copick-utils 0.6.1__tar.gz → 1.0.0__tar.gz

{copick_utils-0.6.1 → copick_utils-1.0.0}/.github/workflows/conventional-commits.yml

@@ -16,4 +16,4 @@ jobs:
   conventional_commit_title:
     runs-on: ubuntu-latest
     steps:
-      - uses: chanzuckerberg/github-actions/.github/actions/conventional-commits@v6.4.0
+      - uses: chanzuckerberg/github-actions/.github/actions/conventional-commits@v6.10.0

{copick_utils-0.6.1 → copick_utils-1.0.0}/.github/workflows/py-formatting.yml

@@ -10,8 +10,8 @@ jobs:
     name: pre-commit checks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.12.5"
       - name: Install action-validator with asdf

{copick_utils-0.6.1 → copick_utils-1.0.0}/.github/workflows/release-please.yml

@@ -43,13 +43,13 @@ jobs:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - name: Checkout ref branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           ref: ${{ github.ref }}
           fetch-depth: 0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           version: "0.7.13"
           python-version: "3.12"

copick_utils-1.0.0/.release-please.manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "1.0.0"
+}

copick_utils-1.0.0/CHANGELOG.md

@@ -0,0 +1,36 @@
+# Changelog
+
+## [1.0.0](https://github.com/copick/copick-utils/compare/copick-utils-v0.6.1...copick-utils-v1.0.0) (2025-10-16)
+
+
+### ⚠ BREAKING CHANGES
+
+* Conversion, logical and processing commands for copick-utils CLI ([#24](https://github.com/copick/copick-utils/issues/24))
+
+### ✨ Features
+
+* Conversion, logical and processing commands for copick-utils CLI ([#24](https://github.com/copick/copick-utils/issues/24)) ([d455fd2](https://github.com/copick/copick-utils/commit/d455fd217f4cd4edf18cfe8da48d951799fa272a))
+
+
+### 🐞 Bug Fixes
+
+* bump actions/checkout from 4 to 5 ([#22](https://github.com/copick/copick-utils/issues/22)) ([287ac56](https://github.com/copick/copick-utils/commit/287ac566545d5c8b496dfdc0ae7e18456337de52))
+* bump actions/setup-python from 5 to 6 ([#25](https://github.com/copick/copick-utils/issues/25)) ([f3ed071](https://github.com/copick/copick-utils/commit/f3ed071dafa9469daee9f62a9a06319de4c76d63))
+* bump astral-sh/setup-uv from 6 to 7 ([#30](https://github.com/copick/copick-utils/issues/30)) ([b3028ef](https://github.com/copick/copick-utils/commit/b3028ef908f0e0d42cf418abb5169ab3a87556eb))
+* bump chanzuckerberg/github-actions from 6.4.0 to 6.5.0 ([#20](https://github.com/copick/copick-utils/issues/20)) ([13056ae](https://github.com/copick/copick-utils/commit/13056ae6ee0fc0132c20b5f0539614c9d4d4aa24))
+* bump chanzuckerberg/github-actions from 6.5.0 to 6.6.0 ([#23](https://github.com/copick/copick-utils/issues/23)) ([2c6a994](https://github.com/copick/copick-utils/commit/2c6a99497098073cecb52b5094da9f6ede040c4a))
+* bump chanzuckerberg/github-actions from 6.6.0 to 6.10.0 ([#29](https://github.com/copick/copick-utils/issues/29)) ([bb50f1e](https://github.com/copick/copick-utils/commit/bb50f1ee9070cf33cee6d78e64aefe5063e5f0eb))
+
+## [0.6.1](https://github.com/copick/copick-utils/compare/copick-utils-v0.6.0...copick-utils-v0.6.1) (2025-07-16)
+
+
+### 🐞 Bug Fixes
+
+* bump actions/checkout from 3 to 4 ([#19](https://github.com/copick/copick-utils/issues/19)) ([570072f](https://github.com/copick/copick-utils/commit/570072f708ea47b54d00fcc24451401896c91e25))
+* bump actions/setup-python from 4 to 5 ([#17](https://github.com/copick/copick-utils/issues/17)) ([95c4784](https://github.com/copick/copick-utils/commit/95c47842e6a271ae40f69a9f9a578ef55d3d318b))
+* bump asdf-vm/actions from 3 to 4 ([#18](https://github.com/copick/copick-utils/issues/18)) ([039b576](https://github.com/copick/copick-utils/commit/039b5761c4bc6b128f1bfef1aa2e7bf612f42ea3))
+
+
+### 🧹 Miscellaneous Chores
+
+* Set up CI for copick-utils ([#14](https://github.com/copick/copick-utils/issues/14)) ([0fbcfbb](https://github.com/copick/copick-utils/commit/0fbcfbb5bc12261da52e0850531195049328c2f9))

