copick-utils 0.6.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

copick_utils/__init__.py

@@ -1,3 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Kyle Harrington <czi@kyleharrington.com>
 #
 # SPDX-License-Identifier: MIT
+__version__ = "1.0.0"

copick_utils/cli/__init__.py

@@ -0,0 +1,33 @@
+"""CLI commands for copick-utils."""
+
+from .conversion_commands import (
+    mesh2picks,
+    mesh2seg,
+    picks2ellipsoid,
+    picks2mesh,
+    picks2plane,
+    picks2seg,
+    picks2sphere,
+    picks2surface,
+    seg2mesh,
+    seg2picks,
+)
+from .processing_commands import fit_spline, separate_components, skeletonize
+
+__all__ = [
+    # Conversion commands
+    "picks2seg",
+    "seg2picks",
+    "mesh2seg",
+    "seg2mesh",
+    "picks2mesh",
+    "mesh2picks",
+    "picks2surface",
+    "picks2plane",
+    "picks2sphere",
+    "picks2ellipsoid",
+    # Processing commands
+    "separate_components",
+    "skeletonize",
+    "fit_spline",
+]

copick_utils/cli/clipmesh.py

@@ -0,0 +1,161 @@
+import click
+import copick
+from click_option_group import optgroup
+from copick.cli.util import add_config_option, add_debug_option
+from copick.util.log import get_logger
+from copick.util.uri import parse_copick_uri
+
+from copick_utils.cli.util import (
+    add_distance_options,
+    add_input_option,
+    add_output_option,
+    add_reference_mesh_option,
+    add_reference_seg_option,
+    add_workers_option,
+)
+from copick_utils.util.config_models import create_reference_config
+
+
+@click.command(
+    context_settings={"show_default": True},
+    short_help="Limit meshes to vertices within distance of a reference surface.",
+    no_args_is_help=True,
+)
+@add_config_option
+@optgroup.group("\nInput Options", help="Options related to the input meshes.")
+@optgroup.option(
+    "--run-names",
+    "-r",
+    multiple=True,
+    help="Specific run names to process (default: all runs).",
+)
+@add_input_option("mesh")
+@optgroup.group("\nReference Options", help="Options for reference surface (provide either mesh or segmentation).")
+@add_reference_mesh_option(required=False)
+@add_reference_seg_option(required=False)
+@optgroup.group("\nTool Options", help="Options related to this tool.")
+@add_distance_options
+@add_workers_option
+@optgroup.group("\nOutput Options", help="Options related to output meshes.")
+@add_output_option("mesh", default_tool="clipmesh")
+@optgroup.option(
+    "--individual-meshes/--no-individual-meshes",
+    "-im",
+    is_flag=True,
+    default=False,
+    help="Create individual meshes for each instance (enables {instance_id} placeholder).",
+)
+@add_debug_option
+def clipmesh(
+    config,
+    run_names,
+    input_uri,
+    ref_mesh_uri,
+    ref_seg_uri,
+    max_distance,
+    mesh_voxel_spacing,
+    workers,
+    output_uri,
+    individual_meshes,
+    debug,
+):
+    """
+    Limit meshes to vertices within a certain distance of a reference surface.
+
+    \b
+    URI Format:
+        Meshes: object_name:user_id/session_id
+        Segmentations: name:user_id/session_id@voxel_spacing
+
+    \b
+    The reference surface can be either a mesh or a segmentation.
+    Only mesh vertices within the specified distance will be kept.
+
+    \b
+    Examples:
+        # Limit mesh to vertices near reference mesh surface
+        copick logical clipmesh -i "membrane:user1/full-001" -rm "boundary:user1/boundary-001" -o "membrane:clipmesh/limited-001" --max-distance 50.0
+
+        # Limit using segmentation as reference
+        copick logical clipmesh -i "membrane:user1/full-001" -rs "mask:user1/mask-001@10.0" -o "membrane:clipmesh/limited-001" --max-distance 100.0
+    """
