chore: Remove unused codepaths.

src/copick_utils/cli/segop.py

@@ -79,12 +79,6 @@ def segop(
     Note: All segmentations are converted to binary for boolean operations.
     Voxel spacing applies globally to all inputs and output.
 
-    \b
-    Single-Input Pattern Expansion (union only):
-        When providing a single -i flag with a pattern, the union operation will
-        expand the pattern within each run and merge all matching segmentations.
-        This is useful for combining multiple versions/annotations within each run.
-
     \b
     Examples:
         # Single-input union: merge all matching segmentations within each run

src/copick_utils/converters/__init__.py

@@ -1,35 +1,25 @@
 """Converters for different copick data types."""
 
-from copick_utils.converters.ellipsoid_from_picks import ellipsoid_from_picks, ellipsoid_from_picks_batch
-from copick_utils.converters.mesh_from_picks import mesh_from_picks, mesh_from_picks_batch
-from copick_utils.converters.mesh_from_segmentation import mesh_from_segmentation, mesh_from_segmentation_batch
-from copick_utils.converters.picks_from_mesh import picks_from_mesh, picks_from_mesh_batch
-from copick_utils.converters.picks_from_segmentation import picks_from_segmentation, picks_from_segmentation_batch
-from copick_utils.converters.plane_from_picks import plane_from_picks, plane_from_picks_batch
-from copick_utils.converters.segmentation_from_mesh import segmentation_from_mesh, segmentation_from_mesh_batch
-from copick_utils.converters.segmentation_from_picks import segmentation_from_picks, segmentation_from_picks_batch
-from copick_utils.converters.sphere_from_picks import sphere_from_picks, sphere_from_picks_batch
-from copick_utils.converters.surface_from_picks import surface_from_picks, surface_from_picks_batch
+from copick_utils.converters.ellipsoid_from_picks import ellipsoid_from_picks
+from copick_utils.converters.mesh_from_picks import mesh_from_picks
+from copick_utils.converters.mesh_from_segmentation import mesh_from_segmentation
+from copick_utils.converters.picks_from_mesh import picks_from_mesh
+from copick_utils.converters.picks_from_segmentation import picks_from_segmentation
+from copick_utils.converters.plane_from_picks import plane_from_picks
+from copick_utils.converters.segmentation_from_mesh import segmentation_from_mesh
+from copick_utils.converters.segmentation_from_picks import segmentation_from_picks
+from copick_utils.converters.sphere_from_picks import sphere_from_picks
+from copick_utils.converters.surface_from_picks import surface_from_picks
 
 __all__ = [
     "mesh_from_segmentation",
-    "mesh_from_segmentation_batch",
     "picks_from_segmentation",
-    "picks_from_segmentation_batch",
     "picks_from_mesh",
-    "picks_from_mesh_batch",
     "segmentation_from_mesh",
-    "segmentation_from_mesh_batch",
     "segmentation_from_picks",
-    "segmentation_from_picks_batch",
     "mesh_from_picks",
-    "mesh_from_picks_batch",
     "sphere_from_picks",
-    "sphere_from_picks_batch",
     "ellipsoid_from_picks",
-    "ellipsoid_from_picks_batch",
     "plane_from_picks",
-    "plane_from_picks_batch",
     "surface_from_picks",
-    "surface_from_picks_batch",
 ]

src/copick_utils/converters/ellipsoid_from_picks.py

@@ -7,8 +7,6 @@
 
 from copick_utils.converters.converter_common import (
     cluster,
-    create_batch_converter,
-    create_batch_worker,
     store_mesh_with_stats,
     validate_points,
 )
@@ -315,20 +313,7 @@ def create_ellipsoid_from_points(cluster_points):
         return None
 
 
-# Create worker function using common infrastructure
-_ellipsoid_from_picks_worker = create_batch_worker(ellipsoid_from_picks, "ellipsoid", min_points=6)
-
-
-# Create batch converter using common infrastructure
-ellipsoid_from_picks_batch = create_batch_converter(
-    ellipsoid_from_picks,
-    "Converting picks to ellipsoid meshes",
-    "ellipsoid",
-    min_points=6,
-)
-
 # Lazy batch converter for new architecture
-
 ellipsoid_from_picks_lazy_batch = create_lazy_batch_converter(
     converter_func=ellipsoid_from_picks,
     task_description="Converting picks to ellipsoid meshes",

