junifer 0.0.6.dev51__py3-none-any.whl → 0.0.6.dev88__py3-none-any.whl

junifer/markers/functional_connectivity/__init__.py

@@ -3,17 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .functional_connectivity_parcels import FunctionalConnectivityParcels
-from .functional_connectivity_spheres import FunctionalConnectivitySpheres
-from .crossparcellation_functional_connectivity import CrossParcellationFC
-from .edge_functional_connectivity_parcels import EdgeCentricFCParcels
-from .edge_functional_connectivity_spheres import EdgeCentricFCSpheres
+import lazy_loader as lazy
 
 
-__all__ = [
-    "FunctionalConnectivityParcels",
-    "FunctionalConnectivitySpheres",
-    "CrossParcellationFC",
-    "EdgeCentricFCParcels",
-    "EdgeCentricFCSpheres",
-]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/markers/functional_connectivity/__init__.pyi

@@ -0,0 +1,13 @@
+__all__ = [
+    "FunctionalConnectivityParcels",
+    "FunctionalConnectivitySpheres",
+    "CrossParcellationFC",
+    "EdgeCentricFCParcels",
+    "EdgeCentricFCSpheres",
+]
+
+from .functional_connectivity_parcels import FunctionalConnectivityParcels
+from .functional_connectivity_spheres import FunctionalConnectivitySpheres
+from .crossparcellation_functional_connectivity import CrossParcellationFC
+from .edge_functional_connectivity_parcels import EdgeCentricFCParcels
+from .edge_functional_connectivity_spheres import EdgeCentricFCSpheres

junifer/markers/reho/__init__.py

@@ -3,8 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .reho_parcels import ReHoParcels
-from .reho_spheres import ReHoSpheres
+import lazy_loader as lazy
 
 
-__all__ = ["ReHoParcels", "ReHoSpheres"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/markers/reho/__init__.pyi

@@ -0,0 +1,4 @@
+__all__ = ["ReHoParcels", "ReHoSpheres"]
+
+from .reho_parcels import ReHoParcels
+from .reho_spheres import ReHoSpheres

junifer/markers/temporal_snr/__init__.py

@@ -3,8 +3,7 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from .temporal_snr_parcels import TemporalSNRParcels
-from .temporal_snr_spheres import TemporalSNRSpheres
+import lazy_loader as lazy
 
 
-__all__ = ["TemporalSNRParcels", "TemporalSNRSpheres"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/markers/temporal_snr/__init__.pyi

@@ -0,0 +1,4 @@
+__all__ = ["TemporalSNRParcels", "TemporalSNRSpheres"]
+
+from .temporal_snr_parcels import TemporalSNRParcels
+from .temporal_snr_spheres import TemporalSNRSpheres

junifer/pipeline/__init__.py

@@ -3,15 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from . import registry
-from .pipeline_step_mixin import PipelineStepMixin
-from .update_meta_mixin import UpdateMetaMixin
-from .workdir_manager import WorkDirManager
+import lazy_loader as lazy
 
 
-__all__ = [
-    "registry",
-    "PipelineStepMixin",
-    "UpdateMetaMixin",
-    "WorkDirManager",
-]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/pipeline/__init__.pyi

@@ -0,0 +1,13 @@
+__all__ = [
+    "registry",
+    "PipelineStepMixin",
+    "UpdateMetaMixin",
+    "WorkDirManager",
+    "MarkerCollection",
+]
+
+from . import registry
+from .pipeline_step_mixin import PipelineStepMixin
+from .update_meta_mixin import UpdateMetaMixin
+from .workdir_manager import WorkDirManager
+from .marker_collection import MarkerCollection

junifer/{markers/collection.py → pipeline/marker_collection.py}

@@ -7,16 +7,16 @@
 from collections import Counter
 from typing import TYPE_CHECKING, Dict, List, Optional
 
-from ..datareader.default import DefaultDataReader
-from ..markers.base import BaseMarker
+from ..datareader import DefaultDataReader
 from ..pipeline import PipelineStepMixin, WorkDirManager
-from ..preprocess.base import BasePreprocessor
-from ..storage.base import BaseFeatureStorage
 from ..utils import logger, raise_error
 
 
 if TYPE_CHECKING:
     from junifer.datagrabber import BaseDataGrabber
+    from junifer.markers import BaseMarker
+    from junifer.preprocess import BasePreprocessor
+    from junifer.storage import BaseFeatureStorage
 