+    from copick_utils.logical.distance_operations import limit_mesh_by_distance_lazy_batch
+
+    logger = get_logger(__name__, debug=debug)
+
+    # Validate that exactly one reference type is provided
+    if not ref_mesh_uri and not ref_seg_uri:
+        raise click.BadParameter("Must provide either --ref-mesh or --ref-seg")
+    if ref_mesh_uri and ref_seg_uri:
+        raise click.BadParameter("Cannot provide both --ref-mesh and --ref-seg")
+
+    root = copick.from_file(config)
+    run_names_list = list(run_names) if run_names else None
+
+    # Determine reference type and URI
+    reference_uri = ref_mesh_uri or ref_seg_uri
+    reference_type = "mesh" if ref_mesh_uri else "segmentation"
+
+    # Create config directly from URIs with additional params for distance operations
+    try:
+        task_config = create_reference_config(
+            input_uri=input_uri,
+            input_type="mesh",
+            output_uri=output_uri,
+            output_type="mesh",
+            reference_uri=reference_uri,
+            reference_type=reference_type,
+            additional_params={"max_distance": max_distance, "mesh_voxel_spacing": mesh_voxel_spacing},
+            command_name="clipmesh",
+        )
+    except ValueError as e:
+        raise click.BadParameter(str(e)) from e
+
+    # Extract parameters for logging
+    input_params = parse_copick_uri(input_uri, "mesh")
+    output_params = parse_copick_uri(output_uri, "mesh")
+    ref_params = parse_copick_uri(reference_uri, reference_type)
+
+    logger.info(f"Limiting meshes by distance for object '{input_params['object_name']}'")
+    logger.info(f"Source mesh pattern: {input_params['user_id']}/{input_params['session_id']}")
+    if reference_type == "mesh":
+        logger.info(f"Reference mesh: {ref_params['object_name']} ({ref_params['user_id']}/{ref_params['session_id']})")
+    else:
+        logger.info(
+            f"Reference segmentation: {ref_params['name']} ({ref_params['user_id']}/{ref_params['session_id']})",
+        )
+    logger.info(f"Maximum distance: {max_distance} angstroms")
+    logger.info(
+        f"Target mesh template: {output_params['object_name']} ({output_params['user_id']}/{output_params['session_id']})",
+    )
+
+    # Parallel discovery and processing - no sequential bottleneck!
+    results = limit_mesh_by_distance_lazy_batch(
+        root=root,
+        config=task_config,
+        run_names=run_names_list,
+        workers=workers,
+    )
+
+    successful = sum(1 for result in results.values() if result and result.get("processed", 0) > 0)
+    total_vertices = sum(result.get("vertices_created", 0) for result in results.values() if result)
+    total_faces = sum(result.get("faces_created", 0) for result in results.values() if result)
+    total_processed = sum(result.get("processed", 0) for result in results.values() if result)
+
+    # Collect all errors
+    all_errors = []
+    for result in results.values():
+        if result and result.get("errors"):
+            all_errors.extend(result["errors"])
+
+    logger.info(f"Completed: {successful}/{len(results)} runs processed successfully")
+    logger.info(f"Total distance limiting operations completed: {total_processed}")
+    logger.info(f"Total vertices created: {total_vertices}")
+    logger.info(f"Total faces created: {total_faces}")
+
+    if all_errors:
+        logger.warning(f"Encountered {len(all_errors)} errors during processing")
+        for error in all_errors[:5]:  # Show first 5 errors
+            logger.warning(f"  - {error}")
+        if len(all_errors) > 5:
+            logger.warning(f"  ... and {len(all_errors) - 5} more errors")

