Refactor plugin code for general view import

Repurposes the code from plugins.py (now deprecated) to register the
different view factories. To maintain compatability, added a "view_name"
attribute which is the name that gets added to the registry.
Additionally, the import code tries to import from the path if a search
path is provided, otherwise will search the sys.path for existing
modules with the "niftyone_" prefix.

Author: kaitj

src/niftyone/__init__.py

@@ -1,19 +1,11 @@
 """Large-scale neuroimaging visualization using FiftyOne."""
 
-# Import all plugins. In particular this should register user's custom generators
-from . import plugins
-from ._version import __version__, __version_tuple__
+from pathlib import Path
 
-# Register existing views
-from .figures.dwi import (
-    DwiPerShell,
-    QSpaceShells,
-    SignalPerVolume,
-)
-from .figures.func import CarpetPlot, MeanStd
-from .figures.multi_view import (
-    SliceVideo,
-    ThreeView,
-    ThreeViewVideo,
-)
+from ._version import __version__, __version_tuple__
+from .figures.factory import __file__ as factory_path
+from .figures.factory import register_views
 from .runner import Runner
+
+# Register all default views
+register_views(search_path=str(Path(factory_path).parent))

src/niftyone/__main__.py

@@ -28,6 +28,7 @@ def main() -> None:
                 sub=args.participant_label,
                 index_path=args.index,
                 qc_dir=args.qc_dir,
+                plugin_dir=args.plugin_dir,
                 config=args.config,
                 workers=args.workers,
                 overwrite=args.overwrite,

src/niftyone/analysis_levels/participant.py

@@ -35,6 +35,7 @@ def participant(
     sub: str | None = None,
     index_path: Path | None = None,
     qc_dir: Path | None = None,
+    plugin_dir: Path | None = None,
     config: Path | None = None,
     workers: int = 1,
     overwrite: bool = False,
@@ -60,11 +61,17 @@ def participant(
         f"\n\tsubject: {sub}"
         f"\n\tindex: {index_path}"
         f"\n\tqc: {qc_dir}"
+        f"\n\tplugin: {plugin_dir}"
         f"\n\tconfig: {config}"
         f"\n\tworkers: {workers}"
         f"\n\toverwrite: {overwrite}"
     )
 
+    # Register any plugin figure views
+    factory.register_views(
+        search_path=str(plugin_dir) if plugin_dir else None, plugin_prefix="niftyone_"
+    )
+
     logging.info("Loading dataset index")
     index = bids2table(bids_dir, index_path=index_path, workers=workers)
 

src/niftyone/cli.py

@@ -86,6 +86,14 @@ def _add_participant_args(self) -> None:
             default=None,
             help="pre-computed QC metrics if available",
         )
+        self.participant_level.add_argument(
+            "--plugin-dir",
+            metavar="PATH",
+            type=Path,
+            default=None,
+            help="directory to search for plugins in;plugins should be "
+            "prepended with 'niftyone_'",
+        )
         self.participant_level.add_argument(
             "--config",
             metavar="PATH",

src/niftyone/figures/dwi.py

@@ -1,22 +1,22 @@
 """Factories associated with diffusion data."""
 
 from niclips.figures import dwi
-from niftyone.figures.factory import View, register
+from niftyone.figures.factory import View
 
 
-@register("qspace_shells")
 class QSpaceShells(View):
     entities = {"ext": ".mp4", "extra_entities": {"figure": "qspace"}}
     view_fn = staticmethod(dwi.visualize_qspace)
+    view_name = "qspace_shells"
 
 
-@register("three_view_shell_video")
 class DwiPerShell(View):
     entities = {"ext": ".mp4", "extra_entities": {"figure": "bval"}}
     view_fn = staticmethod(dwi.three_view_per_shell)
+    view_name = "three_view_shell_video"
 
 
-@register("signal_per_volume")
 class SignalPerVolume(View):
     entities = {"ext": ".mp4", "extra_entities": {"figure": "signalPerVolume"}}
     view_fn = staticmethod(dwi.signal_per_volume)
+    view_name = "signal_per_volume"

src/niftyone/figures/factory.py

@@ -1,9 +1,13 @@
 """Factory module for creating different figures."""
 
+import importlib.util
+import inspect
 import logging
+import pkgutil
 from abc import ABC
 from functools import reduce
 from pathlib import Path
+from types import ModuleType
 from typing import Any, Callable, Generic, TypeVar
 
 import matplotlib.pyplot as plt
@@ -20,62 +24,12 @@
 view_registry: dict[str, type["View"]] = {}
 
 
-def register(name: str) -> Callable[[type[T]], type[T]]:
-    """Function to register view to registry."""
-
-    def decorator(cls: type[T]) -> type[T]:
-        view_registry[name] = cls
-        return cls
-
-    return decorator
-
-
-def create_view(
-    view: str,
-    view_kwargs: dict[str, Any] | None,
-    join_entities: list[str],
-    queries: list[str],
-) -> "View":
-    """Function to create view."""
-    if view_kwargs is None:
-        view_kwargs = {}
-
-    try:
-        view_cls = view_registry[view]
-        view_instance = view_cls(queries, join_entities, view_kwargs)
-        return view_instance
-    except KeyError:
-        msg = f"Factory for '{view}' for not found in registry."
-        raise KeyError(msg)
-
-
-def create_views(config: dict[str, Any]) -> list["View"]:
-    """Create selected views dynamically from config with default settings."""
-    views: list["View"] = []
-
-    for group in config.get("figures", {}).values():
-        queries = group.get("queries", [])
-        join_entities = group.get("join_entities", ["sub", "ses"])
-        views_map = group.get("views", {})
-
-        for view, view_kwargs in views_map.items():
-            views.append(
-                create_view(
-                    view=view,
-                    view_kwargs=view_kwargs,
-                    join_entities=join_entities,
-                    queries=queries,
-                )
-            )
-
-    return views
-
-
 class View(ABC, Generic[T]):
     """Base view class."""
 
