Integrate Curator instructions to the Crash example

examples/structural_mechanics/crash/README.md

@@ -121,6 +121,68 @@ This will install:
 - lasso-python (for LS-DYNA file parsing),
 - torch_geometric and torch_scatter (for GNN operations),
 
+## Data Preprocessing
+
+`PhysicsNeMo` has a related project to help with data processing, called
+[PhysicsNeMo-Curator](https://github.com/NVIDIA/physicsnemo-curator).
+Using `PhysicsNeMo-Curator`, crash simulation data from LS-DYNA can be processed into training-ready formats easily.
+
+Currently, this can be used to preprocess d3plot files into VTP.
+
+### Quick Start
+
+Install PhysicsNeMo-Curator following
+[these instructions](https://github.com/NVIDIA/physicsnemo-curator?tab=readme-ov-file#installation-and-usage).
+
+Process your LS-DYNA data:
+
+```bash
+export PYTHONPATH=$PYTHONPATH:examples &&
+physicsnemo-curator-etl                                    \
+    --config-dir=examples/config                           \
+    --config-name=crash_etl                                \
+    etl.source.input_dir=/data/crash_sims/                 \
+    etl.sink.output_dir=/data/crash_processed_vtp/         \
+    etl.processing.num_processes=4
+```
+
+This will process all LS-DYNA runs in `/data/crash_sims/` and output VTP files to `/data/crash_processed_vtp/`.
+
+### Input Data Structure
+
+The Curator expects your LS-DYNA data organized as:
+
+```
+crash_sims/
+├── Run100/
+│   ├── d3plot          # Required: binary mesh/displacement data
+│   └── run100.k        # Optional: part thickness definitions
+├── Run101/
+│   ├── d3plot
+│   └── run101.k
+└── ...
+```
+
+### Output Formats
+
+#### VTP Format (Recommended for this example)
+
+Produces single VTP file per run with all timesteps as displacement fields:
+
+```
+crash_processed_vtp/
+├── Run100.vtp
+├── Run101.vtp
+└── ...
+```
+
+Each VTP contains:
+- Reference coordinates at t=0
+- Displacement fields: `displacement_t0.000`, `displacement_t0.005`, etc.
+- Node thickness values
+
+This format is directly compatible with the VTP reader in this example.
+
 ## Training
 
 Training is managed via Hydra configurations located in conf/.

