
-    runs-on: ubuntu-latest
+    # We lint on Windows so we can lint wx code.
+    runs-on: windows-latest
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
           python-version: "3.13"
-      - uses: tox-dev/action-pre-commit-uv@v1
-        with:
-          extra_args: --all-files --verbose
+      - run: uvx pre-commit run --all-files --verbose
 
   test:
-    name: test ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.gfx }}
+    name: test ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.gfx }} ${{ matrix.canvas }}
     runs-on: ${{ matrix.os }}
-    env:
-      UV_FROZEN: 1
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.13"]
         gfx: [pygfx, vispy]
+        canvas: [pyqt, jupyter, wx]
+        exclude:
+          # glfw.GLFWError: (65545) b'NSGL: Failed to find a suitable pixel format'
+          # (Under the hood GLFW gives vispy the OpenGL context.)
+          - os: macos-latest
+            canvas: jupyter
+            gfx: vispy
+          # wxpython does not build wheels for ubuntu or macos-latest py3.10
+          - os: ubuntu-latest
+            canvas: wx
+          - os: macos-latest
+            canvas: wx
+            python-version: "3.10"
+          # FIXME: On CI: AttributeError: 'Shared' object has no attribute '_device'. Did you mean: 'device'?
+          # Related to pygfx v0.13.0
+          # Tests pass locally
+          - os: windows-latest
+            gfx: pygfx
+        include:
+          - python-version: "3.11"
+            gfx: pygfx
+            canvas: pyqt
+            os: ubuntu-latest
+          - python-version: "3.12"
+            gfx: pygfx
+            canvas: pyqt
+            os: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v4
@@ -61,7 +85,7 @@ jobs:
           sudo apt install -y libegl1-mesa-dev libgl1-mesa-dri libxcb-xfixes0-dev mesa-vulkan-drivers
 
       - name: Install dependencies
-        run: uv sync --no-dev --group test --extra ${{ matrix.gfx }} ${{ matrix.python-version != '3.10' && '--extra imgui' || '' }}
+        run: uv sync --no-dev --group test --extra ${{ matrix.gfx }} --extra ${{matrix.canvas}} ${{ matrix.python-version != '3.10' && '--extra imgui' || '' }} ${{ matrix.canvas == 'pyqt' && '--group testqt' || '' }}
 
       - name: Test
         shell: bash
@@ -70,7 +94,7 @@ jobs:
       - name: Upload coverage
         uses: actions/upload-artifact@v4
         with:
-          name: covreport-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.gfx }}
+          name: covreport-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.gfx }}-${{ matrix.canvas }}
           path: ./.coverage*
           include-hidden-files: true
 

.gitignore

@@ -109,3 +109,5 @@ ENV/
 # IDE settings
 .vscode/
 .idea/
+
+uv.lock

.pre-commit-config.yaml

@@ -27,26 +27,26 @@ repos:
         language: system
         types_or: [python, pyi]
         require_serial: true
-        entry: uv run ruff format --force-exclude
+        entry: uv run --active ruff format --force-exclude
       - id: ruff-check
         name: ruff check
         language: system
         types_or: [python, pyi]
         require_serial: true
-        entry: uv run ruff check --force-exclude
+        entry: uv run --active ruff check --force-exclude
         args: [--output-format=full, --show-fixes, --exit-non-zero-on-fix]
       - id: mypy
         name: mypy
         language: system
         types_or: [python, pyi]
         require_serial: true
-        entry: uv run mypy
+        entry: uv run --active mypy
       - id: pyright
         name: pyright
         language: system
         types_or: [python, pyi]
         require_serial: true
-        entry: uv run pyright
+        entry: uv run --active pyright
 