copick_utils/cli/clippicks.py

@@ -0,0 +1,154 @@
+"""CLI commands for distance-based limiting operations."""
+
+import click
+import copick
+from click_option_group import optgroup
+from copick.cli.util import add_config_option, add_debug_option
+from copick.util.log import get_logger
+from copick.util.uri import parse_copick_uri
+
+from copick_utils.cli.util import (
+    add_distance_options,
+    add_input_option,
+    add_output_option,
+    add_reference_mesh_option,
+    add_reference_seg_option,
+    add_workers_option,
+)
+from copick_utils.util.config_models import create_reference_config
+
+
+@click.command(
+    context_settings={"show_default": True},
+    short_help="Limit picks to those within distance of a reference surface.",
+    no_args_is_help=True,
+)
+@add_config_option
+@optgroup.group("\nInput Options", help="Options related to the input picks.")
+@optgroup.option(
+    "--run-names",
+    "-r",
+    multiple=True,
+    help="Specific run names to process (default: all runs).",
+)
+@add_input_option("picks")
+@optgroup.group("\nReference Options", help="Options for reference surface (provide either mesh or segmentation).")
+@add_reference_mesh_option(required=False)
+@add_reference_seg_option(required=False)
+@optgroup.group("\nTool Options", help="Options related to this tool.")
+@add_distance_options
+@add_workers_option
+@optgroup.group("\nOutput Options", help="Options related to output picks.")
+@add_output_option("picks", default_tool="clippicks")
+@add_debug_option
+def clippicks(
+    config,
+    run_names,
+    input_uri,
+    ref_mesh_uri,
+    ref_seg_uri,
+    max_distance,
+    mesh_voxel_spacing,
+    workers,
+    output_uri,
+    debug,
+):
+    """
+    Limit picks to those within a certain distance of a reference surface.
+
+    \b
+    URI Format:
+        Picks: object_name:user_id/session_id
+        Meshes: object_name:user_id/session_id
+        Segmentations: name:user_id/session_id@voxel_spacing
+
+    \b
+    The reference surface can be either a mesh or a segmentation.
+    Only picks within the specified distance will be kept.
+
+    \b
+    Examples:
+        # Limit picks to those near reference mesh surface
+        copick logical clippicks -i "ribosome:user1/all-001" -rm "boundary:user1/boundary-001" -o "ribosome:clippicks/limited-001" --max-distance 50.0
+
+        # Limit using segmentation as reference
+        copick logical clippicks -i "ribosome:user1/all-001" -rs "mask:user1/mask-001@10.0" -o "ribosome:clippicks/limited-001" --max-distance 100.0
+    """
+    from copick_utils.logical.distance_operations import limit_picks_by_distance_lazy_batch
+
+    logger = get_logger(__name__, debug=debug)
+
+    # Validate that exactly one reference type is provided
+    if not ref_mesh_uri and not ref_seg_uri:
+        raise click.BadParameter("Must provide either --ref-mesh or --ref-seg")
+    if ref_mesh_uri and ref_seg_uri:
+        raise click.BadParameter("Cannot provide both --ref-mesh and --ref-seg")
+
+    root = copick.from_file(config)
+    run_names_list = list(run_names) if run_names else None
+
+    # Determine reference type and URI
+    reference_uri = ref_mesh_uri or ref_seg_uri
+    reference_type = "mesh" if ref_mesh_uri else "segmentation"
+
+    # Create config directly from URIs with additional params
+    try:
+        task_config = create_reference_config(
+            input_uri=input_uri,
+            input_type="picks",
+            output_uri=output_uri,
+            output_type="picks",
+            reference_uri=reference_uri,
+            reference_type=reference_type,
+            additional_params={"max_distance": max_distance, "mesh_voxel_spacing": mesh_voxel_spacing},
+            command_name="clippicks",
+        )
+    except ValueError as e:
+        raise click.BadParameter(str(e)) from e
+
+    # Extract parameters for logging
+    input_params = parse_copick_uri(input_uri, "picks")
+    output_params = parse_copick_uri(output_uri, "picks")
+    ref_params = parse_copick_uri(reference_uri, reference_type)
+
+    logger.info(f"Limiting picks by distance for object '{input_params['object_name']}'")
+    logger.info(f"Source picks pattern: {input_params['user_id']}/{input_params['session_id']}")
+    if reference_type == "mesh":
+        logger.info(f"Reference mesh: {ref_params['object_name']} ({ref_params['user_id']}/{ref_params['session_id']})")
+    else:
+        logger.info(
+            f"Reference segmentation: {ref_params['name']} ({ref_params['user_id']}/{ref_params['session_id']})",
+        )
+    logger.info(f"Maximum distance: {max_distance} angstroms")
+    logger.info(
+        f"Target picks template: {output_params['object_name']} ({output_params['user_id']}/{output_params['session_id']})",
+    )
+
+    # Parallel discovery and processing - no sequential bottleneck!
+    results = limit_picks_by_distance_lazy_batch(
+        root=root,
+        config=task_config,
+        run_names=run_names_list,
+        workers=workers,
+    )
+
+    successful = sum(1 for result in results.values() if result and result.get("processed", 0) > 0)
+    total_points = sum(result.get("points_created", 0) for result in results.values() if result)
+    total_processed = sum(result.get("processed", 0) for result in results.values() if result)
+
+    # Collect all errors
+    all_errors = []
+    for result in results.values():
+        if result and result.get("errors"):
+            all_errors.extend(result["errors"])
+
+    logger.info(f"Completed: {successful}/{len(results)} runs processed successfully")
+    logger.info(f"Total distance limiting operations completed: {total_processed}")
+    logger.info(f"Total points created: {total_points}")
+
+    if all_errors:
+        logger.warning(f"Encountered {len(all_errors)} errors during processing")
+        for error in all_errors[:5]:  # Show first 5 errors
+            logger.warning(f"  - {error}")
+        if len(all_errors) > 5:
+            logger.warning(f"  ... and {len(all_errors) - 5} more errors")

