copick-utils 0.6.1__py3-none-any.whl → 1.0.1__py3-none-any.whl

copick_utils/process/filter_components.py

@@ -0,0 +1,306 @@
+"""Filter connected components in segmentations by size."""
+
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
+
+import numpy as np
+from copick.util.log import get_logger
+from scipy.ndimage import generate_binary_structure, label
+
+if TYPE_CHECKING:
+    from copick.models import CopickRoot, CopickRun, CopickSegmentation
+
+logger = get_logger(__name__)
+
+
+def _filter_components_by_size(
+    seg: np.ndarray,
+    voxel_spacing: float,
+    connectivity: str = "all",
+    min_size: Optional[float] = None,
+    max_size: Optional[float] = None,
+) -> Tuple[np.ndarray, int, int, list]:
+    """
+    Filter connected components in a segmentation by size.
+
+    Args:
+        seg: Binary mask segmentation (numpy array)
+        voxel_spacing: Voxel spacing in angstroms
+        connectivity: Connectivity for connected components (default: "all")
+                     "face" = face connectivity (6-connected in 3D)
+                     "face-edge" = face+edge connectivity (18-connected in 3D)
+                     "all" = face+edge+corner connectivity (26-connected in 3D)
+        min_size: Minimum component volume in cubic angstroms (ų) to keep (None = no minimum)
+        max_size: Maximum component volume in cubic angstroms (ų) to keep (None = no maximum)
+
+    Returns:
+        Tuple of (seg_filtered, num_kept, num_removed, component_info)
+        - seg_filtered: Filtered segmentation with only components passing size criteria
+        - num_kept: Number of components kept
+        - num_removed: Number of components removed
+        - component_info: List of dicts with info about each component
+    """
+    # Map connectivity string to numeric value
+    connectivity_map = {
+        "face": 1,
+        "face-edge": 2,
+        "all": 3,
+    }
+    connectivity_value = connectivity_map.get(connectivity, 3)
+
+    # Define connectivity structure
+    struct = generate_binary_structure(seg.ndim, connectivity_value)
+
+    # Label connected components
+    labeled_seg, num_components = label(seg, structure=struct)
+
+    # Calculate voxel volume in cubic angstroms
+    voxel_volume = voxel_spacing**3
+
+    # Initialize output
+    seg_filtered = np.zeros_like(seg, dtype=bool)
+
+    component_info = []
+    num_kept = 0
+    num_removed = 0
+
+    # Check each component
+    for component_id in range(1, num_components + 1):
+        # Extract this component
+        component_mask = labeled_seg == component_id
+        component_voxels = int(np.sum(component_mask))
+        component_volume = component_voxels * voxel_volume
+
+        # Apply size filtering
+        passes_filter = True
+        if min_size is not None and component_volume < min_size:
+            passes_filter = False
+        if max_size is not None and component_volume > max_size:
+            passes_filter = False
+
+        # Store information
+        info = {
+            "component_id": component_id,
+            "voxels": component_voxels,
+            "volume": component_volume,
+            "kept": passes_filter,
+        }
+        component_info.append(info)
+
+        # Keep or remove component
+        if passes_filter:
+            seg_filtered = np.logical_or(seg_filtered, component_mask)
+            num_kept += 1
+        else:
+            num_removed += 1
+
+    return seg_filtered.astype(np.uint8), num_kept, num_removed, component_info
+
+
+def filter_segmentation_components(
+    segmentation: "CopickSegmentation",
+    run: "CopickRun",
+    object_name: str,
+    session_id: str,
+    user_id: str,
+    voxel_spacing: float,
+    is_multilabel: bool = False,
+    connectivity: str = "all",
+    min_size: Optional[float] = None,
+    max_size: Optional[float] = None,
+    **kwargs,
+) -> Optional[Tuple["CopickSegmentation", Dict[str, int]]]:
+    """
+    Filter connected components in a segmentation by size.
+
+    Args:
+        segmentation: Input CopickSegmentation object
+        run: CopickRun object
+        object_name: Name for the output segmentation
+        session_id: Session ID for the output segmentation
+        user_id: User ID for the output segmentation
+        voxel_spacing: Voxel spacing for the output segmentation in angstroms
+        is_multilabel: Whether the segmentation is multilabel
+        connectivity: Connectivity for connected components (default: "all")
+                     "face" = 6-connected, "face-edge" = 18-connected, "all" = 26-connected
+        min_size: Minimum component volume in cubic angstroms (ų) to keep (None = no minimum)
+        max_size: Maximum component volume in cubic angstroms (ų) to keep (None = no maximum)
+        **kwargs: Additional keyword arguments
+
+    Returns:
+        Tuple of (CopickSegmentation object, stats dict) or None if operation failed.
