swcstudio 0.2.0__py3-none-any.whl

swcstudio/__init__.py

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+"""swcstudio package entrypoint.
+
+Layers:
+- swcstudio.core: shared algorithm/data logic
+- swcstudio.tools: tool + feature modules
+- swcstudio.api: public Python API
+- swcstudio.cli: terminal interface
+- swcstudio.gui: desktop GUI interface
+"""
+
+from importlib.metadata import PackageNotFoundError, version as _pkg_version
+
+try:
+    __version__ = _pkg_version("swcstudio")
+except PackageNotFoundError:
+    # Local source checkout before installation.
+    __version__ = "0.1.0"
+
+__all__ = ["api", "core", "tools", "plugins", "cli", "gui", "__version__"]

swcstudio/api.py

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+"""Public library API for swcstudio.
+
+All interfaces (GUI, CLI, and external Python callers) should import these
+functions or the corresponding tool/feature modules.
+"""
+
+from __future__ import annotations
+
+from swcstudio.core.auto_typing import BatchOptions
+from swcstudio.plugins import (
+    autoload_plugins_from_environment,
+    get_plugin,
+    list_all_feature_methods,
+    list_feature_methods,
+    list_plugins,
+    load_plugin_module,
+    load_plugins,
+    register_method,
+    register_plugin_manifest,
+    register_plugin_method,
+    unregister_method,
+    unregister_plugin,
+)
+from swcstudio.tools.batch_processing.features.auto_typing import run_folder as batch_auto_typing
+from swcstudio.tools.batch_processing.features.index_clean import run_folder as batch_index_clean_folder
+from swcstudio.tools.batch_processing.features.simplification import (
+    run_folder as batch_simplify_folder,
+)
+from swcstudio.tools.batch_processing.features.batch_validation import (
+    validate_folder as batch_validate_folder,
+)
+from swcstudio.tools.batch_processing.features.radii_cleaning import (
+    clean_folder as batch_radii_cleaning,
+    clean_path as radii_clean_path,
+)
+from swcstudio.tools.batch_processing.features.swc_splitter import (
+    split_folder as batch_split_folder,
+)
+from swcstudio.tools.geometry_editing.features.operations import (
+    disconnect_branch as geometry_disconnect_branch,
+    delete_node as geometry_delete_node,
+    delete_subtree as geometry_delete_subtree,
+    insert_node_between as geometry_insert_node_between,
+    move_node_absolute as geometry_move_node_absolute,
+    move_subtree_absolute as geometry_move_subtree_absolute,
+    reconnect_branch as geometry_reconnect_branch,
+    reindex_dataframe_with_map as geometry_reindex_dataframe_with_map,
+)
+from swcstudio.tools.morphology_editing.features.dendrogram_editing import (
+    reassign_subtree_types,
+    reassign_subtree_types_in_file,
+)
+from swcstudio.tools.morphology_editing.features.manual_label import (
+    set_node_type_file as morphology_set_node_type_file,
+    set_node_type_text as morphology_set_node_type_text,
+)
+from swcstudio.tools.morphology_editing.features.manual_radii import (
+    set_node_radius_file as morphology_set_node_radius_file,
+    set_node_radius_text as morphology_set_node_radius_text,
+)
+from swcstudio.tools.morphology_editing.features.simplification import (
+    simplify_file as morphology_smart_decimation_file,
+    simplify_swc_text as morphology_smart_decimation_text,
+)
+from swcstudio.tools.validation.features.auto_fix import auto_fix_file, auto_fix_text
+from swcstudio.tools.validation.features.index_clean import (
+    index_clean_file as validation_index_clean_file,
+    index_clean_text as validation_index_clean_text,
+)
+from swcstudio.tools.validation.features.auto_typing import (
+    auto_label_file as validation_auto_label_file,
+    run_file as validation_auto_typing_file,
+)
+from swcstudio.tools.validation.features.run_checks import (
+    validate_file as validation_run_file,
+    validate_text as validation_run_text,
+)
+from swcstudio.tools.visualization.features.mesh_editing import (
+    build_mesh_from_file,
+    build_mesh_from_text,
+)
+
+__all__ = [
+    "BatchOptions",
+    "batch_validate_folder",
+    "batch_split_folder",
+    "batch_auto_typing",
+    "batch_simplify_folder",
+    "batch_index_clean_folder",
+    "batch_radii_cleaning",
+    "radii_clean_path",
+    "auto_fix_text",
+    "auto_fix_file",
+    "validation_index_clean_text",
+    "validation_index_clean_file",
+    "validation_auto_typing_file",
+    "validation_run_text",
+    "validation_run_file",
+    "build_mesh_from_text",
+    "build_mesh_from_file",
+    "reassign_subtree_types",
+    "reassign_subtree_types_in_file",
+    "morphology_set_node_type_text",
+    "morphology_set_node_type_file",
+    "morphology_set_node_radius_text",
+    "morphology_set_node_radius_file",
+    "validation_auto_label_file",
+    "morphology_smart_decimation_text",
+    "morphology_smart_decimation_file",
+    "geometry_move_node_absolute",
+    "geometry_move_subtree_absolute",
+    "geometry_reconnect_branch",
+    "geometry_disconnect_branch",
+    "geometry_delete_node",
+    "geometry_delete_subtree",
+    "geometry_insert_node_between",
+    "geometry_reindex_dataframe_with_map",
+    "load_plugin_module",
+    "load_plugins",
+    "autoload_plugins_from_environment",
+    "register_plugin_manifest",
+    "register_plugin_method",
+    "unregister_plugin",
+    "list_plugins",
+    "get_plugin",
+    "register_method",
+    "unregister_method",
+    "list_feature_methods",
+    "list_all_feature_methods",
+]

swcstudio/cli/__init__.py

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+"""CLI package for swcstudio."""
+
+__all__ = ["cli"]