Performance: use ImageData when grid has uniform axis spacing

.github/workflows/docker.yml

@@ -15,20 +15,20 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' || github.event_name == 'workflow_dispatch' || ( github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository )
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Log into the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: token
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Extract metadata for the Docker image
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
       - name: Build and push the Docker image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: .
           file: Dockerfile

.github/workflows/release.yml

@@ -6,9 +6,9 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.9"
       - name: Install dependencies

.github/workflows/test.yml

@@ -16,9 +16,9 @@ jobs:
       matrix:
         python-version: [3.9, "3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -36,11 +36,11 @@ jobs:
       #   run: |
       #     make doctest
       - name: Stash coverage
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage.xml
           path: coverage.xml
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: coverage.xml

pvxarray/io.py

@@ -34,7 +34,8 @@ def image_data_to_dataset(mesh):
     def gen_coords(i):
         coords = (
             np.cumsum(np.insert(np.full(mesh.dimensions[i] - 1, mesh.spacing[i]), 0, 0))
-            + mesh.origin[i]  # noqa: W503
+            + mesh.origin[i]
+            + mesh.offset[i]  # noqa: W503
         )
         return coords
 

pvxarray/rectilinear.py

@@ -1,6 +1,7 @@
 from typing import Dict, Optional
 import warnings
 
+import numpy as np
 import pyvista as pv
 
 from pvxarray.errors import DataCopyWarning
@@ -14,20 +15,47 @@ def mesh(
     order: Optional[str] = "C",
     component: Optional[str] = None,
     scales: Optional[Dict] = None,
-):
+) -> pv.RectilinearGrid | pv.ImageData:
     if order is None:
         order = "C"
-    self._mesh = pv.RectilinearGrid()
+
     ndim = 3 - (x, y, z).count(None)
     if ndim < 1:
         raise ValueError("You must specify at least one dimension as X, Y, or Z.")
     # Construct the mesh
     if x is not None:
-        self._mesh.x = self._get_array(x, scale=(scales and scales.get(x)) or 1)
+        xx = self._get_array(x, scale=(scales and scales.get(x)) or 1)
+    else:
+        xx = np.array([0.0])
     if y is not None:
-        self._mesh.y = self._get_array(y, scale=(scales and scales.get(y)) or 1)
+        yy = self._get_array(y, scale=(scales and scales.get(y)) or 1)
+    else:
+        yy = np.array([0.0])
     if z is not None:
-        self._mesh.z = self._get_array(z, scale=(scales and scales.get(z)) or 1)
+        zz = self._get_array(z, scale=(scales and scales.get(z)) or 1)
+    else:
+        zz = np.array([0.0])
+
+    dx = np.diff(xx)
+    dy = np.diff(yy)
+    dz = np.diff(zz)
+
+    ddx = dx[0] if len(dx) and dx[0] > 0 else 1.0
+    ddy = dy[0] if len(dy) and dy[0] > 0 else 1.0
+    ddz = dz[0] if len(dz) and dz[0] > 0 else 1.0
+
+    if np.allclose(dx, ddx) and np.allclose(dy, ddy) and np.allclose(dz, ddz):
+        self._mesh = pv.ImageData(
+            origin=(xx[0], yy[0], zz[0]),
+            spacing=(ddx, ddy, ddz),
+            dimensions=(len(xx), len(yy), len(zz)),
+        )
+    else:
+        self._mesh = pv.RectilinearGrid()
+        self._mesh.x = xx
+        self._mesh.y = yy
+        self._mesh.z = zz
+
     # Handle data values
     values = self.data
     values_dim = values.ndim

tests/test_dataset_io.py

@@ -45,12 +45,14 @@ def test_read_vtr(vtr_path):
 
 def test_read_vti(vti_path):
     ds = xr.open_dataset(vti_path, engine="pyvista")
-    truth = ImageData(vti_path).cast_to_rectilinear_grid()
+    truth = ImageData(vti_path)
+    truth_r = truth.cast_to_rectilinear_grid()
     assert np.allclose(ds["RTData"].values.ravel(), truth["RTData"].ravel())
-    assert np.allclose(ds["x"].values, truth.x)
-    assert np.allclose(ds["y"].values, truth.y)
-    assert np.allclose(ds["z"].values, truth.z)
-    assert ds["RTData"].pyvista.mesh(x="x", y="y", z="z") == truth
+    assert np.allclose(ds["x"].values, truth_r.x)
+    assert np.allclose(ds["y"].values, truth_r.y)
+    assert np.allclose(ds["z"].values, truth_r.z)
+    im = ds["RTData"].pyvista.mesh(x="x", y="y", z="z")
+    assert im.cast_to_rectilinear_grid() == truth_r
 
 
 def test_read_vts(vts_path):
@@ -89,10 +91,8 @@ def test_convert_vti(vti_path):
     mesh = ds["RTData"].pyvista.mesh(x="x", y="y", z="z")
     assert np.array_equal(ds["RTData"].values.ravel(), truth["RTData"].ravel())
     assert np.may_share_memory(ds["RTData"].values.ravel(), truth["RTData"].ravel())
-    assert np.array_equal(mesh.x, truth_r.x)
-    assert np.array_equal(mesh.y, truth_r.y)
-    assert np.array_equal(mesh.z, truth_r.z)
-    assert mesh == truth_r
+    # assert np.array_equal(mesh.points, truth_r.points)
+    assert mesh.cast_to_rectilinear_grid() == truth_r
 
 
 def test_convert_vts(vts_path):