+        Stats dict contains 'voxels_kept', 'components_kept', 'components_removed'.
+    """
+    try:
+        # Load segmentation array
+        seg_array = segmentation.numpy()
+
+        if seg_array is None:
+            logger.error("Could not load segmentation data")
+            return None
+
+        if seg_array.size == 0:
+            logger.error("Empty segmentation data")
+            return None
+
+        # Convert to boolean array
+        bool_seg = seg_array.astype(bool)
+
+        # Filter components
+        result_array, num_kept, num_removed, component_info = _filter_components_by_size(
+            bool_seg,
+            voxel_spacing=voxel_spacing,
+            connectivity=connectivity,
+            min_size=min_size,
+            max_size=max_size,
+        )
+
+        # Create output segmentation
+        output_seg = run.new_segmentation(
+            name=object_name,
+            user_id=user_id,
+            session_id=session_id,
+            is_multilabel=is_multilabel,
+            voxel_size=voxel_spacing,
+            exist_ok=True,
+        )
+
+        # Store the result
+        output_seg.from_numpy(result_array)
+
+        stats = {
+            "voxels_kept": int(np.sum(result_array)),
+            "components_kept": num_kept,
+            "components_removed": num_removed,
+            "components_total": num_kept + num_removed,
+        }
+        logger.info(
+            f"Filtered components: kept {stats['components_kept']}/{stats['components_total']}, "
+            f"removed {stats['components_removed']} ({stats['voxels_kept']} voxels remaining)",
+        )
+        return output_seg, stats
+
+    except Exception as e:
+        logger.error(f"Error filtering segmentation components: {e}")
+        return None
+
+
+def _filter_components_worker(
+    run: "CopickRun",
+    segmentation_name: str,
+    segmentation_user_id: str,
+    segmentation_session_id: str,
+    voxel_spacing: float,
+    connectivity: str,
+    min_size: Optional[float],
+    max_size: Optional[float],
+    output_user_id: str,
+    output_session_id: str,
+    is_multilabel: bool,
+    root: "CopickRoot",
+) -> Dict[str, Any]:
+    """Worker function for batch component filtering."""
+    try:
+        # Get segmentation
+        segmentations = run.get_segmentations(
+            name=segmentation_name,
+            user_id=segmentation_user_id,
+            session_id=segmentation_session_id,
+            voxel_size=voxel_spacing,
+        )
+
+        if not segmentations:
+            return {"processed": 0, "errors": [f"No segmentation found for {run.name}"]}
+
+        segmentation = segmentations[0]
+
+        # Filter components
+        result = filter_segmentation_components(
+            segmentation=segmentation,
+            run=run,
+            object_name=segmentation_name,
+            session_id=output_session_id,
+            user_id=output_user_id,
+            voxel_spacing=voxel_spacing,
+            is_multilabel=is_multilabel,
+            connectivity=connectivity,
+            min_size=min_size,
+            max_size=max_size,
+        )
+
+        if result is None:
+            return {"processed": 0, "errors": [f"Failed to filter components for {run.name}"]}
+
+        output_seg, stats = result
+
+        return {
+            "processed": 1,
+            "errors": [],
+            "voxels_kept": stats["voxels_kept"],
+            "components_kept": stats["components_kept"],
+            "components_removed": stats["components_removed"],
+            "components_total": stats["components_total"],
+        }
+
+    except Exception as e:
+        return {"processed": 0, "errors": [f"Error processing {run.name}: {e}"]}
+
+
+def filter_components_batch(
+    root: "CopickRoot",
+    segmentation_name: str,
+    segmentation_user_id: str,
+    segmentation_session_id: str,
+    voxel_spacing: float,
+    connectivity: str = "all",
+    min_size: Optional[float] = None,
+    max_size: Optional[float] = None,
+    output_user_id: str = "filter-components",
+    output_session_id: str = "filtered",
+    is_multilabel: bool = False,
+    run_names: Optional[List[str]] = None,
+    workers: int = 8,
+) -> Dict[str, Any]:
+    """
+    Batch filter connected components by size across multiple runs.
