copick-utils 0.6.1__py3-none-any.whl → 1.0.0__py3-none-any.whl

copick_utils/converters/mesh_from_picks.py

@@ -0,0 +1,209 @@
+from typing import TYPE_CHECKING, Any, Dict, Optional, Tuple
+
+import numpy as np
+import trimesh as tm
+from copick.util.log import get_logger
+
+from copick_utils.converters.converter_common import (
+    cluster,
+    create_batch_converter,
+    create_batch_worker,
+    store_mesh_with_stats,
+    validate_points,
+)
+from copick_utils.converters.lazy_converter import create_lazy_batch_converter
+
+if TYPE_CHECKING:
+    from copick.models import CopickMesh, CopickRun
+
+logger = get_logger(__name__)
+
+
+def convex_hull_mesh(points: np.ndarray) -> tm.Trimesh:
+    """Create a convex hull mesh from points.
+
+    Args:
+        points: Nx3 array of points.
+
+    Returns:
+        Trimesh object representing the convex hull.
+    """
+    if len(points) < 4:
+        raise ValueError("Need at least 4 points to create a convex hull")
+
+    # Use trimesh's convex hull function instead of scipy
+    hull_mesh = tm.convex.convex_hull(points)
+    return hull_mesh
+
+
+def alpha_shape_mesh(points: np.ndarray, alpha: float) -> tm.Trimesh:
+    """Create an alpha shape mesh from points.
+
+    Args:
+        points: Nx3 array of points.
+        alpha: Alpha parameter controlling the shape detail.
+
+    Returns:
+        Trimesh object representing the alpha shape.
+    """
+    logger.warning("Alpha shape mode is currently disabled, falling back to convex hull")
+    return convex_hull_mesh(points)
+
+
+def mesh_from_picks(
+    points: np.ndarray,
+    run: "CopickRun",
+    object_name: str,
+    session_id: str,
+    user_id: str,
+    mesh_type: str = "convex_hull",
+    alpha: Optional[float] = None,
+    use_clustering: bool = False,
+    clustering_method: str = "dbscan",
+    clustering_params: Optional[Dict[str, Any]] = None,
+    all_clusters: bool = False,
+    individual_meshes: bool = False,
+    session_id_template: Optional[str] = None,
+) -> Optional[Tuple["CopickMesh", Dict[str, int]]]:
+    """Create mesh(es) from pick points.
+
+    Args:
+        points: Nx3 array of pick positions.
+        run: Copick run object.
+        object_name: Name of the mesh object.
+        session_id: Session ID for the mesh.
+        user_id: User ID for the mesh.
+        mesh_type: Type of mesh to create ('convex_hull', 'alpha_shape').
+        alpha: Alpha parameter for alpha shapes (required if mesh_type='alpha_shape').
+        use_clustering: Whether to cluster points first.
+        clustering_method: Clustering method ('dbscan', 'kmeans').
+        clustering_params: Parameters for clustering.
+            e.g.
+                - {'eps': 5.0, 'min_samples': 3} for DBSCAN
+                - {'n_clusters': 3} for KMeans
+        all_clusters: If True, use all clusters; if False, use only the largest cluster.
+        individual_meshes: If True, create separate mesh objects for each mesh.
+        session_id_template: Template for individual mesh session IDs.
+
+    Returns:
+        Tuple of (CopickMesh object, stats dict) or None if creation failed.
+        Stats dict contains 'vertices_created' and 'faces_created' totals.
+    """
+    if not validate_points(points, 4, "mesh"):
+        return None
+
+    if clustering_params is None:
+        clustering_params = {}
+
+    # Define mesh creation function
+    def create_mesh_from_points(cluster_points):
+        if mesh_type == "convex_hull":
+            return convex_hull_mesh(cluster_points)
+        elif mesh_type == "alpha_shape":
+            if alpha is None:
+                raise ValueError("Alpha parameter is required for alpha shapes")
+            return alpha_shape_mesh(cluster_points, alpha)
+        else:
+            raise ValueError(f"Unknown mesh type: {mesh_type}")
+
+    # Handle clustering workflow with special mesh logic
+    if use_clustering:
+        point_clusters = cluster(
+            points,
+            clustering_method,
+            min_points_per_cluster=4,  # Meshes need at least 4 points
+            **clustering_params,
+        )
+
+        if not point_clusters:
+            logger.warning("No valid clusters found")
+            return None
+
+        logger.info(f"Found {len(point_clusters)} clusters")
+
+        if all_clusters and len(point_clusters) > 1:
+            if individual_meshes:
+                # Create separate mesh objects for each mesh
+                created_meshes = []
+                total_vertices = 0
+                total_faces = 0
+
+                for i, cluster_points in enumerate(point_clusters):
+                    try:
+                        cluster_mesh = create_mesh_from_points(cluster_points)
+
+                        # Generate session ID using template if provided
+                        if session_id_template:
+                            mesh_session_id = session_id_template.format(
+                                base_session_id=session_id,
+                                instance_id=i,
+                            )
+                        else:
+                            mesh_session_id = f"{session_id}-{i:03d}"
+
+                        copick_mesh = run.new_mesh(object_name, mesh_session_id, user_id, exist_ok=True)
+                        copick_mesh.mesh = cluster_mesh
+                        copick_mesh.store()
+                        created_meshes.append(copick_mesh)
+                        total_vertices += len(cluster_mesh.vertices)
+                        total_faces += len(cluster_mesh.faces)
+                        logger.info(
+                            f"Created individual mesh {i} with {len(cluster_mesh.vertices)} vertices",
+                        )
+                    except Exception as e:
+                        logger.error(f"Failed to create mesh {i}: {e}")
+                        continue
+
+                # Return the first mesh and total stats
+                if created_meshes:
+                    stats = {"vertices_created": total_vertices, "faces_created": total_faces}
+                    return created_meshes[0], stats
+                else:
+                    return None
+            else:
+                # Create meshes from all clusters and combine them
+                all_meshes = []
+                for cluster_points in point_clusters:
+                    cluster_mesh = create_mesh_from_points(cluster_points)
+                    all_meshes.append(cluster_mesh)
+
+                # Combine all meshes
+                combined_mesh = tm.util.concatenate(all_meshes)
+        else:
+            # Use largest cluster
+            cluster_sizes = [len(cluster) for cluster in point_clusters]
+            largest_cluster_idx = np.argmax(cluster_sizes)
+            points_to_use = point_clusters[largest_cluster_idx]
+            logger.info(f"Using largest cluster with {len(points_to_use)} points")
+
+            combined_mesh = create_mesh_from_points(points_to_use)
+    else:
+        # Use all points without clustering
+        combined_mesh = create_mesh_from_points(points)
+
+    # Store mesh and return stats
+    try:
+        return store_mesh_with_stats(run, combined_mesh, object_name, session_id, user_id, "mesh")
+    except Exception as e:
+        logger.critical(f"Error creating mesh: {e}")
+        return None
+
+
+# Create worker function using common infrastructure
+_mesh_from_picks_worker = create_batch_worker(mesh_from_picks, "mesh", "picks", min_points=4)
+
+
+# Create batch converter using common infrastructure
+mesh_from_picks_batch = create_batch_converter(
+    mesh_from_picks,
+    "Converting picks to meshes",
+    "mesh",
+    "picks",
+    min_points=4,
+)
+
+# Lazy batch converter for new architecture
+mesh_from_picks_lazy_batch = create_lazy_batch_converter(
+    converter_func=mesh_from_picks,
+    task_description="Converting picks to meshes",
+)

