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

copick_utils/logical/distance_operations.py

@@ -0,0 +1,604 @@
+"""Distance-based limiting operations for meshes, segmentations, and picks."""
+
+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, CopickPicks, CopickRun, CopickSegmentation
+
+logger = get_logger(__name__)
+
+
+def _create_distance_field_from_segmentation(segmentation_array: np.ndarray, voxel_spacing: float) -> np.ndarray:
+    """
+    Create Euclidean distance field from reference segmentation using distance transform.
+
+    Args:
+        segmentation_array: Binary reference segmentation array
+        voxel_spacing: Voxel spacing of the segmentation
+
+    Returns:
+        Distance field array with exact Euclidean distances in physical units
+    """
+    from scipy import ndimage
+
+    # Convert reference to binary
+    binary_ref = (segmentation_array > 0).astype(bool)
+
+    # Compute distance transform (distances to nearest foreground voxel)
+    # We want distances FROM the segmentation, so use the inverse
+    distance_field_voxels = ndimage.distance_transform_edt(~binary_ref)
+
+    # Convert from voxel units to physical units
+    distance_field = distance_field_voxels * voxel_spacing
+
+    return distance_field
+
+
+def _create_distance_field_from_mesh(
+    mesh: tm.Trimesh,
+    target_shape: tuple,
+    target_voxel_spacing: float,
+    mesh_voxel_spacing: float = None,
+) -> np.ndarray:
+    """
+    Create Euclidean distance field from reference mesh using voxelization and distance transform.
+
+    Args:
+        mesh: Reference trimesh object
+        target_shape: Shape of target array
+        target_voxel_spacing: Voxel spacing of target
+        mesh_voxel_spacing: Voxel spacing for mesh voxelization (defaults to target_voxel_spacing)
+
+    Returns:
+        Distance field array with exact Euclidean distances in physical units
+    """
+    if mesh_voxel_spacing is None:
+        mesh_voxel_spacing = target_voxel_spacing
+
+    # Calculate voxelization grid size based on target shape and spacing
+    physical_size = np.array(target_shape) * target_voxel_spacing
+    voxel_grid_shape = np.ceil(physical_size / mesh_voxel_spacing).astype(int)
+
+    # Voxelize the mesh
+    try:
+        # Use trimesh's voxelization
+        voxel_grid = mesh.voxelized(pitch=mesh_voxel_spacing)
+        voxelized_array = voxel_grid.matrix
+    except Exception as e:
+        logger.warning(f"Trimesh voxelization failed: {e}. Using fallback method.")
+        # Fallback: create a simple voxelization by checking mesh bounds
+        bounds = mesh.bounds
+        origin = bounds[0]
+
+        # Create coordinate grids
+        x_coords = np.arange(voxel_grid_shape[0]) * mesh_voxel_spacing + origin[0]
+        y_coords = np.arange(voxel_grid_shape[1]) * mesh_voxel_spacing + origin[1]
+        z_coords = np.arange(voxel_grid_shape[2]) * mesh_voxel_spacing + origin[2]
+
+        xx, yy, zz = np.meshgrid(x_coords, y_coords, z_coords, indexing="ij")
+        points = np.column_stack([xx.ravel(), yy.ravel(), zz.ravel()])
+
+        # Check which points are inside the mesh
+        inside = mesh.contains(points)
+        voxelized_array = inside.reshape(voxel_grid_shape)
+
+    # Resample to target resolution if needed
+    if mesh_voxel_spacing != target_voxel_spacing:
+        from scipy.ndimage import zoom
+
+        zoom_factor = mesh_voxel_spacing / target_voxel_spacing
+        voxelized_array = zoom(voxelized_array.astype(float), zoom_factor, order=0) > 0.5
+
+    # Ensure shape matches target
+    if voxelized_array.shape != target_shape:
+        # Crop or pad to match target shape
+        result = np.zeros(target_shape, dtype=bool)
+
+        # Calculate valid regions for copying
+        copy_shape = np.minimum(voxelized_array.shape, target_shape)
+        slices_src = tuple(slice(0, s) for s in copy_shape)
+        slices_dst = tuple(slice(0, s) for s in copy_shape)
+
+        result[slices_dst] = voxelized_array[slices_src]
+        voxelized_array = result
+
+    # Create distance field using distance transform
+    return _create_distance_field_from_segmentation(voxelized_array.astype(np.uint8), target_voxel_spacing)
+
+
+def limit_mesh_by_distance(
+    mesh: "CopickMesh",
+    run: "CopickRun",
+    output_object_name: str,
+    output_session_id: str,
+    output_user_id: str,
+    reference_mesh: Optional["CopickMesh"] = None,
+    reference_segmentation: Optional["CopickSegmentation"] = None,
+    max_distance: float = 100.0,
+    mesh_voxel_spacing: float = None,
+    **kwargs,
+) -> Optional[Tuple["CopickMesh", Dict[str, int]]]:
+    """
+    Limit a mesh to vertices within a certain distance of a reference surface.