examples/structural_mechanics/crash/tests/test_vtp_reader.py

@@ -0,0 +1,222 @@
+# SPDX-FileCopyrightText: Copyright (c) 2023 - 2025 NVIDIA CORPORATION & AFFILIATES.
+# SPDX-FileCopyrightText: All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import tempfile
+import numpy as np
+import pyvista as pv
+import pytest
+from pathlib import Path
+
+# Import functions from vtp_reader
+import sys
+
+sys.path.insert(0, str(Path(__file__).parent.parent))
+from vtp_reader import (
+    load_vtp_file,
+    extract_mesh_connectivity_from_polydata,
+    build_edges_from_mesh_connectivity,
+)
+
+
+@pytest.fixture
+def simple_vtp_file():
+    """Create a simple VTP file for testing."""
+    # Create a simple quad mesh (2x2 grid)
+    points = np.array(
+        [
+            [0, 0, 0],
+            [1, 0, 0],
+            [0, 1, 0],
+            [1, 1, 0],
+        ],
+        dtype=np.uint8,
+    )
+
+    # Single quad cell
+    faces = np.array([4, 0, 1, 3, 2])  # quad with 4 vertices
+
+    mesh = pv.PolyData(points, faces, force_float=False)
+
+    # Add displacement fields for 3 timesteps
+    mesh.point_data["displacement_t0.000"] = np.array(
+        [
+            [0, 0, 0],
+            [0, 0, 0],
+            [0, 0, 0],
+            [0, 0, 0],
+        ],
+        dtype=np.uint8,
+    )
+
+    mesh.point_data["displacement_t0.005"] = np.array(
+        [
+            [1, 0, 0],
+            [1, 0, 0],
+            [1, 0, 0],
+            [1, 0, 0],
+        ],
+        dtype=np.uint8,
+    )
+
+    mesh.point_data["displacement_t0.010"] = np.array(
+        [
+            [2, 0, 0],
+            [2, 0, 0],
+            [2, 0, 0],
+            [2, 0, 0],
+        ],
+        dtype=np.uint8,
+    )
+
+    # Add thickness as additional point data
+    mesh.point_data["thickness"] = np.array([1, 1, 1, 1], dtype=np.uint8)
+
+    # Save to temporary file
+    with tempfile.NamedTemporaryFile(suffix=".vtp", delete=False) as f:
+        temp_path = f.name
+
+    mesh.save(temp_path)
+    yield temp_path
+
+    # Cleanup
+    Path(temp_path).unlink(missing_ok=True)
+
+
+def test_load_vtp_file_basic(simple_vtp_file):
+    """Test basic VTP file loading."""
+    pos_raw, mesh_connectivity, point_data_dict = load_vtp_file(simple_vtp_file)
+
+    # Check positions shape: (timesteps, nodes, 3)
+    assert pos_raw.shape == (3, 4, 3), f"Expected shape (3, 4, 3), got {pos_raw.shape}"
+
+    # Check mesh connectivity
+    assert len(mesh_connectivity) == 1, f"Expected 1 cell, got {len(mesh_connectivity)}"
+    assert len(mesh_connectivity[0]) == 4, (
+        f"Expected quad with 4 vertices, got {len(mesh_connectivity[0])}"
+    )
+
+    # Check point data dict contains thickness
+    assert "thickness" in point_data_dict, "Thickness not found in point_data_dict"
+    assert point_data_dict["thickness"].shape == (4,), (
+        f"Expected thickness shape (4,), got {point_data_dict['thickness'].shape}"
+    )
+
+
+def test_load_vtp_file_displacements(simple_vtp_file):
+    """Test that displacements are correctly applied."""
+    pos_raw, _, _ = load_vtp_file(simple_vtp_file)
+
+    # First timestep should be reference coords (displacement = 0)
+    expected_t0 = np.array(
+        [
+            [0, 0, 0],
+            [1, 0, 0],
+            [0, 1, 0],
+            [1, 1, 0],
+        ]
+    )
+    np.testing.assert_array_almost_equal(pos_raw[0], expected_t0, decimal=5)
+
+    # Second timestep should include displacement
+    expected_t1 = expected_t0 + np.array([[1, 0, 0]] * 4)
+    np.testing.assert_array_almost_equal(pos_raw[1], expected_t1, decimal=5)
+
+    # Third timestep
+    expected_t2 = expected_t0 + np.array([[2, 0, 0]] * 4)
+    np.testing.assert_array_almost_equal(pos_raw[2], expected_t2, decimal=5)
+
+
+def test_extract_mesh_connectivity():
+    """Test mesh connectivity extraction from PolyData."""
+    points = np.array(
+        [
+            [0, 0, 0],
+            [1, 0, 0],
+            [1, 1, 0],
+            [0, 1, 0],
+        ]
+    )
+
+    # Create a single quad
+    faces = np.array([4, 0, 1, 2, 3])
+    poly = pv.PolyData(points, faces, force_float=False)
+
+    connectivity = extract_mesh_connectivity_from_polydata(poly)
+
+    assert len(connectivity) == 1, f"Expected 1 cell, got {len(connectivity)}"
+    assert len(connectivity[0]) == 4, f"Expected 4 vertices, got {len(connectivity[0])}"
+    assert connectivity[0] == [0, 1, 2, 3], (
+        f"Expected [0, 1, 2, 3], got {connectivity[0]}"
+    )
+
+
+def test_build_edges_from_mesh_connectivity():
+    """Test edge building from mesh connectivity."""
+    # Single quad: should produce 4 edges
+    mesh_connectivity = [[0, 1, 2, 3]]
+    edges = build_edges_from_mesh_connectivity(mesh_connectivity)
+
+    expected_edges = {(0, 1), (1, 2), (2, 3), (0, 3)}
+    assert edges == expected_edges, f"Expected {expected_edges}, got {edges}"
+
+
+def test_point_data_extraction(simple_vtp_file):
+    """Test that non-displacement point data is extracted correctly."""
+    _, _, point_data_dict = load_vtp_file(simple_vtp_file)
+
+    # Should have thickness
+    assert "thickness" in point_data_dict, "Thickness not in point_data_dict"
+
+    # Should NOT have displacement fields
+    assert "displacement_t0.000" not in point_data_dict, (
+        "Displacement fields should not be in point_data_dict"
+    )
+    assert "displacement_t0.005" not in point_data_dict, (
+        "Displacement fields should not be in point_data_dict"
+    )
+
+    # Check thickness values
+    expected_thickness = np.array([1, 1, 1, 1], dtype=np.uint8)
+    np.testing.assert_array_almost_equal(
+        point_data_dict["thickness"], expected_thickness, decimal=5
+    )
+
+
+def test_missing_displacement_fields():
+    """Test that missing displacement fields raises appropriate error."""
+    # Create VTP without displacement fields
+    points = np.array([[0, 0, 0], [1, 0, 0], [0, 1, 0]])
+    faces = np.array([3, 0, 1, 2])
+    mesh = pv.PolyData(points, faces, force_float=False)
+
+    with tempfile.NamedTemporaryFile(suffix=".vtp", delete=False) as f:
+        temp_path = f.name
+
+    mesh.save(temp_path)
+
+    try:
+        with pytest.raises(ValueError, match="No displacement fields found"):
+            load_vtp_file(temp_path)
+    finally:
+        Path(temp_path).unlink(missing_ok=True)
+
+
+def test_empty_mesh_connectivity():
+    """Test edge building with empty connectivity."""
+    mesh_connectivity = []
+    edges = build_edges_from_mesh_connectivity(mesh_connectivity)
+
+    assert len(edges) == 0, f"Expected 0 edges for empty connectivity, got {len(edges)}"