copick_utils/cli/clipseg.py

@@ -0,0 +1,163 @@
+import click
+import copick
+from click_option_group import optgroup
+from copick.cli.util import add_config_option, add_debug_option
+from copick.util.log import get_logger
+from copick.util.uri import parse_copick_uri
+
+from copick_utils.cli.util import (
+    add_distance_options,
+    add_input_option,
+    add_output_option,
+    add_reference_mesh_option,
+    add_reference_seg_option,
+    add_workers_option,
+)
+from copick_utils.util.config_models import create_reference_config
+
+
+@click.command(
+    context_settings={"show_default": True},
+    short_help="Limit segmentations to voxels within distance of a reference surface.",
+    no_args_is_help=True,
+)
+@add_config_option
+@optgroup.group("\nInput Options", help="Options related to the input segmentations.")
+@optgroup.option(
+    "--run-names",
+    "-r",
+    multiple=True,
+    help="Specific run names to process (default: all runs).",
+)
+@add_input_option("segmentation")
+@optgroup.group("\nReference Options", help="Options for reference surface (provide either mesh or segmentation).")
+@add_reference_mesh_option(required=False)
+@add_reference_seg_option(required=False)
+@optgroup.group("\nTool Options", help="Options related to this tool.")
+@add_distance_options
+@add_workers_option
+@optgroup.group("\nOutput Options", help="Options related to output segmentations.")
+@add_output_option("segmentation", default_tool="clipseg")
+@add_debug_option
+def clipseg(
+    config,
+    run_names,
+    input_uri,
+    ref_mesh_uri,
+    ref_seg_uri,
+    max_distance,
+    mesh_voxel_spacing,
+    workers,
+    output_uri,
+    debug,
+):
+    """
+    Limit segmentations to voxels within a certain distance of a reference surface.
+
+    \b
+    URI Format:
+        Segmentations: name:user_id/session_id@voxel_spacing
+        Meshes: object_name:user_id/session_id
+
+    \b
+    The reference surface can be either a mesh or another segmentation.
+    Only segmentation voxels within the specified distance will be kept.
+
+    \b
+    Examples:
+        # Limit segmentation to voxels near reference mesh
+        copick logical clipseg -i "membrane:user1/full-001@10.0" -rm "boundary:user1/boundary-001" -o "membrane:clipseg/limited-001@10.0" --max-distance 50.0
+
+        # Limit using another segmentation as reference
+        copick logical clipseg -i "membrane:user1/full-001@10.0" -rs "mask:user1/mask-001@10.0" -o "membrane:clipseg/limited-001@10.0" --max-distance 100.0
+    """
+    from copick_utils.logical.distance_operations import limit_segmentation_by_distance_lazy_batch
+
+    logger = get_logger(__name__, debug=debug)
+
+    # Validate that exactly one reference type is provided
+    if not ref_mesh_uri and not ref_seg_uri:
+        raise click.BadParameter("Must provide either --ref-mesh or --ref-seg")
+    if ref_mesh_uri and ref_seg_uri:
+        raise click.BadParameter("Cannot provide both --ref-mesh and --ref-seg")
+
+    root = copick.from_file(config)
+    run_names_list = list(run_names) if run_names else None
+
+    # Determine reference type and URI
+    reference_uri = ref_mesh_uri or ref_seg_uri
+    reference_type = "mesh" if ref_mesh_uri else "segmentation"
+
+    # Extract voxel_spacing and multilabel from output for additional_params
+    output_params_temp = parse_copick_uri(output_uri, "segmentation")
+    voxel_spacing_output = output_params_temp["voxel_spacing"]
+    if isinstance(voxel_spacing_output, str):
+        voxel_spacing_output = float(voxel_spacing_output)
+    multilabel_output = output_params_temp.get("multilabel") or False
+
+    # Create config directly from URIs with additional params and smart defaults
+    try:
+        task_config = create_reference_config(
+            input_uri=input_uri,
+            input_type="segmentation",
+            output_uri=output_uri,