src/copick_utils/converters/mesh_from_picks.py

@@ -6,8 +6,6 @@
 
 from copick_utils.converters.converter_common import (
     cluster,
-    create_batch_converter,
-    create_batch_worker,
     store_mesh_with_stats,
     validate_points,
 )
@@ -189,19 +187,6 @@ def create_mesh_from_points(cluster_points):
         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,

src/copick_utils/converters/mesh_from_segmentation.py

@@ -7,8 +7,6 @@
 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
@@ -99,19 +97,6 @@ def mesh_from_segmentation(
         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,

src/copick_utils/converters/picks_from_mesh.py

@@ -1,4 +1,4 @@
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Sequence, Tuple
+from typing import TYPE_CHECKING, Any, Dict, Optional, Sequence, Tuple
 
 import numpy as np
 import trimesh as tm
@@ -8,7 +8,7 @@
 from copick_utils.converters.lazy_converter import create_lazy_batch_converter
 
 if TYPE_CHECKING:
-    from copick.models import CopickMesh, CopickPicks, CopickRoot, CopickRun
+    from copick.models import CopickMesh, CopickPicks, CopickRun
 
 logger = get_logger(__name__)
 
@@ -459,82 +459,6 @@ def picks_from_mesh_standard(
         return None
 
 
-def picks_from_mesh_batch(
-    root: "CopickRoot",
-    mesh_object_name: str,
-    mesh_user_id: str,
-    mesh_session_id: str,
-    sampling_type: str,
-    n_points: int,
-    pick_object_name: str,
-    pick_session_id: str,
-    pick_user_id: str,
-    voxel_spacing: float,
-    tomo_type: str = "wbp",
-    min_dist: Optional[float] = None,
-    edge_dist: float = 32.0,
-    include_normals: bool = False,
-    random_orientations: bool = False,
-    seed: Optional[int] = None,
-    run_names: Optional[List[str]] = None,
-    workers: int = 8,
-) -> Dict[str, Any]:
-    """
-    Batch convert meshes to picks across multiple runs.
-
-    Args:
-        root: The copick root containing runs to process.
-        mesh_object_name: Name of the mesh object to sample from.
-        mesh_user_id: User ID of the mesh to convert.
-        mesh_session_id: Session ID of the mesh to convert.
-        sampling_type: Type of sampling ('inside', 'surface', 'outside', 'vertices').
-        n_points: Number of points to sample (ignored for 'vertices' type).
-        pick_object_name: Name of the object for created picks.
-        pick_session_id: Session ID for created picks.
-        pick_user_id: User ID for created picks.
-        voxel_spacing: Voxel spacing for coordinate scaling.
-        tomo_type: Tomogram type for getting volume dimensions. Default is 'wbp'.
-        min_dist: Minimum distance between points. If None, uses 2 * voxel_spacing.
-        edge_dist: Distance from volume edges in voxels. Default is 32.0.
-        include_normals: Include surface normals as orientations (surface sampling only). Default is False.
-        random_orientations: Generate random orientations for points. Default is False.
-        seed: Random seed for reproducible results.
-        run_names: List of run names to process. If None, processes all runs.
-        workers: Number of worker processes. Default is 8.
-
-    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=_picks_from_mesh_worker,
-        root=root,
-        runs=runs_to_process,
-        workers=workers,
-        task_desc="Converting meshes to picks",
-        mesh_object_name=mesh_object_name,
-        mesh_user_id=mesh_user_id,
-        mesh_session_id=mesh_session_id,
-        sampling_type=sampling_type,
-        n_points=n_points,
-        pick_object_name=pick_object_name,
-        pick_session_id=pick_session_id,
-        pick_user_id=pick_user_id,
-        voxel_spacing=voxel_spacing,
-        tomo_type=tomo_type,
-        min_dist=min_dist,
-        edge_dist=edge_dist,
-        include_normals=include_normals,
-        random_orientations=random_orientations,
-        seed=seed,
-    )
-
-    return results
-
-
 # Lazy batch converter for new architecture
 picks_from_mesh_lazy_batch = create_lazy_batch_converter(
     converter_func=picks_from_mesh_standard,

src/copick_utils/converters/picks_from_segmentation.py

@@ -7,10 +7,6 @@
 from skimage.morphology import ball, binary_dilation, binary_erosion
 from skimage.segmentation import watershed
 
-from copick_utils.converters.converter_common import (
-    create_batch_converter,
-    create_batch_worker,
-)
 from copick_utils.converters.lazy_converter import create_lazy_batch_converter
 
 if TYPE_CHECKING:
@@ -148,19 +144,6 @@ def picks_from_segmentation(
         return None
 