+
+    Args:
+        mesh: CopickMesh to limit
+        reference_mesh: Reference CopickMesh (either this or reference_segmentation must be provided)
+        reference_segmentation: Reference CopickSegmentation
+        run: CopickRun object
+        output_object_name: Name for the output mesh
+        output_session_id: Session ID for the output mesh
+        output_user_id: User ID for the output mesh
+        max_distance: Maximum distance from reference surface
+        mesh_voxel_spacing: Voxel spacing for mesh voxelization (defaults to 10.0)
+        **kwargs: Additional keyword arguments
+
+    Returns:
+        Tuple of (CopickMesh object, stats dict) or None if operation failed.
+        Stats dict contains 'vertices_created' and 'faces_created'.
+    """
+    try:
+        if reference_mesh is None and reference_segmentation is None:
+            raise ValueError("Either reference_mesh or reference_segmentation must be provided")
+
+        # Get the target mesh
+        target_mesh = mesh.mesh
+        if target_mesh is None:
+            logger.error("Could not load target mesh data")
+            return None
+
+        # Handle Scene objects
+        if isinstance(target_mesh, tm.Scene):
+            if len(target_mesh.geometry) == 0:
+                logger.error("Target mesh is empty")
+                return None
+            target_mesh = tm.util.concatenate(list(target_mesh.geometry.values()))
+
+        # Create distance field from reference
+        # Use mesh bounds to define coordinate space
+        mesh_bounds = np.array([target_mesh.vertices.min(axis=0), target_mesh.vertices.max(axis=0)])
+
+        # Add padding for max_distance
+        padding = max_distance * 1.1
+        mesh_bounds[0] -= padding
+        mesh_bounds[1] += padding
+
+        field_voxel_spacing = mesh_voxel_spacing if mesh_voxel_spacing is not None else 10.0
+        field_size = mesh_bounds[1] - mesh_bounds[0]
+        field_shape = np.ceil(field_size / field_voxel_spacing).astype(int)
+
+        if reference_mesh is not None:
+            ref_mesh = reference_mesh.mesh
+            if ref_mesh is None:
+                logger.error("Could not load reference mesh data")
+                return None
+
+            if isinstance(ref_mesh, tm.Scene):
+                if len(ref_mesh.geometry) == 0:
+                    logger.error("Reference mesh is empty")
+                    return None
+                ref_mesh = tm.util.concatenate(list(ref_mesh.geometry.values()))
+
+            # Create distance field from mesh
+            distance_field = _create_distance_field_from_mesh(
+                ref_mesh,
+                field_shape,
+                field_voxel_spacing,
+                mesh_voxel_spacing,
+            )
+
+        else:  # reference_segmentation is not None
+            ref_seg_array = reference_segmentation.numpy()
+            if ref_seg_array is None or ref_seg_array.size == 0:
+                logger.error("Could not load reference segmentation data")
+                return None
+
+            # Convert segmentation to field coordinate space
+            seg_indices = np.array(np.where(ref_seg_array > 0)).T
+            seg_physical = seg_indices * reference_segmentation.voxel_size
+            field_coords = np.floor((seg_physical - mesh_bounds[0]) / field_voxel_spacing).astype(int)
+
+            # Create voxelized reference in field space
+            voxelized_ref = np.zeros(field_shape, dtype=bool)
+            valid_coords = (field_coords >= 0).all(axis=1) & (field_coords < field_shape).all(axis=1)
+            if np.any(valid_coords):
+                valid_field_coords = field_coords[valid_coords]