+            output_type="segmentation",
+            reference_uri=reference_uri,
+            reference_type=reference_type,
+            additional_params={
+                "max_distance": max_distance,
+                "mesh_voxel_spacing": mesh_voxel_spacing,
+                "voxel_spacing": voxel_spacing_output,
+                "is_multilabel": multilabel_output,
+            },
+            command_name="clipseg",
+        )
+    except ValueError as e:
+        raise click.BadParameter(str(e)) from e
+
+    # Extract parameters for logging
+    input_params = parse_copick_uri(input_uri, "segmentation")
+    output_params = parse_copick_uri(output_uri, "segmentation")
+    ref_params = parse_copick_uri(reference_uri, reference_type)
+
+    logger.info(f"Limiting segmentations by distance for '{input_params['name']}'")
+    logger.info(f"Source segmentation pattern: {input_params['user_id']}/{input_params['session_id']}")
+    if reference_type == "mesh":
+        logger.info(f"Reference mesh: {ref_params['object_name']} ({ref_params['user_id']}/{ref_params['session_id']})")
+    else:
+        logger.info(
+            f"Reference segmentation: {ref_params['name']} ({ref_params['user_id']}/{ref_params['session_id']})",
+        )
+    logger.info(f"Maximum distance: {max_distance} angstroms")
+    logger.info(
+        f"Target segmentation template: {output_params['name']} ({output_params['user_id']}/{output_params['session_id']})",
+    )
+
+    # Parallel discovery and processing - no sequential bottleneck!
+    results = limit_segmentation_by_distance_lazy_batch(
+        root=root,
+        config=task_config,
+        run_names=run_names_list,
+        workers=workers,
+    )
+
+    successful = sum(1 for result in results.values() if result and result.get("processed", 0) > 0)
+    total_voxels = sum(result.get("voxels_created", 0) for result in results.values() if result)
+    total_processed = sum(result.get("processed", 0) for result in results.values() if result)
+
+    # Collect all errors
+    all_errors = []
+    for result in results.values():
+        if result and result.get("errors"):
+            all_errors.extend(result["errors"])
+
+    logger.info(f"Completed: {successful}/{len(results)} runs processed successfully")
+    logger.info(f"Total distance limiting operations completed: {total_processed}")
+    logger.info(f"Total voxels created: {total_voxels}")
+
+    if all_errors:
+        logger.warning(f"Encountered {len(all_errors)} errors during processing")
+        for error in all_errors[:5]:  # Show first 5 errors
+            logger.warning(f"  - {error}")
+        if len(all_errors) > 5:
+            logger.warning(f"  ... and {len(all_errors) - 5} more errors")

copick_utils/cli/conversion_commands.py

@@ -0,0 +1,32 @@
+"""CLI commands for data conversion between different copick formats.
+
+This module imports all conversion commands from specialized files for better organization.
+"""
+
+from copick_utils.cli.mesh2picks import mesh2picks
+from copick_utils.cli.mesh2seg import mesh2seg
+from copick_utils.cli.picks2ellipsoid import picks2ellipsoid
+from copick_utils.cli.picks2mesh import picks2mesh
+from copick_utils.cli.picks2plane import picks2plane
+from copick_utils.cli.picks2seg import picks2seg
+from copick_utils.cli.picks2sphere import picks2sphere
+from copick_utils.cli.picks2surface import picks2surface
+from copick_utils.cli.seg2mesh import seg2mesh
+from copick_utils.cli.seg2picks import seg2picks
+
+# All commands are now available for import by the main CLI
+__all__ = [
+    # Picks to mesh commands
+    "picks2mesh",
+    "picks2sphere",
+    "picks2ellipsoid",
+    "picks2plane",
+    "picks2surface",
+    # Mesh to picks commands
+    "mesh2picks",
+    # Segmentation conversion commands
+    "picks2seg",
+    "seg2picks",
+    "mesh2seg",
+    "seg2mesh",
+]