junifer 0.0.6.dev219__py3-none-any.whl → 0.0.6.dev248__py3-none-any.whl

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -4,11 +4,12 @@
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 import pandas as pd
 
 from ...api.decorators import register_marker
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import logger, raise_error
 from ..base import BaseMarker
 from ..parcel_aggregation import ParcelAggregation
@@ -49,9 +50,9 @@ class CrossParcellationFC(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "functional_connectivity": "matrix",
         },

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -5,11 +5,12 @@
 
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
 from ...external.nilearn import JuniferConnectivityMeasure
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import raise_error
 from ..base import BaseMarker
 
@@ -51,9 +52,9 @@ class FunctionalConnectivityBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "scikit-learn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "scikit-learn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "functional_connectivity": "matrix",
         },

junifer/markers/parcel_aggregation.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 import numpy as np
 from nilearn.image import math_img
@@ -13,6 +13,7 @@ from nilearn.maskers import NiftiMasker
 from ..api.decorators import register_marker
 from ..data import get_data
 from ..stats import get_aggfunc_by_name
+from ..typing import Dependencies, MarkerInOutMappings
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
@@ -61,9 +62,9 @@ class ParcelAggregation(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "numpy"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "T1w": {
             "aggregation": "vector",
         },

junifer/markers/reho/_afni_reho.py

@@ -8,22 +8,20 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Dict,
-    List,
     Optional,
     Tuple,
-    Union,
 )
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import ExternalDependencies
 from ...utils import logger, run_ext_cmd
 from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["AFNIReHo"]
@@ -37,7 +35,7 @@ class AFNIReHo(metaclass=Singleton):
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "afni",
             "commands": ["3dReHo", "3dAFNItoNIFTI"],

junifer/markers/reho/_junifer_reho.py

@@ -9,7 +9,6 @@ from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Set,
     Tuple,
 )
 
@@ -20,12 +19,13 @@ from nilearn import image as nimg
 from nilearn import masking as nmask
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies
 from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["JuniferReHo"]
@@ -38,7 +38,7 @@ class JuniferReHo(metaclass=Singleton):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nilearn", "scipy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nilearn", "scipy"}
 
     def __del__(self) -> None:
         """Terminate the class."""

junifer/markers/reho/reho_base.py

@@ -10,13 +10,11 @@ from typing import (
     Any,
     ClassVar,
     Dict,
-    List,
     Optional,
     Tuple,
-    Type,
-    Union,
 )
 
+from ...typing import ConditionalDependencies, MarkerInOutMappings
 from ...utils import logger, raise_error
 from ..base import BaseMarker
 from ._afni_reho import AFNIReHo
@@ -24,7 +22,7 @@ from ._junifer_reho import JuniferReHo
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 __all__ = ["ReHoBase"]
 
@@ -51,7 +49,7 @@ class ReHoBase(BaseMarker):
 
     """
 
-    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+    _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
         {
             "using": "afni",
             "depends_on": AFNIReHo,
@@ -62,7 +60,7 @@ class ReHoBase(BaseMarker):
         },
     ]
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "reho": "vector",
         },

junifer/markers/sphere_aggregation.py

@@ -4,12 +4,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from ..api.decorators import register_marker
 from ..data import get_data
 from ..external.nilearn import JuniferNiftiSpheresMasker
 from ..stats import get_aggfunc_by_name
+from ..typing import Dependencies, MarkerInOutMappings
 from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
@@ -66,9 +67,9 @@ class SphereAggregation(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn", "numpy"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "T1w": {
             "aggregation": "vector",
         },

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -5,10 +5,11 @@
 
 
 from abc import abstractmethod
-from typing import Any, ClassVar, Dict, List, Optional, Set, Union
+from typing import Any, ClassVar, Dict, List, Optional, Union
 
 from nilearn import image as nimg
 
+from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import raise_error
 from ..base import BaseMarker
 