+                voxelized_ref[valid_field_coords[:, 0], valid_field_coords[:, 1], valid_field_coords[:, 2]] = True
+
+            distance_field = _create_distance_field_from_segmentation(
+                voxelized_ref.astype(np.uint8),
+                field_voxel_spacing,
+            )
+
+        # Convert mesh vertex coordinates to field indices
+        vertex_field_coords = (target_mesh.vertices - mesh_bounds[0]) / field_voxel_spacing
+        vertex_field_indices = np.floor(vertex_field_coords).astype(int)
+
+        # Check which vertices are within field bounds
+        valid_vertices = (vertex_field_indices >= 0).all(axis=1) & (vertex_field_indices < field_shape).all(axis=1)
+
+        if not np.any(valid_vertices):
+            logger.warning("No mesh vertices within distance field bounds")
+            return None
+
+        # Get distances for valid vertices
+        valid_indices = vertex_field_indices[valid_vertices]
+        vertex_distances = distance_field[valid_indices[:, 0], valid_indices[:, 1], valid_indices[:, 2]]
+
+        # Find vertices within distance threshold
+        distance_valid = vertex_distances <= max_distance
+
+        # Combine bounds validity and distance validity
+        final_valid = np.zeros(len(target_mesh.vertices), dtype=bool)
+        final_valid[valid_vertices] = distance_valid
+
+        if not np.any(final_valid):
+            logger.warning(f"No vertices within {max_distance} units of reference surface")
+            return None
+
+        # Create a new mesh with only valid vertices and their faces
+        valid_vertex_indices = np.where(final_valid)[0]
+
+        # Create a mapping from old vertex indices to new ones
+        vertex_mapping = {}
+        new_vertices = []
+        for new_idx, old_idx in enumerate(valid_vertex_indices):
+            vertex_mapping[old_idx] = new_idx
+            new_vertices.append(target_mesh.vertices[old_idx])
+
+        new_vertices = np.array(new_vertices)
+
+        # Filter faces to only include those with all vertices in the valid set
+        valid_faces = []
+        for face in target_mesh.faces:
+            if all(vertex in vertex_mapping for vertex in face):
+                new_face = [vertex_mapping[vertex] for vertex in face]
+                valid_faces.append(new_face)
+
+        if len(valid_faces) == 0:
+            logger.warning("No valid faces after distance filtering")
+            return None
+
+        new_faces = np.array(valid_faces)
+
+        # Create the limited mesh
+        limited_mesh = tm.Trimesh(vertices=new_vertices, faces=new_faces)
+
+        # Store the result
+        copick_mesh, stats = store_mesh_with_stats(
+            run=run,
+            mesh=limited_mesh,
+            object_name=output_object_name,
+            session_id=output_session_id,
+            user_id=output_user_id,
+            shape_name="distance-limited mesh",
+        )
+
+        logger.info(f"Limited mesh to {stats['vertices_created']} vertices within {max_distance} units")
+        return copick_mesh, stats
+
+    except Exception as e:
+        logger.error(f"Error limiting mesh by distance: {e}")
+        return None
+
+
+def limit_segmentation_by_distance(
+    segmentation: "CopickSegmentation",
+    run: "CopickRun",
+    output_object_name: str,
+    output_session_id: str,
+    output_user_id: str,
+    reference_mesh: Optional["CopickMesh"] = None,
+    reference_segmentation: Optional["CopickSegmentation"] = None,
+    max_distance: float = 100.0,
+    voxel_spacing: float = 10.0,
+    mesh_voxel_spacing: float = None,
+    is_multilabel: bool = False,
+    **kwargs,
+) -> Optional[Tuple["CopickSegmentation", Dict[str, int]]]:
+    """
+    Limit a segmentation to voxels within a certain distance of a reference surface.