 
-# Create worker function using common infrastructure
-_picks_from_segmentation_worker = create_batch_worker(picks_from_segmentation, "picks", "segmentation", min_points=0)
-
-
-# Create batch converter using common infrastructure
-picks_from_segmentation_batch = create_batch_converter(
-    picks_from_segmentation,
-    "Converting segmentations to picks",
-    "picks",
-    "segmentation",
-    min_points=0,
-)
-
 # Lazy batch converter for new architecture
 picks_from_segmentation_lazy_batch = create_lazy_batch_converter(
     converter_func=picks_from_segmentation,

src/copick_utils/converters/plane_from_picks.py

@@ -7,8 +7,6 @@
 
 from copick_utils.converters.converter_common import (
     cluster,
-    create_batch_converter,
-    create_batch_worker,
     store_mesh_with_stats,
     validate_points,
 )
@@ -232,18 +230,6 @@ def create_plane_from_points(cluster_points):
         return None
 
 
-# Create worker function using common infrastructure
-_plane_from_picks_worker = create_batch_worker(plane_from_picks, "plane", min_points=3)
-
-
-# Create batch converter using common infrastructure
-plane_from_picks_batch = create_batch_converter(
-    plane_from_picks,
-    "Converting picks to plane meshes",
-    "plane",
-    min_points=3,
-)
-
 # Lazy batch converter for new architecture
 plane_from_picks_lazy_batch = create_lazy_batch_converter(
     converter_func=plane_from_picks,

src/copick_utils/converters/segmentation_from_mesh.py

@@ -8,10 +8,6 @@
 from copick.util.log import get_logger
 from trimesh.ray.ray_triangle import RayMeshIntersector
 
-from copick_utils.converters.converter_common import (
-    create_batch_converter,
-    create_batch_worker,
-)
 from copick_utils.converters.lazy_converter import create_lazy_batch_converter
 
 if TYPE_CHECKING:
@@ -271,19 +267,6 @@ def segmentation_from_mesh(
         return None
 
 
-# Create worker function using common infrastructure
-_segmentation_from_mesh_worker = create_batch_worker(segmentation_from_mesh, "segmentation", "mesh", min_points=0)
-
-
-# Create batch converter using common infrastructure
-segmentation_from_mesh_batch = create_batch_converter(
-    segmentation_from_mesh,
-    "Converting meshes to segmentations",
-    "segmentation",
-    "mesh",
-    min_points=0,
-)
-
 # Lazy batch converter for new architecture
 segmentation_from_mesh_lazy_batch = create_lazy_batch_converter(
     converter_func=segmentation_from_mesh,

src/copick_utils/converters/segmentation_from_picks.py

@@ -5,10 +5,6 @@
 from copick.util.log import get_logger
 from scipy.ndimage import zoom
 
-from copick_utils.converters.converter_common import (
-    create_batch_converter,
-    create_batch_worker,
-)
 from copick_utils.converters.lazy_converter import create_lazy_batch_converter
 
 if TYPE_CHECKING:
@@ -277,19 +273,6 @@ def segmentation_from_picks(
         return None
 
 
-# Create worker function using common infrastructure
-_segmentation_from_picks_worker = create_batch_worker(segmentation_from_picks, "segmentation", "picks", min_points=1)
-
-
-# Create batch converter using common infrastructure
-segmentation_from_picks_batch = create_batch_converter(
-    segmentation_from_picks,
-    "Converting picks to segmentations",
-    "segmentation",
-    "picks",
-    min_points=1,
-)
-
 # Lazy batch converter for new architecture
 segmentation_from_picks_lazy_batch = create_lazy_batch_converter(
     converter_func=segmentation_from_picks,

src/copick_utils/converters/sphere_from_picks.py

@@ -7,8 +7,6 @@
 
 from copick_utils.converters.converter_common import (
     cluster,
-    create_batch_converter,
-    create_batch_worker,
     store_mesh_with_stats,
     validate_points,
 )
@@ -287,18 +285,6 @@ def sphere_from_picks(
         return None
 
 
-# Create worker function using common infrastructure
-_sphere_from_picks_worker = create_batch_worker(sphere_from_picks, "sphere", min_points=4)
-
-
-# Create batch converter using common infrastructure
-sphere_from_picks_batch = create_batch_converter(
-    sphere_from_picks,
-    "Converting picks to sphere meshes",
-    "sphere",
-    min_points=4,
-)
-
 # Lazy batch converter for new architecture
 sphere_from_picks_lazy_batch = create_lazy_batch_converter(
     converter_func=sphere_from_picks,