 
 __all__ = ["MarkerCollection"]
@@ -45,10 +45,10 @@ class MarkerCollection:
 
     def __init__(
         self,
-        markers: List[BaseMarker],
+        markers: List["BaseMarker"],
         datareader: Optional[PipelineStepMixin] = None,
-        preprocessors: Optional[List[BasePreprocessor]] = None,
-        storage: Optional[BaseFeatureStorage] = None,
+        preprocessors: Optional[List["BasePreprocessor"]] = None,
+        storage: Optional["BaseFeatureStorage"] = None,
     ):
         # Check that the markers have different names
         marker_names = [m.name for m in markers]

junifer/pipeline/registry.py

@@ -5,6 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import importlib
 from typing import TYPE_CHECKING, Dict, List, Optional, Union
 
 from ..utils.logging import logger, raise_error
@@ -28,8 +29,64 @@ _VALID_STEPS: List[str] = [
     "storage",
 ]
 
+# Step to sub-package mapping
+_STEP_TO_SUBPKG_MAPPINGS = {
+    "datagrabber": "datagrabber",
+    "datareader": "datareader",
+    "preprocessing": "preprocess",
+    "marker": "markers",
+    "storage": "storage",
+}
+
 # Define registry for valid steps
-_REGISTRY: Dict[str, Dict[str, type]] = {x: {} for x in _VALID_STEPS}
+_REGISTRY: Dict[str, Dict[str, Union[str, type]]] = {
+    "datagrabber": {
+        "HCP1200": "HCP1200",
+        "BaseDataGrabber": "BaseDataGrabber",
+        "DataladAOMICID1000": "DataladAOMICID1000",
+        "DataladAOMICPIOP1": "DataladAOMICPIOP1",
+        "DataladAOMICPIOP2": "DataladAOMICPIOP2",
+        "DataladDataGrabber": "DataladDataGrabber",
+        "DataladHCP1200": "DataladHCP1200",
+        "DMCC13Benchmark": "DMCC13Benchmark",
+        "MultipleDataGrabber": "MultipleDataGrabber",
+        "PatternDataGrabber": "PatternDataGrabber",
+        "PatternDataladDataGrabber": "PatternDataladDataGrabber",
+    },
+    "datareader": {
+        "DefaultDataReader": "DefaultDataReader",
+    },
+    "preprocessing": {
+        "BasePreprocessor": "BasePreprocessor",
+        "Smoothing": "Smoothing",
+        "SpaceWarper": "SpaceWarper",
+        "fMRIPrepConfoundRemove": "fMRIPrepConfoundRemove",
+    },
+    "marker": {
+        "ALFFParcels": "ALFFParcels",
+        "ALFFSpheres": "ALFFSpheres",
+        "BaseMarker": "BaseMarker",
+        "BrainPrint": "BrainPrint",
+        "CrossParcellationFC": "CrossParcellationFC",
+        "EdgeCentricFCParcels": "EdgeCentricFCParcels",
+        "EdgeCentricFCSpheres": "EdgeCentricFCSpheres",
+        "FunctionalConnectivityParcels": "FunctionalConnectivityParcels",
+        "FunctionalConnectivitySpheres": "FunctionalConnectivitySpheres",
+        "ParcelAggregation": "ParcelAggregation",
+        "ReHoParcels": "ReHoParcels",
+        "ReHoSpheres": "ReHoSpheres",
+        "RSSETSMarker": "RSSETSMarker",
+        "SphereAggregation": "SphereAggregation",
+        "TemporalSNRParcels": "TemporalSNRParcels",
+        "TemporalSNRSpheres": "TemporalSNRSpheres",
+    },
+    "storage": {
+        "BaseFeatureStorage": "BaseFeatureStorage",
+        "HDF5FeatureStorage": "HDF5FeatureStorage",
+        "PandasBaseFeatureStorage": "PandasBaseFeatureStorage",
+        "SQLiteFeatureStorage": "SQLiteFeatureStorage",
+    },
+}
 
 
 def register(step: str, name: str, klass: type) -> None:
@@ -112,7 +169,18 @@ def get_class(step: str, name: str) -> type:
     if name not in _REGISTRY[step]:
         raise_error(msg=f"Invalid name: {name}", klass=ValueError)
 
-    return _REGISTRY[step][name]
+    # Check if first-time import, then import it
+    if isinstance(_REGISTRY[step][name], str):
+        klass = getattr(
+            importlib.import_module(
+                f"junifer.{_STEP_TO_SUBPKG_MAPPINGS[step]}"
+            ),
+            name,
+        )
+    else:
+        klass = _REGISTRY[step][name]
+
+    return klass
 
 
 def build(

junifer/{markers/tests/test_collection.py → pipeline/tests/test_marker_collection.py}

@@ -1,4 +1,4 @@
-"""Provide tests for marker collection."""
+"""Provide tests for MarkerCollection."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -12,10 +12,9 @@ from numpy.testing import assert_array_equal
 from junifer.datareader.default import DefaultDataReader
 from junifer.markers import (
     FunctionalConnectivityParcels,
-    MarkerCollection,
     ParcelAggregation,
 )
-from junifer.pipeline import PipelineStepMixin
+from junifer.pipeline import MarkerCollection, PipelineStepMixin
 from junifer.preprocess import fMRIPrepConfoundRemover
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import (

junifer/preprocess/__init__.py

@@ -5,15 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .base import BasePreprocessor
-from .confounds import fMRIPrepConfoundRemover
-from .warping import SpaceWarper
-from .smoothing import Smoothing
+import lazy_loader as lazy
 