+
+    Args:
+        segmentation: CopickSegmentation to limit
+        reference_mesh: Reference CopickMesh (either this or reference_segmentation must be provided)
+        reference_segmentation: Reference CopickSegmentation
+        run: CopickRun object
+        output_object_name: Name for the output segmentation
+        output_session_id: Session ID for the output segmentation
+        output_user_id: User ID for the output segmentation
+        max_distance: Maximum distance from reference surface
+        voxel_spacing: Voxel spacing for the output segmentation
+        mesh_voxel_spacing: Voxel spacing for mesh voxelization (defaults to target voxel spacing)
+        is_multilabel: Whether the segmentation is multilabel
+        **kwargs: Additional keyword arguments
+
+    Returns:
+        Tuple of (CopickSegmentation object, stats dict) or None if operation failed.
+        Stats dict contains 'voxels_created'.
+    """
+    try:
+        if reference_mesh is None and reference_segmentation is None:
+            raise ValueError("Either reference_mesh or reference_segmentation must be provided")
+
+        # Load target segmentation
+        seg_array = segmentation.numpy()
+        if seg_array is None or seg_array.size == 0:
+            logger.error("Could not load target segmentation data")
+            return None
+
+        # Create distance field from reference
+        if reference_mesh is not None:
+            ref_mesh = reference_mesh.mesh
+            if ref_mesh is None:
+                logger.error("Could not load reference mesh data")
+                return None
+
+            if isinstance(ref_mesh, tm.Scene):
+                if len(ref_mesh.geometry) == 0:
+                    logger.error("Reference mesh is empty")
+                    return None
+                ref_mesh = tm.util.concatenate(list(ref_mesh.geometry.values()))
+
+            # Create distance field from mesh
+            distance_field = _create_distance_field_from_mesh(
+                ref_mesh,
+                seg_array.shape,
+                segmentation.voxel_size,
+                mesh_voxel_spacing,
+            )
+
+        else:  # reference_segmentation is not None
+            ref_seg_array = reference_segmentation.numpy()
+            if ref_seg_array is None or ref_seg_array.size == 0:
+                logger.error("Could not load reference segmentation data")
+                return None
+
+            # Handle different voxel spacings between reference and target
+            if abs(reference_segmentation.voxel_size - segmentation.voxel_size) > 1e-6:
+                # Resample reference segmentation to match target
+                from scipy.ndimage import zoom
+
+                zoom_factor = reference_segmentation.voxel_size / segmentation.voxel_size
+                ref_seg_array = zoom(ref_seg_array.astype(float), zoom_factor, order=0) > 0.5
+
+                # Crop or pad to match target shape
+                if ref_seg_array.shape != seg_array.shape:
+                    result = np.zeros(seg_array.shape, dtype=bool)
+                    copy_shape = np.minimum(ref_seg_array.shape, seg_array.shape)
+                    slices = tuple(slice(0, s) for s in copy_shape)
+                    result[slices] = ref_seg_array[slices]
+                    ref_seg_array = result
+
+            # Create distance field from segmentation
+            distance_field = _create_distance_field_from_segmentation(ref_seg_array, segmentation.voxel_size)
+
+        # Apply distance threshold to create mask
+        distance_mask = distance_field <= max_distance
+
+        # Apply mask to target segmentation
+        output_array = seg_array * distance_mask
+
+        if np.sum(output_array > 0) == 0:
+            logger.warning(f"No voxels within {max_distance} units of reference surface")
+            return None
+
+        # Create output segmentation
+        output_seg = run.new_segmentation(
+            name=output_object_name,
+            user_id=output_user_id,
+            session_id=output_session_id,
+            is_multilabel=is_multilabel,
+            voxel_size=voxel_spacing,
+            exist_ok=True,
+        )
+
+        # Store the result
+        output_seg.from_numpy(output_array)
+
+        stats = {"voxels_created": int(np.sum(output_array > 0))}
+        logger.info(f"Limited segmentation to {stats['voxels_created']} voxels within {max_distance} units")
+        return output_seg, stats
+
+    except Exception as e:
+        logger.error(f"Error limiting segmentation by distance: {e}")
+        return None
+
+
+def limit_picks_by_distance(
+    picks: "CopickPicks",
+    run: "CopickRun",
+    pick_object_name: str,
+    pick_session_id: str,
+    pick_user_id: str,
+    reference_mesh: Optional["CopickMesh"] = None,
+    reference_segmentation: Optional["CopickSegmentation"] = None,
+    max_distance: float = 100.0,
+    mesh_voxel_spacing: float = None,
+    **kwargs,
+) -> Optional[Tuple["CopickPicks", Dict[str, int]]]:
+    """
+    Limit picks to those within a certain distance of a reference surface.