   - repo: https://github.com/crate-ci/typos
     rev: v1.34.0

examples/basic_mesh.py

@@ -0,0 +1,92 @@
+import cmap
+import numpy as np
+
+import scenex as snx
+from scenex.app.events import (
+    Event,
+    MouseButton,
+    MouseMoveEvent,
+    MousePressEvent,
+)
+from scenex.utils.controllers import PanZoomController
+
+
+# Create a more complex mesh - a grid of vertices
+def create_grid_mesh(
+    size: int = 10, spacing: float = 0.2
+) -> tuple[np.ndarray, np.ndarray]:
+    """Create a grid mesh with given size and spacing."""
+    vertices = []
+    faces = []
+
+    # Create vertices in a grid
+    for i in range(size):
+        for j in range(size):
+            x = i * spacing
+            y = j * spacing
+            z = 0.0
+            vertices.append([x, y, z])
+
+    # Create triangular faces
+    for i in range(size - 1):
+        for j in range(size - 1):
+            # Current vertex indices
+            v0 = i * size + j
+            v1 = i * size + (j + 1)
+            v2 = (i + 1) * size + j
+            v3 = (i + 1) * size + (j + 1)
+
+            # Two triangles per grid square
+            faces.append([v0, v1, v2])
+            faces.append([v1, v3, v2])
+
+    return np.array(vertices), np.array(faces)
+
+
+# Create the mesh
+original_vertices, original_faces = create_grid_mesh(size=15, spacing=0.15)
+
+mesh = snx.Mesh(
+    vertices=original_vertices, faces=original_faces, color=cmap.Color("cyan")
+)
+
+view = snx.View(
+    scene=snx.Scene(children=[mesh]),
+    camera=snx.Camera(controller=PanZoomController(), interactive=True),
+)
+
+
+def event_filter(event: Event) -> bool:
+    """Interactive mesh manipulation based on mouse events."""
+    if isinstance(event, MouseMoveEvent):
+        if intersections := event.world_ray.intersections(view.scene):
+            # Find mesh intersection
+            for node, _distance in intersections:
+                if isinstance(node, snx.Mesh):
+                    # Remove the intersected face
+                    indices = [i for i, _d in node.intersecting_faces(event.world_ray)]
+                    node.faces = np.delete(node.faces, indices, axis=0)
+            return True
+    elif isinstance(event, MousePressEvent):
+        if event.buttons & MouseButton.LEFT:
+            # Reset the mesh on click
+            mesh.vertices = original_vertices.copy()
+            mesh.faces = original_faces.copy()
+            return True
+
+    return False
+
+
+# Set up the event filter
+view.set_event_filter(event_filter)
+
+# Show and position camera
+snx.use("vispy")
+snx.show(view)
+
+print("Interactive Mesh Demo:")
+print("- Move mouse over mesh to delete intersected faces")
+print("- Left click to reset all faces")
+print("- Use mouse to pan/zoom the camera")
+
+snx.run()

examples/basic_scene.py

@@ -2,6 +2,7 @@
 import numpy as np
 
 import scenex as snx
+from scenex.utils.controllers import PanZoomController
 
 try:
     from scenex.imgui import add_imgui_controls
@@ -28,6 +29,7 @@
             ),
         ]
     ),
+    camera=snx.Camera(controller=PanZoomController(), interactive=True),
 )
 
 # example of adding an object to a scene
@@ -41,6 +43,7 @@
 # snx.use("vispy")
 
 snx.show(view)
+
 if add_imgui_controls is not None:
     add_imgui_controls(view)
 snx.run()

examples/basic_volume.py

@@ -1,6 +1,9 @@
 import numpy as np
 
 import scenex as snx
+from scenex.model._transform import Transform
+from scenex.utils import projections
+from scenex.utils.controllers import OrbitController
 
 try:
     from imageio.v2 import volread
@@ -16,11 +19,28 @@
             snx.Volume(
                 data=data,
                 clims=(data.min(), data.max()),
-            ),
+            )
         ]
     ),
-    camera=snx.Camera(type="perspective"),
+    camera=snx.Camera(interactive=True),
 )
 