     entities: dict[str, Any] | None = None
     view_fn: Callable[[nib.Nifti1Image, Path], Image | Figure | None] | None = None
+    view_name: str | None = None  # Name for registry (defaults to class)
 
     def __init__(
         self,
@@ -162,3 +116,78 @@ def create(
             self.view_fn(img, out_path, **self.view_kwargs)
 
         plt.close("all")
+
+
+def create_view(
+    view: str,
+    view_kwargs: dict[str, Any] | None,
+    join_entities: list[str],
+    queries: list[str],
+) -> "View":
+    """Function to create view."""
+    if view_kwargs is None:
+        view_kwargs = {}
+
+    try:
+        view_cls = view_registry[view]
+        view_instance = view_cls(queries, join_entities, view_kwargs)
+        return view_instance
+    except KeyError:
+        msg = f"Factory for '{view}' for not found in registry."
+        raise KeyError(msg)
+
+
+def create_views(config: dict[str, Any]) -> list["View"]:
+    """Create selected views dynamically from config with default settings."""
+    views: list["View"] = []
+
+    for group in config.get("figures", {}).values():
+        queries = group.get("queries", [])
+        join_entities = group.get("join_entities", ["sub", "ses"])
+        views_map = group.get("views", {})
+
+        for view, view_kwargs in views_map.items():
+            views.append(
+                create_view(
+                    view=view,
+                    view_kwargs=view_kwargs,
+                    join_entities=join_entities,
+                    queries=queries,
+                )
+            )
+
+    return views
+
+
+def register(cls: type[T]) -> type[T]:
+    """Function to add view to registry."""
+    view_registry[cls.view_name or cls.__name__] = cls
+    return cls
+
+
+def register_views(search_path: str | None, plugin_prefix: str | None = None) -> None:
+    """Register all views."""
+
+    def _import_module(module_name: str) -> ModuleType:
+        """Import module."""
+        if search_path is not None:
+            module_path = Path(search_path) / f"{module_name}.py"
+            spec = importlib.util.spec_from_file_location(module_name, module_path)
+            if spec is None or spec.loader is None:
+                raise ImportError(f"Unable to load {module_name}")
+            module = importlib.util.module_from_spec(spec)
+            spec.loader.exec_module(module)
+        else:
+            module = importlib.import_module(module_name)
+        return module
+
+    for _, module_name, _ in pkgutil.iter_modules(
+        path=[search_path] if search_path else None
+    ):
+        if plugin_prefix is None or module_name.startswith(plugin_prefix):
+            print(plugin_prefix, module_name)
+            module = _import_module(module_name=module_name)
+
+            for _, obj in inspect.getmembers(module, inspect.isclass):
+                if issubclass(obj, View) and obj is not View:
+                    register(obj)

src/niftyone/figures/func.py

@@ -1,16 +1,16 @@
 """Factories associated with functional data."""
 
 from niclips.figures import bold
-from niftyone.figures.factory import View, register
+from niftyone.figures.factory import View
 
 
-@register("carpet_plot")
 class CarpetPlot(View):
     entities = {"ext": ".png", "extra_entities": {"figure": "carpet"}}
     view_fn = staticmethod(bold.carpet_plot)
+    view_name = "carpet_plot"
 
 
-@register("mean_std")
 class MeanStd(View):
     entities = {"ext": ".png", "extra_entities": {"figure": "meanStd"}}
     view_fn = staticmethod(bold.bold_mean_std)
+    view_name = "mean_std"

src/niftyone/figures/multi_view.py

@@ -1,22 +1,22 @@
 """Factories associated with multi-view."""
 
 from niclips.figures import multi_view
-from niftyone.figures.factory import View, register
+from niftyone.figures.factory import View
 
 
-@register("three_view")
 class ThreeView(View):
     entities = {"ext": ".png", "extra_entities": {"figure": "threeView"}}
     view_fn = staticmethod(multi_view.three_view_frame)
+    view_name = "three_view"
 
 
-@register("slice_video")
 class SliceVideo(View):
     entities = {"ext": ".mp4", "extra_entities": {"figure": "sliceVideo"}}
     view_fn = staticmethod(multi_view.slice_video)
+    view_name = "slice_video"
 
 
-@register("three_view_video")
 class ThreeViewVideo(View):
     entities = {"ext": ".mp4", "extra_entities": {"figure": "threeViewVideo"}}
     view_fn = staticmethod(multi_view.three_view_video)
+    view_name = "three_view_video"

src/niftyone/plugins.py

@@ -58,6 +58,8 @@ def setup_registry():
     view_registry.clear()
 
     class TestView(View):
+        view_name = "test_view"
+
         def create(
             self,
             records: pd.Series,
@@ -66,7 +68,7 @@ def create(
         ) -> None:
             pass
 
-    register("test_view")(TestView)
+    register(TestView)
     yield
     view_registry.clear()