+
+    Args:
+        picks: CopickPicks to limit
+        reference_mesh: Reference CopickMesh (either this or reference_segmentation must be provided)
+        reference_segmentation: Reference CopickSegmentation
+        run: CopickRun object
+        pick_object_name: Name for the output picks
+        pick_session_id: Session ID for the output picks
+        pick_user_id: User ID for the output picks
+        max_distance: Maximum distance from reference surface
+        mesh_voxel_spacing: Voxel spacing for mesh voxelization (defaults to 10.0)
+        **kwargs: Additional keyword arguments
+
+    Returns:
+        Tuple of (CopickPicks object, stats dict) or None if operation failed.
+        Stats dict contains 'points_created'.
+    """
+    try:
+        if reference_mesh is None and reference_segmentation is None:
+            raise ValueError("Either reference_mesh or reference_segmentation must be provided")
+
+        # Load pick data
+        points, transforms = picks.numpy()
+        if points is None or len(points) == 0:
+            logger.error("Could not load pick data")
+            return None
+
+        pick_positions = points[:, :3]  # Use only x, y, z coordinates
+
+        # We need a coordinate space to create the distance field
+        # Use the reference segmentation's coordinate space, or create one for mesh references
+        if reference_segmentation is not None:
+            ref_seg_array = reference_segmentation.numpy()
+            if ref_seg_array is None or ref_seg_array.size == 0:
+                logger.error("Could not load reference segmentation data")
+                return None
+
+            # Use reference segmentation's coordinate space
+            field_voxel_spacing = reference_segmentation.voxel_size
+            distance_field = _create_distance_field_from_segmentation(ref_seg_array, field_voxel_spacing)
+
+            # Convert pick coordinates to voxel indices in reference segmentation space
+            pick_voxel_coords = pick_positions / field_voxel_spacing
+            pick_voxel_indices = np.floor(pick_voxel_coords).astype(int)
+
+        else:  # reference_mesh is not None
+            ref_mesh = reference_mesh.mesh
+            if ref_mesh is None:
+                logger.error("Could not load reference mesh data")
+                return None
+
+            if isinstance(ref_mesh, tm.Scene):
+                if len(ref_mesh.geometry) == 0:
+                    logger.error("Reference mesh is empty")
+                    return None
+                ref_mesh = tm.util.concatenate(list(ref_mesh.geometry.values()))
+
+            # Define coordinate space based on mesh bounds and pick positions
+            all_coords = np.vstack([ref_mesh.vertices, pick_positions])
+            coord_bounds = np.array([all_coords.min(axis=0), all_coords.max(axis=0)])
+
+            # Add padding for max_distance
+            padding = max_distance * 1.1
+            coord_bounds[0] -= padding
+            coord_bounds[1] += padding
+
+            field_voxel_spacing = mesh_voxel_spacing if mesh_voxel_spacing is not None else 10.0
+            field_size = coord_bounds[1] - coord_bounds[0]
+            field_shape = np.ceil(field_size / field_voxel_spacing).astype(int)
+
+            # Create distance field from mesh in this coordinate space
+            distance_field = _create_distance_field_from_mesh(
+                ref_mesh,
+                field_shape,
+                field_voxel_spacing,