+snx.use("vispy")
 snx.show(view)
+
+# Orbit around the center of the volume
+orbit_center = np.mean(np.asarray(view.scene.bounding_box), axis=0)
+
+# Place the camera along the x axis, looking at the orbit center
+view.camera.transform = Transform().translated(orbit_center).translated((300, 0, 0))
+view.camera.look_at(orbit_center, up=(0, 0, 1))
+# Perspective projection for 3D
+view.camera.projection = projections.perspective(
+    fov=70,
+    near=1,
+    far=1_000_000,  # Just need something big
+)
+view.camera.set_event_filter(OrbitController(orbit_center))
+
+
 snx.run()

examples/blending.py

@@ -0,0 +1,96 @@
+"""An example demonstrating different blend modes.
+
+Unaltered, each channel of the volume is blended additively, resulting in transparency.
+
+By clicking on the volume, the blend mode will alternate to an opaque strategy. In this
+case, fragments written by the nuclei channel will always be visible over fragments
+written by the membranes channel (because its draw order is higher).
+"""
+
+import cmap
+import numpy as np
+
+import scenex as snx
+import scenex.model
+from scenex.app.events import Event, MousePressEvent
+from scenex.model._transform import Transform
+from scenex.utils import projections
+from scenex.utils.controllers import OrbitController
+
+try:
+    from imageio.v2 import volread
+
+    url = "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/cells3d.tif"
+    data = np.asarray(volread(url)).astype(np.uint16)[:, :, :, :]
+except ImportError:
+    data = np.random.randint(0, 2, (3, 2, 3, 3)).astype(np.uint16)
+
+data1 = data[:, 0, :, :]
+volume1 = snx.Volume(
+    data=data1,
+    cmap=cmap.Colormap("green"),
+    blending=scenex.model.BlendMode.ADDITIVE,
+    clims=(data1.min(), data1.max()),
+    opacity=0.7,
+    order=1,
+    name="Cell membranes",
+    interactive=True,
+)
+data2 = data[:, 1, :, :]
+volume2 = snx.Volume(
+    data=data2,
+    blending=scenex.model.BlendMode.ADDITIVE,
+    cmap=cmap.Colormap("magenta"),
+    clims=(data2.min(), data2.max()),
+    opacity=0.7,
+    order=2,
+    name="Cell nuclei",
+    interactive=True,
+    transform=Transform().translated((0, 0, 30)),
+)
+
+view = snx.View(
+    scene=snx.Scene(
+        children=[volume1, volume2],
+        interactive=True,
+    ),
+    camera=snx.Camera(interactive=True),
+)
+
+blend_modes = list(scenex.model.BlendMode)
+
+
+def change_blend_mode(event: Event, node: snx.Node) -> bool:
+    """Change the blend mode of a volume when it is clicked."""
+    if isinstance(event, MousePressEvent):
+        idx = blend_modes.index(node.blending)
+        next_idx = (idx + 1) % len(blend_modes)
+
+        print(f"Changing blend mode to {blend_modes[next_idx]}")
+
+        volume1.blending = blend_modes[next_idx]
+        volume2.blending = blend_modes[next_idx]
+    return False
+
+
+volume1.set_event_filter(change_blend_mode)
+
+
+snx.use("vispy")
+snx.show(view)
+
+# Orbit around the center of the volume
+orbit_center = np.mean(np.asarray(view.scene.bounding_box), axis=0)
+
+# Place the camera along the x axis, looking at the orbit center
+view.camera.transform = Transform().translated(orbit_center).translated((300, 0, 0))
+view.camera.look_at(orbit_center, up=(0, 0, 1))
+# Perspective projection for 3D
+view.camera.projection = projections.perspective(
+    fov=70,
+    near=1,
+    far=1_000_000,  # Just need something big
+)
+view.camera.set_event_filter(OrbitController(orbit_center))
+
+snx.run()