{copick_utils-0.6.1 → copick_utils-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: copick-utils
-Version: 0.6.1
+Version: 1.0.0
 Summary: Utilities for copick
 Project-URL: Repository, https://github.com/KyleHarrington/copick-utils.git
 Project-URL: Issues, https://github.com/KyleHarrington/copick-utils/issues
@@ -28,7 +28,20 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Requires-Python: >=3.9
-Requires-Dist: copick>=0.8.0
+Requires-Dist: click
+Requires-Dist: click-option-group
+Requires-Dist: copick>=1.16.0
+Requires-Dist: manifold3d
+Requires-Dist: mapbox-earcut
+Requires-Dist: numpy
+Requires-Dist: rtree
+Requires-Dist: scikit-image
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: shapely
+Requires-Dist: tqdm
+Requires-Dist: trimesh
+Requires-Dist: zarr
 Provides-Extra: dev
 Requires-Dist: black>=25.1.0; extra == 'dev'
 Requires-Dist: hatch-vcs>=0.4.0; extra == 'dev'

{copick_utils-0.6.1 → copick_utils-1.0.0}/pyproject.toml

@@ -19,7 +19,20 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-    "copick>=0.8.0",
+    "copick>=1.16.0",
+    "click",
+    "click-option-group",
+    "numpy",
+    "scipy",
+    "scikit-image",
+    "zarr",
+    "trimesh",
+    "manifold3d",
+    "mapbox-earcut",
+    "tqdm",
+    "scikit-learn",
+    "shapely",
+    "rtree"
 ]
 authors = [
     { name = "Kyle Harrington", email = "czi@kyleharrington.com" },
@@ -44,6 +57,36 @@ dev = [
     "ruff>=0.12.0",
 ]
 
+[project.entry-points."copick.convert.commands"]
+picks2seg = "copick_utils.cli.conversion_commands:picks2seg"
+seg2picks = "copick_utils.cli.conversion_commands:seg2picks"
+mesh2seg = "copick_utils.cli.conversion_commands:mesh2seg"
+seg2mesh = "copick_utils.cli.conversion_commands:seg2mesh"
+mesh2picks = "copick_utils.cli.conversion_commands:mesh2picks"
+picks2mesh = "copick_utils.cli.conversion_commands:picks2mesh"
+picks2sphere = "copick_utils.cli.conversion_commands:picks2sphere"
+picks2ellipsoid = "copick_utils.cli.conversion_commands:picks2ellipsoid"
+picks2plane = "copick_utils.cli.conversion_commands:picks2plane"
+picks2surface = "copick_utils.cli.conversion_commands:picks2surface"
+
+[project.entry-points."copick.process.commands"]
+separate_components = "copick_utils.cli.processing_commands:separate_components"
+filter_components = "copick_utils.cli.processing_commands:filter_components"
+skeletonize = "copick_utils.cli.processing_commands:skeletonize"
+fit_spline = "copick_utils.cli.processing_commands:fit_spline"
+validbox = "copick_utils.cli.processing_commands:validbox"
+hull = "copick_utils.cli.processing_commands:hull"
+
+[project.entry-points."copick.logical.commands"]
+meshop = "copick_utils.cli.logical_commands:meshop"
+segop = "copick_utils.cli.logical_commands:segop"
+enclosed = "copick_utils.cli.logical_commands:enclosed"
+clipmesh = "copick_utils.cli.logical_commands:clipmesh"
+clipseg = "copick_utils.cli.logical_commands:clipseg"
+clippicks = "copick_utils.cli.logical_commands:clippicks"
+picksin = "copick_utils.cli.logical_commands:picksin"
+picksout = "copick_utils.cli.logical_commands:picksout"
+
 [tool.hatch.version]
 path = "src/copick_utils/__init__.py"
 

{copick_utils-0.6.1 → copick_utils-1.0.0}/src/copick_utils/__init__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Kyle Harrington <czi@kyleharrington.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.6.1"
+__version__ = "1.0.0"

copick_utils-1.0.0/src/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-1.0.0/src/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-1.0.0/src/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")