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

copick_utils/cli/validbox.py

@@ -0,0 +1,155 @@
+"""CLI commands for segmentation processing 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 expand_output_uri, parse_copick_uri
+
+from copick_utils.cli.util import add_output_option, add_tomogram_option
+
+
+@click.command(
+    context_settings={"show_default": True},
+    short_help="Generate valid area box meshes for tomographic reconstructions.",
+    no_args_is_help=True,
+)
+@add_config_option
+@optgroup.group("\nInput Options", help="Options related to the input runs.")
+@optgroup.option(
+    "--run-names",
+    "-r",
+    multiple=True,
+    help="Specific run names to process (default: all runs).",
+)
+@add_tomogram_option(required=True)
+@optgroup.group("\nTool Options", help="Options related to this tool.")
+@optgroup.option(
+    "--angle",
+    type=float,
+    default=0.0,
+    help="Rotation angle around Z-axis in degrees.",
+)
+@optgroup.option(
+    "--workers",
+    type=int,
+    default=8,
+    help="Number of worker processes.",
+)
+@optgroup.group("\nOutput Options", help="Options related to output meshes.")
+@add_output_option("mesh", default_tool="validbox")
+@add_debug_option
+def validbox(
+    config,
+    run_names,
+    tomogram_uri,
+    angle,
+    workers,
+    output_uri,
+    debug,
+):
+    """
+    Generate valid area box meshes for tomographic reconstructions.
+
+    \b
+    URI Format:
+        Meshes: object_name:user_id/session_id
+        Tomograms: tomo_type@voxel_spacing
+
+    \b
+    Creates box meshes representing the valid imaging area of tomographic
+    reconstructions. The box dimensions are based on the tomogram voxel dimensions
+    and can be optionally rotated around the Z-axis.
+
+    \b
+    Examples:
+        # Generate validbox meshes for all runs
+        copick process validbox --tomogram wbp@10.0 -o "validbox"
+
+        # Generate with rotation and specific tomogram type
+        copick process validbox -t imod@10.0 --angle 45.0 -o "validbox/rotated"
+    """
+    from copick_utils.process.validbox import validbox_batch
+
+    logger = get_logger(__name__, debug=debug)
+
+    root = copick.from_file(config)
+    run_names_list = list(run_names) if run_names else None
+
+    # Parse tomogram URI to extract tomo_type and voxel_spacing
+    try:
+        tomogram_params = parse_copick_uri(tomogram_uri, "tomogram")
+    except ValueError as e:
+        raise click.BadParameter(f"Invalid tomogram URI: {e}") from e
+
+    tomo_type = tomogram_params["tomo_type"]
+    voxel_spacing = tomogram_params["voxel_spacing"]
+    if isinstance(voxel_spacing, str):
+        voxel_spacing = float(voxel_spacing)
+
+    # Expand output URI with smart defaults (no input, so use synthetic input)
+    try:
+        output_uri = expand_output_uri(
+            output_uri=output_uri,
+            input_uri="validbox:*/*",  # Synthetic input for default object name
+            input_type="mesh",
+            output_type="mesh",
+            command_name="validbox",
+            individual_outputs=False,
+        )
+    except ValueError as e:
+        raise click.BadParameter(f"Error expanding output URI: {e}") from e
+
+    # Parse output URI (now fully expanded)
+    try:
+        output_params = parse_copick_uri(output_uri, "mesh")
+    except ValueError as e:
+        raise click.BadParameter(f"Invalid output URI: {e}") from e
+
+    mesh_object_name_output = output_params["object_name"]
+    mesh_user_id_output = output_params["user_id"]
+    mesh_session_id_output = output_params["session_id"]
+
+    logger.info(f"Generating validbox meshes for object '{mesh_object_name_output}'")
+    logger.info(f"Tomogram: {tomo_type}@{voxel_spacing}")
+    logger.info(f"Rotation angle: {angle} degrees")
+    logger.info(f"Target mesh: {mesh_object_name_output} ({mesh_user_id_output}/{mesh_session_id_output})")
+
+    if run_names_list:
+        logger.info(f"Processing {len(run_names_list)} specific runs")
+    else:
+        logger.info(f"Processing all {len(root.runs)} runs")
+
+    results = validbox_batch(
+        root=root,
+        voxel_spacing=voxel_spacing,
+        mesh_object_name=mesh_object_name_output,
+        mesh_user_id=mesh_user_id_output,
+        mesh_session_id=mesh_session_id_output,
+        tomo_type=tomo_type,
+        angle=angle,
+        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)
+
+    # 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 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/converters/__init__.py

@@ -0,0 +1,35 @@
+"""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
+
+__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",
+]