+                mesh_voxel_spacing,
+            )
+
+            # Convert pick coordinates to voxel indices in this field space
+            pick_voxel_coords = (pick_positions - coord_bounds[0]) / field_voxel_spacing
+            pick_voxel_indices = np.floor(pick_voxel_coords).astype(int)
+
+        # Check which picks are within field bounds
+        valid_picks = (pick_voxel_indices >= 0).all(axis=1) & (pick_voxel_indices < distance_field.shape).all(axis=1)
+
+        if not np.any(valid_picks):
+            logger.warning("No picks within distance field bounds")
+            return None
+
+        # Get distances for valid picks
+        valid_indices = pick_voxel_indices[valid_picks]
+        pick_distances = distance_field[valid_indices[:, 0], valid_indices[:, 1], valid_indices[:, 2]]
+
+        # Find picks within distance threshold
+        distance_valid = pick_distances <= max_distance
+
+        # Combine bounds validity and distance validity
+        final_valid = np.zeros(len(points), dtype=bool)
+        final_valid[valid_picks] = distance_valid
+
+        if not np.any(final_valid):
+            logger.warning(f"No picks within {max_distance} units of reference surface")
+            return None
+
+        # Filter picks
+        valid_points = points[final_valid]
+        valid_transforms = transforms[final_valid] if transforms is not None else None
+
+        # Create output picks
+        output_picks = run.new_picks(pick_object_name, pick_session_id, pick_user_id, exist_ok=True)
+        output_picks.from_numpy(positions=valid_points, transforms=valid_transforms)
+        output_picks.store()
+
+        stats = {"points_created": len(valid_points)}
+        logger.info(f"Limited picks to {stats['points_created']} points within {max_distance} units")
+        return output_picks, stats
+
+    except Exception as e:
+        logger.error(f"Error limiting picks by distance: {e}")
+        return None
+
+
+# Create batch workers
+_limit_mesh_by_distance_worker = create_batch_worker(limit_mesh_by_distance, "mesh", "mesh", min_points=0)
+_limit_segmentation_by_distance_worker = create_batch_worker(
+    limit_segmentation_by_distance,
+    "segmentation",
+    "segmentation",
+    min_points=0,
+)
+_limit_picks_by_distance_worker = create_batch_worker(limit_picks_by_distance, "picks", "picks", min_points=1)
+
+# Create batch converters
+limit_mesh_by_distance_batch = create_batch_converter(
+    limit_mesh_by_distance,
+    "Limiting meshes by distance",
+    "mesh",
+    "mesh",
+    min_points=0,
+)
+
+limit_segmentation_by_distance_batch = create_batch_converter(
+    limit_segmentation_by_distance,
+    "Limiting segmentations by distance",
+    "segmentation",
+    "segmentation",
+    min_points=0,
+)
+
+limit_picks_by_distance_batch = create_batch_converter(
+    limit_picks_by_distance,
+    "Limiting picks by distance",
+    "picks",
+    "picks",
+    min_points=1,
+)
+
+# Lazy batch converters for new architecture
+limit_segmentation_by_distance_lazy_batch = create_lazy_batch_converter(
+    converter_func=limit_segmentation_by_distance,
+    task_description="Limiting segmentations by distance",
+)
+
+limit_picks_by_distance_lazy_batch = create_lazy_batch_converter(
+    converter_func=limit_picks_by_distance,
+    task_description="Limiting picks by distance",
+)
+
+limit_mesh_by_distance_lazy_batch = create_lazy_batch_converter(
+    converter_func=limit_mesh_by_distance,
+    task_description="Limiting meshes by distance",
+)