+
+    Args:
+        root: The copick root containing runs to process
+        segmentation_name: Name of the segmentation to process
+        segmentation_user_id: User ID of the segmentation to process
+        segmentation_session_id: Session ID of the segmentation to process
+        voxel_spacing: Voxel spacing in angstroms
+        connectivity: Connectivity for connected components (default: "all")
+        min_size: Minimum component volume in ų to keep (None = no minimum)
+        max_size: Maximum component volume in ų to keep (None = no maximum)
+        output_user_id: User ID for output segmentations
+        output_session_id: Session ID for output segmentations
+        is_multilabel: Whether the segmentation is multilabel
+        run_names: List of run names to process. If None, processes all runs.
+        workers: Number of worker processes
+
+    Returns:
+        Dictionary with processing results and statistics
+    """
+    from copick.ops.run import map_runs
+
+    runs_to_process = [run.name for run in root.runs] if run_names is None else run_names
+
+    results = map_runs(
+        callback=_filter_components_worker,
+        root=root,
+        runs=runs_to_process,
+        workers=workers,
+        task_desc="Filtering components by size",
+        segmentation_name=segmentation_name,
+        segmentation_user_id=segmentation_user_id,
+        segmentation_session_id=segmentation_session_id,
+        voxel_spacing=voxel_spacing,
+        connectivity=connectivity,
+        min_size=min_size,
+        max_size=max_size,
+        output_user_id=output_user_id,
+        output_session_id=output_session_id,
+        is_multilabel=is_multilabel,
+    )
+
+    return results

copick_utils/process/hull.py

@@ -0,0 +1,106 @@
+"""Compute various hull operations on meshes."""
+from typing import TYPE_CHECKING, Dict, Optional, Tuple
+
+import trimesh as tm
+from copick.util.log import get_logger
+
+from copick_utils.converters.converter_common import create_batch_converter, store_mesh_with_stats
+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 compute_hull(
+    mesh: "CopickMesh",
+    run: "CopickRun",
+    object_name: str,
+    session_id: str,
+    user_id: str,
+    hull_type: str = "convex",
+    **kwargs,
+) -> Optional[Tuple["CopickMesh", Dict[str, int]]]:
+    """
+    Compute hull of a CopickMesh object.
+
+    Args:
+        mesh: CopickMesh object to compute hull for
+        run: CopickRun object
+        object_name: Name for the output mesh
+        session_id: Session ID for the output mesh
+        user_id: User ID for the output mesh
+        hull_type: Type of hull to compute ('convex')
+        **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:
+        # Get trimesh object
+        trimesh_obj = mesh.mesh
+
+        if trimesh_obj is None:
+            logger.error("Could not load mesh data")
+            return None
+
+        # Ensure we have proper Trimesh object
+        if isinstance(trimesh_obj, tm.Scene):
+            if len(trimesh_obj.geometry) == 0:
+                logger.error("Mesh is empty")
+                return None
+            trimesh_obj = trimesh_obj.to_mesh()
+
+        if not isinstance(trimesh_obj, tm.Trimesh):
+            logger.error(f"Expected Trimesh object, got {type(trimesh_obj)}")
+            return None
+
+        # Compute hull based on type
+        if hull_type == "convex":
+            hull_mesh = trimesh_obj.convex_hull
+            shape_name = "convex hull"
+        else:
+            raise ValueError(f"Unknown hull type: {hull_type}")
+
+        if hull_mesh is None:
+            logger.error(f"Failed to compute {hull_type} hull")
+            return None
+
+        if hull_mesh.vertices.shape[0] == 0:
+            logger.error(f"{hull_type.capitalize()} hull resulted in empty mesh")
+            return None
+
+        # Store the result
+        copick_mesh, stats = store_mesh_with_stats(
+            run=run,
+            mesh=hull_mesh,
+            object_name=object_name,
+            session_id=session_id,
+            user_id=user_id,
+            shape_name=shape_name,
+        )
+
+        logger.info(f"Created {hull_type} hull mesh with {stats['vertices_created']} vertices")
+        return copick_mesh, stats
+
+    except Exception as e:
+        logger.error(f"Error computing {hull_type} hull: {e}")
+        return None
+
+
+# Create batch converter
+hull_from_mesh_batch = create_batch_converter(
+    compute_hull,
+    "Computing hull from meshes",
+    "mesh",
+    "mesh",
+    min_points=0,
+)
+
+# Lazy batch converter for new architecture
+hull_lazy_batch = create_lazy_batch_converter(
+    converter_func=compute_hull,
+    task_description="Computing convex hulls",
+)