 
-__all__ = [
-    "BasePreprocessor",
-    "fMRIPrepConfoundRemover",
-    "SpaceWarper",
-    "Smoothing",
-]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/preprocess/__init__.pyi

@@ -0,0 +1,11 @@
+__all__ = [
+    "BasePreprocessor",
+    "fMRIPrepConfoundRemover",
+    "SpaceWarper",
+    "Smoothing",
+]
+
+from .base import BasePreprocessor
+from .confounds import fMRIPrepConfoundRemover
+from .warping import SpaceWarper
+from .smoothing import Smoothing

junifer/preprocess/confounds/__init__.py

@@ -4,7 +4,7 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from .fmriprep_confound_remover import fMRIPrepConfoundRemover
+import lazy_loader as lazy
 
 
-__all__ = ["fMRIPrepConfoundRemover"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/preprocess/confounds/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["fMRIPrepConfoundRemover"]
+
+from .fmriprep_confound_remover import fMRIPrepConfoundRemover

junifer/preprocess/smoothing/__init__.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .smoothing import Smoothing
+import lazy_loader as lazy
 
 
-__all__ = ["Smoothing"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/preprocess/smoothing/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["Smoothing"]
+
+from .smoothing import Smoothing

junifer/preprocess/warping/__init__.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .space_warper import SpaceWarper
+import lazy_loader as lazy
 
 
-__all__ = ["SpaceWarper"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/preprocess/warping/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["SpaceWarper"]
+
+from .space_warper import SpaceWarper

junifer/storage/__init__.py

@@ -4,15 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .base import BaseFeatureStorage
-from .pandas_base import PandasBaseFeatureStorage
-from .sqlite import SQLiteFeatureStorage
-from .hdf5 import HDF5FeatureStorage
+import lazy_loader as lazy
 
 
-__all__ = [
-    "BaseFeatureStorage",
-    "PandasBaseFeatureStorage",
-    "SQLiteFeatureStorage",
-    "HDF5FeatureStorage",
-]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/storage/__init__.pyi

@@ -0,0 +1,11 @@
+__all__ = [
+    "BaseFeatureStorage",
+    "PandasBaseFeatureStorage",
+    "SQLiteFeatureStorage",
+    "HDF5FeatureStorage",
+]
+
+from .base import BaseFeatureStorage
+from .pandas_base import PandasBaseFeatureStorage
+from .sqlite import SQLiteFeatureStorage
+from .hdf5 import HDF5FeatureStorage

junifer/testing/__init__.py

@@ -4,8 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from . import datagrabbers
-from .utils import get_testing_data
+import lazy_loader as lazy
 
 
-__all__ = ["datagrabbers", "get_testing_data"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/testing/__init__.pyi

@@ -0,0 +1,4 @@
+__all__ = ["datagrabbers", "get_testing_data"]
+
+from . import datagrabbers
+from .utils import get_testing_data

junifer/utils/__init__.py

@@ -4,19 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .fs import make_executable
-from .logging import configure_logging, logger, raise_error, warn_with_log
-from .helpers import run_ext_cmd, deep_update
-from ._yaml import yaml
+import lazy_loader as lazy
 
 
-__all__ = [
-    "make_executable",
-    "configure_logging",
-    "logger",
-    "raise_error",
-    "warn_with_log",
-    "run_ext_cmd",
-    "deep_update",
-    "yaml",
-]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/utils/__init__.pyi

@@ -0,0 +1,15 @@
+__all__ = [
+    "make_executable",
+    "configure_logging",
+    "logger",
+    "raise_error",
+    "warn_with_log",
+    "run_ext_cmd",
+    "deep_update",
+    "yaml",
+]
+
+from .fs import make_executable
+from .logging import configure_logging, logger, raise_error, warn_with_log
+from .helpers import run_ext_cmd, deep_update
+from ._yaml import yaml

{junifer-0.0.6.dev51.dist-info → junifer-0.0.6.dev88.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev51
+Version: 0.0.6.dev88
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -42,6 +42,7 @@ Requires-Dist: httpx[http2] ==0.26.0
 Requires-Dist: tqdm ==4.66.1
 Requires-Dist: templateflow >=23.0.0
 Requires-Dist: lapy <2.0.0,>=1.0.0
+Requires-Dist: lazy-loader ==0.4
 Requires-Dist: importlib-metadata ; python_version < "3.9"
 Requires-Dist: looseversion ==1.3.0 ; python_version >= "3.12"
 Provides-Extra: all