copick_utils/converters/mesh_from_segmentation.py

@@ -0,0 +1,119 @@
+"""Convert segmentation volumes to meshes."""
+
+from typing import TYPE_CHECKING, Dict, Optional, Tuple
+
+import numpy as np
+import trimesh as tm
+from copick.util.log import get_logger
+
+from copick_utils.converters.converter_common import (
+    create_batch_converter,
+    create_batch_worker,
+    store_mesh_with_stats,
+)
+from copick_utils.converters.lazy_converter import create_lazy_batch_converter
+
+if TYPE_CHECKING:
+    from copick.models import CopickMesh, CopickRun, CopickSegmentation
+
+logger = get_logger(__name__)
+
+
+def volume_to_mesh(volume: np.ndarray, voxel_spacing: float, level: float = 0.5, step_size: int = 1) -> tm.Trimesh:
+    """
+    Convert a binary volume to a mesh using marching cubes.
+
+    Args:
+        volume: Binary volume array with shape (z, y, x)
+        voxel_spacing: Spacing between voxels in physical units
+        level: Isosurface level for marching cubes
+        step_size: Step size for marching cubes (higher = coarser mesh)
+
+    Returns:
+        Trimesh object representing the mesh
+    """
+    from skimage import measure
+
+    # Generate mesh using marching cubes
+    verts, faces, normals, values = measure.marching_cubes(
+        volume.astype(float),
+        level=level,
+        step_size=step_size,
+        spacing=(voxel_spacing, voxel_spacing, voxel_spacing),
+    )
+
+    # Create trimesh object
+    mesh = tm.Trimesh(vertices=verts, faces=faces, vertex_normals=normals)
+
+    return mesh
+
+
+def mesh_from_segmentation(
+    segmentation: "CopickSegmentation",
+    run: "CopickRun",
+    object_name: str,
+    session_id: str,
+    user_id: str,
+    level: float = 0.5,
+    step_size: int = 1,
+) -> Optional[Tuple["CopickMesh", Dict[str, int]]]:
+    """
+    Convert a CopickSegmentation to a mesh.
+
+    Args:
+        segmentation: CopickSegmentation object to convert
+        run: CopickRun object
+        object_name: Name for the output mesh object
+        session_id: Session ID for the output mesh
+        user_id: User ID for the output mesh
+        level: Isosurface level for marching cubes
+        step_size: Step size for marching cubes
+
+    Returns:
+        Tuple of (CopickMesh object, stats dict) or None if creation failed.
+        Stats dict contains 'vertices_created' and 'faces_created'.
+    """
+    try:
+        # Load the volume from the segmentation
+        volume = segmentation.numpy()
+
+        if volume is None or volume.size == 0:
+            logger.error("Empty or invalid volume")
+            return None
+
+        # Get voxel spacing from segmentation
+        voxel_spacing = segmentation.voxel_size
+
+        # Convert volume to mesh
+        mesh = volume_to_mesh(volume, voxel_spacing, level, step_size)
+
+        if mesh.vertices.size == 0:
+            logger.error("Empty mesh generated")
+            return None
+
+        # Store mesh and return stats
+        return store_mesh_with_stats(run, mesh, object_name, session_id, user_id, "mesh")
+
+    except Exception as e:
+        logger.error(f"Error creating mesh: {e}")
+        return None
+
+
+# Create worker function using common infrastructure
+_mesh_from_segmentation_worker = create_batch_worker(mesh_from_segmentation, "mesh", "segmentation", min_points=0)
+
+
+# Create batch converter using common infrastructure
+mesh_from_segmentation_batch = create_batch_converter(
+    mesh_from_segmentation,
+    "Converting segmentations to meshes",
+    "mesh",
+    "segmentation",
+    min_points=0,
+)
+
+# Lazy batch converter for new architecture
+mesh_from_segmentation_lazy_batch = create_lazy_batch_converter(
+    converter_func=mesh_from_segmentation,
+    task_description="Converting segmentations to meshes",
+)