@@ -37,9 +38,9 @@ class TemporalSNRBase(BaseMarker):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
-    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings] = {
         "BOLD": {
             "tsnr": "vector",
         },

junifer/onthefly/_brainprint.py

@@ -3,23 +3,20 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import TYPE_CHECKING, Dict, Optional, Type
+from typing import Dict, Optional
 
 import numpy as np
 import pandas as pd
 
+from ..typing import StorageLike
 from ..utils import raise_error
 
 
-if TYPE_CHECKING:
-    from junifer.storage import BaseFeatureStorage
-
-
 __all__ = ["normalize", "reweight"]
 
 
 def normalize(
-    storage: Type["BaseFeatureStorage"],
+    storage: StorageLike,
     features: Dict[str, Dict[str, Optional[str]]],
     kind: str,
 ) -> pd.DataFrame:
@@ -89,7 +86,7 @@ def normalize(
 
 
 def reweight(
-    storage: Type["BaseFeatureStorage"],
+    storage: StorageLike,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,
 ) -> pd.DataFrame:

junifer/onthefly/read_transform.py

@@ -4,22 +4,19 @@
 # License: AGPL
 
 
-from typing import TYPE_CHECKING, Dict, Optional, Tuple, Type
+from typing import Dict, Optional, Tuple
 
 import pandas as pd
 
+from ..typing import StorageLike
 from ..utils import logger, raise_error, warn_with_log
 
 
-if TYPE_CHECKING:
-    from junifer.storage import BaseFeatureStorage
-
-
 __all__ = ["read_transform"]
 
 
 def read_transform(
-    storage: Type["BaseFeatureStorage"],
+    storage: StorageLike,
     transform: str,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,

junifer/pipeline/marker_collection.py

@@ -5,20 +5,14 @@
 # License: AGPL
 
 from collections import Counter
-from typing import TYPE_CHECKING, Dict, List, Optional
+from typing import Dict, List, Optional
 
 from ..datareader import DefaultDataReader
 from ..pipeline import PipelineStepMixin, WorkDirManager
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 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 +39,10 @@ class MarkerCollection:
 
     def __init__(
         self,
-        markers: List["BaseMarker"],
+        markers: List[MarkerLike],
         datareader: Optional[PipelineStepMixin] = None,
-        preprocessors: Optional[List["BasePreprocessor"]] = None,
-        storage: Optional["BaseFeatureStorage"] = None,
+        preprocessors: Optional[List[PreprocessorLike]] = None,
+        storage: Optional[StorageLike] = None,
     ):
         # Check that the markers have different names
         marker_names = [m.name for m in markers]
@@ -111,7 +105,7 @@ class MarkerCollection:
 
         return None if self._storage else out
 
-    def validate(self, datagrabber: "BaseDataGrabber") -> None:
+    def validate(self, datagrabber: DataGrabberLike) -> None:
         """Validate the pipeline.
 
         Without doing any computation, check if the marker collection can

junifer/pipeline/pipeline_component_registry.py

@@ -6,18 +6,13 @@
 # License: AGPL
 
 import importlib
-from typing import TYPE_CHECKING, Dict, List, Mapping, Optional, Union
+from typing import Dict, List, Mapping, Optional, Union
 
+from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error
 from ..utils.singleton import Singleton
 
 
-if TYPE_CHECKING:
-    from ..datagrabber import BaseDataGrabber
-    from ..storage import BaseFeatureStorage
-    from .pipeline_step_mixin import PipelineStepMixin
-
-
 __all__ = ["PipelineComponentRegistry"]
 
 
@@ -241,7 +236,7 @@ class PipelineComponentRegistry(metaclass=Singleton):
         name: str,
         baseclass: type,
         init_params: Optional[Dict] = None,
-    ) -> Union["BaseDataGrabber", "PipelineStepMixin", "BaseFeatureStorage"]:
+    ) -> Union[DataGrabberLike, PreprocessorLike, MarkerLike, StorageLike]:
         """Build an instance of class registered as ``name``.
 
         Parameters

junifer/pipeline/pipeline_step_mixin.py

@@ -196,10 +196,14 @@ class PipelineStepMixin:
                     for dependency in obj._CONDITIONAL_DEPENDENCIES:
                         if dependency["using"] == obj.using:
                             depends_on = dependency["depends_on"]
-                            # Check dependencies
-                            _check_dependencies(depends_on)
-                            # Check external dependencies
-                            _check_ext_dependencies(depends_on)
+                            # Conditional to make `using="auto"` work
+                            if not isinstance(depends_on, list):
+                                depends_on = [depends_on]
+                            for entry in depends_on:
+                                # Check dependencies
+                                _check_dependencies(entry)
+                                # Check external dependencies
+                                _check_ext_dependencies(entry)
 
         # Check dependencies
         _check_dependencies(self)

junifer/pipeline/tests/test_pipeline_step_mixin.py

@@ -5,12 +5,17 @@
 # License: AGPL
 
 import warnings
-from typing import ClassVar, Dict, List, Set, Type, Union
+from typing import ClassVar, Dict, List
 
 import pytest
 
 from junifer.pipeline.pipeline_step_mixin import PipelineStepMixin
 from junifer.pipeline.utils import _check_afni
+from junifer.typing import (
+    ConditionalDependencies,
+    Dependencies,
+    ExternalDependencies,
+)
 
 
 def test_PipelineStepMixin_correct_dependencies() -> None:
@@ -19,7 +24,7 @@ def test_PipelineStepMixin_correct_dependencies() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _DEPENDENCIES: ClassVar[Set[str]] = {"math"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"math"}
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -40,7 +45,7 @@ def test_PipelineStepMixin_incorrect_dependencies() -> None:
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _DEPENDENCIES: ClassVar[Set[str]] = {"foobar"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"foobar"}
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -65,7 +70,7 @@ def test_PipelineStepMixin_correct_ext_dependencies() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, str]]] = [{"name": "afni"}]
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [{"name": "afni"}]
 
         def validate_input(self, input: List[str]) -> List[str]:
             return input
@@ -89,7 +94,7 @@ def test_PipelineStepMixin_ext_deps_correct_commands() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
             {"name": "afni", "commands": ["3dReHo"]}
         ]
 
@@ -117,7 +122,7 @@ def test_PipelineStepMixin_ext_deps_incorrect_commands() -> None:
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
             {"name": "afni", "commands": ["3d"]}
         ]
 
@@ -141,7 +146,7 @@ def test_PipelineStepMixin_incorrect_ext_dependencies() -> None:
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, bool]]]] = [
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
             {"name": "foobar", "optional": True}
         ]
 
@@ -163,14 +168,12 @@ def test_PipelineStepMixin_correct_conditional_dependencies() -> None:
     """Test fit-transform with correct conditional dependencies."""
 
     class Dependency:
-        _DEPENDENCIES: ClassVar[Set[str]] = {"math"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"math"}
 
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _CONDITIONAL_DEPENDENCIES: ClassVar[
-            List[Dict[str, Union[str, Type]]]
-        ] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "math",
                 "depends_on": Dependency,
@@ -196,14 +199,12 @@ def test_PipelineStepMixin_incorrect_conditional_dependencies() -> None:
     """Test fit-transform with incorrect conditional dependencies."""
 
     class Dependency:
-        _DEPENDENCIES: ClassVar[Set[str]] = {"math"}
+        _DEPENDENCIES: ClassVar[Dependencies] = {"math"}
 
     class IncorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _CONDITIONAL_DEPENDENCIES: ClassVar[
-            List[Dict[str, Union[str, Type]]]
-        ] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "math",
                 "depends_on": Dependency,
@@ -231,14 +232,12 @@ def test_PipelineStepMixin_correct_conditional_ext_dependencies() -> None:
     """Test fit-transform with correct conditional external dependencies."""
 
     class ExternalDependency:
-        _EXT_DEPENDENCIES: ClassVar[List[Dict[str, str]]] = [{"name": "afni"}]
+        _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [{"name": "afni"}]
 
     class CorrectMixer(PipelineStepMixin):
         """Test class for validation."""
 
-        _CONDITIONAL_DEPENDENCIES: ClassVar[
-            List[Dict[str, Union[str, Type]]]
-        ] = [
+        _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
             {
                 "using": "afni",
                 "depends_on": ExternalDependency,

junifer/pipeline/tests/test_workdir_manager.py

@@ -103,6 +103,7 @@ def test_workdir_manager_get_and_delete_tempdir(tmp_path: Path) -> None:
     # Should remove temporary directory
     assert workdir_mgr.root_tempdir is None
 
+
 def test_workdir_manager_no_cleanup(tmp_path: Path) -> None:
     """Test WorkDirManager correctly bypasses cleanup.
 

junifer/pipeline/update_meta_mixin.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Dict
+from typing import Dict, List, Union
 
 
 __all__ = ["UpdateMetaMixin"]
@@ -15,14 +15,14 @@ class UpdateMetaMixin:
 
     def update_meta(
         self,
-        input: Dict,
+        input: Union[Dict, List[Dict]],
         step_name: str,
     ) -> None:
         """Update metadata.
 
         Parameters
         ----------
-        input : dict
+        input : dict or list of dict
             The data object to update.
         step_name : str
             The name of the pipeline step.
@@ -36,17 +36,21 @@ class UpdateMetaMixin:
         for k, v in vars(self).items():
             if not k.startswith("_"):
                 t_meta[k] = v
-        # Add "meta" to the step's local context dict
-        if "meta" not in input:
-            input["meta"] = {}
-        # Add step name
-        input["meta"][step_name] = t_meta
-        # Add step dependencies
-        if "dependencies" not in input["meta"]:
-            input["meta"]["dependencies"] = set()
-        # Update step dependencies
-        dependencies = getattr(self, "_DEPENDENCIES", set())
-        if dependencies is not None:
-            if not isinstance(dependencies, (set, list)):
-                dependencies = {dependencies}
-            input["meta"]["dependencies"].update(dependencies)
+        # Conditional for list dtype vals like Warp
+        if not isinstance(input, list):
+            input = [input]
+        for entry in input:
+            # Add "meta" to the step's entry's local context dict
+            if "meta" not in entry:
+                entry["meta"] = {}
+            # Add step name
+            entry["meta"][step_name] = t_meta
+            # Add step dependencies
+            if "dependencies" not in entry["meta"]:
+                entry["meta"]["dependencies"] = set()
+            # Update step dependencies
+            dependencies = getattr(self, "_DEPENDENCIES", set())
+            if dependencies is not None:
+                if not isinstance(dependencies, (set, list)):
+                    dependencies = {dependencies}
+                entry["meta"]["dependencies"].update(dependencies)

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -11,7 +11,6 @@ from typing import (
     Dict,
     List,
     Optional,
-    Set,
     Tuple,
     Union,
 )
@@ -23,6 +22,7 @@ from nilearn._utils.niimg_conversions import check_niimg_4d
 
 from ...api.decorators import register_preprocessor
 from ...data import get_data
+from ...typing import Dependencies
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 
@@ -152,7 +152,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nilearn"}
 
     def __init__(
         self,

junifer/preprocess/smoothing/_afni_smoothing.py

@@ -6,20 +6,18 @@
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Dict,
-    List,
-    Set,
     Union,
 )
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies, ExternalDependencies
 from ...utils import logger, run_ext_cmd
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["AFNISmoothing"]
@@ -32,14 +30,14 @@ class AFNISmoothing:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "afni",
             "commands": ["3dBlurToFWHM"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nibabel"}
 
     def preprocess(
         self,