examples/structural_mechanics/crash/vtp_reader.py

@@ -55,13 +55,14 @@ def extract_mesh_connectivity_from_polydata(poly: pv.PolyData):
 
 
 def load_vtp_file(vtp_path):
-    """Load positions over time and connectivity from a single VTP file.
+    """Load positions over time, connectivity, and other point data from a single VTP file.
 
     Expects displacement fields in point_data named like:
       - displacement_t0.000, displacement_t0.005, ..., displacement_t0.100
     Returns:
         pos_raw: (timesteps, num_nodes, 3) absolute positions (coords + displacement_t)
         mesh_connectivity: list[list[int]]
+        point_data_dict: dict of other point data arrays (e.g., thickness)
     """
     poly = pv.read(vtp_path)
     if not isinstance(poly, pv.PolyData):
@@ -104,7 +105,14 @@ def natural_key(name):
 
     pos_raw = np.stack(pos_list, axis=0)
     mesh_connectivity = extract_mesh_connectivity_from_polydata(poly)
-    return pos_raw, mesh_connectivity
+
+    # Extract all other point data fields (not displacement fields)
+    point_data_dict = {}
+    for name in poly.point_data.keys():
+        if not name.startswith("displacement_"):
+            point_data_dict[name] = np.asarray(poly.point_data[name])
+
+    return pos_raw, mesh_connectivity, point_data_dict
 
 
 def build_edges_from_mesh_connectivity(mesh_connectivity):
@@ -178,7 +186,7 @@ def process_vtp_data(data_dir, num_samples=2, write_vtp=False, logger=None):
         output_dir = f"./output_{os.path.splitext(os.path.basename(vtp_path))[0]}"
         os.makedirs(output_dir, exist_ok=True)
 
-        pos_raw, mesh_connectivity = load_vtp_file(vtp_path)
+        pos_raw, mesh_connectivity, point_data_dict = load_vtp_file(vtp_path)
 
         # Use unfiltered data
         filtered_pos_raw = pos_raw
@@ -200,7 +208,11 @@ def process_vtp_data(data_dir, num_samples=2, write_vtp=False, logger=None):
             write_vtp=write_vtp,
             logger=logger,
         )
-        point_data_all.append({"coords": mesh_pos_all})
+
+        # Create record with coords and all other point data fields
+        record = {"coords": mesh_pos_all}
+        record.update(point_data_dict)  # Add thickness and any other fields
+        point_data_all.append(record)
 
         processed_runs += 1
         if processed_runs >= num_samples: