docs/changes/newsfragments/239.enh

@@ -0,0 +1 @@
+Improve logging consistency of components by `Synchon Mandal`_

docs/extending/index.rst

@@ -23,6 +23,7 @@ DataGrabbers, Preprocessors, Markers, etc.,  following the *junifer* way.
    :caption: Contents:
 
    extension
+   logging
    datagrabber
    marker
    preprocessor

docs/extending/logging.rst

@@ -0,0 +1,38 @@
+.. include:: ../links.inc
+
+.. _logging_in_extension:
+
+Logging in a ``junifer`` extension
+==================================
+
+It is important to have proper logging in your code and ``junifer`` makes it trivial to do so for your extensions.
+
+For DataGrabber:
+
+.. code-block:: python
+
+   from junifer.datagrabber import logger
+
+
+For Preprocessor:
+
+.. code-block:: python
+
+   from junifer.preprocess import logger
+
+
+For Marker:
+
+.. code-block:: python
+
+   from junifer.marker import logger
+
+
+For Storage:
+
+.. code-block:: python
+
+   from junifer.storage import logger
+
+
+Importing the correct logger will give you a properly set up logger which will fit right in with the rest of ``junifer``\'s log output.

junifer/api/functions.py

@@ -10,6 +10,8 @@ import os
 import shutil
 from pathlib import Path
 
+import structlog
+
 from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from ..datagrabber import BaseDataGrabber
 from ..markers import BaseMarker
@@ -27,11 +29,14 @@ from ..typing import (
     PreprocessorLike,
     StorageLike,
 )
-from ..utils import logger, raise_error, warn_with_log, yaml
+from ..utils import raise_error, warn_with_log, yaml
 
 
 __all__ = ["collect", "list_elements", "queue", "reset", "run"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="api")
+
 
 def _get_datagrabber(datagrabber_config: dict) -> DataGrabberLike:
     """Get DataGrabber.

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -9,12 +9,13 @@ from pathlib import Path
 from typing import Any
 
 from ...typing import Elements
-from ...utils import logger, make_executable, raise_error, run_ext_cmd
+from ...utils import make_executable, raise_error, run_ext_cmd
 from .queue_context_adapter import (
     EnvKind,
     EnvShell,
     QueueContextAdapter,
     QueueContextEnv,
+    logger,
 )
 
 

junifer/api/queue_context/htcondor_adapter.py

@@ -10,12 +10,13 @@ from pathlib import Path
 from typing import Any
 
 from ...typing import Elements
-from ...utils import logger, make_executable, raise_error, run_ext_cmd
+from ...utils import make_executable, raise_error, run_ext_cmd
 from .queue_context_adapter import (
     EnvKind,
     EnvShell,
     QueueContextAdapter,
     QueueContextEnv,
+    logger,
 )
 
 

junifer/api/queue_context/queue_context_adapter.py

@@ -19,6 +19,7 @@ else:
 from abc import ABC, abstractmethod
 from enum import Enum
 
+import structlog
 from pydantic import BaseModel, ConfigDict
 
 from ...utils import raise_error
@@ -26,6 +27,9 @@ from ...utils import raise_error
 
 __all__ = ["EnvKind", "EnvShell", "QueueContextAdapter", "QueueContextEnv"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="api")
+
 
 class EnvKind(str, Enum):
     """Accepted Python environment kind."""

junifer/cli/parser.py

@@ -10,13 +10,17 @@ import sys
 from pathlib import Path
 
 import pandas as pd
+import structlog
 
 from ..typing import Elements
-from ..utils import logger, raise_error, warn_with_log, yaml
+from ..utils import raise_error, warn_with_log, yaml
 
 
 __all__ = ["parse_elements", "parse_yaml"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="cli")
+
 
 def parse_yaml(filepath: str | Path) -> dict:  # noqa: C901
     """Parse YAML.

junifer/data/coordinates/_ants_coordinates_warper.py

@@ -9,7 +9,7 @@ import numpy as np
 from numpy.typing import ArrayLike
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 __all__ = ["ANTsCoordinatesWarper"]
@@ -46,6 +46,9 @@ class ANTsCoordinatesWarper:
             The transformed coordinates.
 
         """
+        # Imported here to avoid circular import
+        from ._coordinates import logger
+
         logger.debug("Using ANTs for coordinates transformation")
 
         # Create element-specific tempdir for storing post-warping assets

junifer/data/coordinates/_coordinates.py

@@ -9,10 +9,11 @@ from typing import Any
 
 import numpy as np
 import pandas as pd
+import structlog
 from junifer_data import get
 from numpy.typing import ArrayLike
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import JUNIFER_DATA_PARAMS, get_dataset_path, get_native_warper
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
@@ -21,6 +22,9 @@ from ._fsl_coordinates_warper import FSLCoordinatesWarper
 
 __all__ = ["CoordinatesRegistry"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 class CoordinatesRegistry(BasePipelineDataRegistry):
     """Class for coordinates data registry.

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -9,7 +9,7 @@ import numpy as np
 from numpy.typing import ArrayLike
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 __all__ = ["FSLCoordinatesWarper"]
@@ -46,6 +46,9 @@ class FSLCoordinatesWarper:
             The transformed coordinates.
 
         """
+        # Imported here to avoid circular import
+        from ._coordinates import logger
+
         logger.debug("Using FSL for coordinates transformation")
 
         # Create element-specific tempdir for storing post-warping assets

junifer/data/maps/_ants_maps_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -71,6 +71,9 @@ class ANTsMapsWarper:
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._maps import logger
+
         # Create element-scoped tempdir so that warped maps is
         # available later as nibabel stores file path reference for
         # loading on computation

junifer/data/maps/_fsl_maps_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -53,6 +53,9 @@ class FSLMapsWarper:
             The transformed maps image.
 
         """
+        # Imported here to avoid circular import
+        from ._maps import logger
+
         logger.debug("Using FSL for maps transformation")
 
         # Create element-scoped tempdir so that warped maps is

junifer/data/maps/_maps.py

@@ -9,9 +9,10 @@ from typing import TYPE_CHECKING, Any, Optional
 import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
+import structlog
 from junifer_data import get
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import (
     JUNIFER_DATA_PARAMS,
@@ -29,6 +30,9 @@ if TYPE_CHECKING:
 
 __all__ = ["MapsRegistry"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 class MapsRegistry(BasePipelineDataRegistry):
     """Class for maps data registry.

junifer/data/masks/_ants_mask_warper.py

@@ -10,7 +10,7 @@ import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -92,6 +92,9 @@ class ANTsMaskWarper:
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._masks import logger
+
         # Create element-scoped tempdir so that warped mask is
         # available later as nibabel stores file path reference for
         # loading on computation

junifer/data/masks/_fsl_mask_warper.py

@@ -10,7 +10,7 @@ import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -74,6 +74,9 @@ class FSLMaskWarper:
             The transformed mask image.
 
         """
+        # Imported here to avoid circular import
+        from ._masks import logger
+
         logger.debug("Using FSL for mask transformation")
 
         # Create element-scoped tempdir so that warped mask is

junifer/data/masks/_masks.py

@@ -15,6 +15,7 @@ from typing import (
 import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
+import structlog
 from junifer_data import get
 from nilearn.masking import (
     compute_background_mask,
@@ -22,7 +23,7 @@ from nilearn.masking import (
     intersect_masks,
 )
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
 from ..utils import (
@@ -41,6 +42,9 @@ if TYPE_CHECKING:
 
 __all__ = ["MaskRegistry", "compute_brain_mask"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 def compute_brain_mask(
     target_data: dict[str, Any],

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -71,6 +71,9 @@ class ANTsParcellationWarper:
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._parcellations import logger
+
         # Create element-scoped tempdir so that warped parcellation is
         # available later as nibabel stores file path reference for
         # loading on computation

junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -53,6 +53,9 @@ class FSLParcellationWarper:
             The transformed parcellation image.
 
         """
+        # Imported here to avoid circular import
+        from ._parcellations import logger
+
         logger.debug("Using FSL for parcellation transformation")
 
         # Create element-scoped tempdir so that warped parcellation is

junifer/data/parcellations/_parcellations.py

@@ -13,9 +13,10 @@ import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
 import pandas as pd
+import structlog
 from junifer_data import get
 
-from ...utils import logger, raise_error, warn_with_log
+from ...utils import raise_error, warn_with_log
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import (
     JUNIFER_DATA_PARAMS,
@@ -36,6 +37,9 @@ __all__ = [
     "merge_parcellations",
 ]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 class ParcellationRegistry(BasePipelineDataRegistry):
     """Class for parcellation data registry.
@@ -58,8 +62,12 @@ class ParcellationRegistry(BasePipelineDataRegistry):
         # The built-in parcellations are files that are shipped with the
         # junifer-data dataset.
         # Make built-in and external dictionaries for validation later
-        self._builtin = {}
+        self._builtin: dict[
-        self._external = {}
+            str, dict[str, str | int | Path | list[str] | list[int]]
+        ] = {}
+        self._external: dict[
+            str, dict[str, str | int | Path | list[str] | list[int]]
+        ] = {}
 
         # Add SUIT
         self._builtin.update(

junifer/data/template_spaces.py

@@ -8,15 +8,19 @@ from typing import Any, Union
 
 import nibabel as nib
 import numpy as np
+import structlog
 from junifer_data import get
 from templateflow import api as tflow
 
-from ..utils import logger, raise_error
+from ..utils import raise_error
 from .utils import JUNIFER_DATA_PARAMS, closest_resolution, get_dataset_path
 
 
 __all__ = ["get_template", "get_xfm"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 def get_xfm(src: str, dst: str) -> Path:  # pragma: no cover
     """Fetch warp files to convert from ``src`` to ``dst``.

junifer/data/utils.py

@@ -8,8 +8,9 @@ from collections.abc import MutableMapping
 from pathlib import Path
 
 import numpy as np
+import structlog
 
-from ..utils import config, logger, raise_error
+from ..utils import config, raise_error
 
 
 __all__ = [
@@ -21,6 +22,8 @@ __all__ = [
     "get_native_warper",
 ]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
 
 # junifer-data version constant
 JUNIFER_DATA_VERSION = "7"

junifer/datagrabber/__init__.pyi

@@ -26,10 +26,11 @@ __all__ = [
     "DataType",
     "ConfoundsFormat",
     "register_confounds_format",
+    "logger",
 ]
 
 # These 4 need to be in this order, otherwise it is a circular import
-from .base import BaseDataGrabber, DataType
+from .base import BaseDataGrabber, DataType, logger
 from .datalad_base import DataladDataGrabber
 from .pattern import (
     PatternDataGrabber,

junifer/datagrabber/base.py

@@ -11,16 +11,20 @@ from enum import Enum
 from pathlib import Path
 from typing import Annotated, Any
 
+import structlog
 from aenum import Enum as AEnum
 from pydantic import BaseModel, BeforeValidator, ConfigDict, Field
 
 from ..pipeline import UpdateMetaMixin
 from ..typing import Element, Elements
-from ..utils import ensure_list, logger, raise_error
+from ..utils import ensure_list, raise_error
 
 
 __all__ = ["BaseDataGrabber", "DataType"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="datagrabber", step="datagrabber")
+
 
 class DataType(str, AEnum):
     """Accepted data type."""
@@ -64,11 +68,16 @@ class BaseDataGrabber(BaseModel, ABC, UpdateMetaMixin):
     datadir: Path
 
     def model_post_init(self, context: Any):  # noqa: D102
-        logger.debug("Initializing BaseDataGrabber")
-        logger.debug(f"\tdatadir = {self.datadir}")
-        logger.debug(f"\ttypes = {self.types}")
         # Run extra validation for datagrabbers and fail early if needed
         self.validate_datagrabber_params()
+        # Convert to correct data type
+        self.types = [
+            DataType(t) if isinstance(t, str) else t for t in self.types
+        ]
+        logger.info(
+            f"Parameters: {self.model_dump(mode='json')}",
+            component=self.__class__.__name__,
+        )
 
     def validate_datagrabber_params(self) -> None:
         """Run extra logical validation for datagrabber.

junifer/datagrabber/datalad_base.py

@@ -20,8 +20,8 @@ from pydantic import AnyUrl, Field, field_validator
 from ..api.decorators import register_datagrabber
 from ..pipeline import WorkDirManager
 from ..typing import Element
-from ..utils import config, logger, raise_error, warn_with_log
+from ..utils import config, raise_error, warn_with_log
-from .base import BaseDataGrabber
+from .base import BaseDataGrabber, logger
 
 
 __all__ = ["DataladDataGrabber"]

junifer/datagrabber/pattern.py

@@ -16,8 +16,8 @@ from pydantic import Field
 
 from ..api.decorators import register_datagrabber
 from ..typing import DataGrabberPatterns, Elements
-from ..utils import logger, raise_error
+from ..utils import raise_error
-from .base import BaseDataGrabber
+from .base import BaseDataGrabber, logger
 from .pattern_validation_mixin import PatternValidationMixin
 
 

junifer/datagrabber/pattern_datalad.py

@@ -8,7 +8,7 @@
 from pydantic import ConfigDict
 
 from ..api.decorators import register_datagrabber
-from ..utils import logger
+from .base import logger
 from .datalad_base import DataladDataGrabber
 from .pattern import PatternDataGrabber
 

junifer/datagrabber/pattern_validation_mixin.py

@@ -16,9 +16,9 @@ from collections.abc import Iterator, MutableMapping
 
 from aenum import extend_enum
 
-from ..datagrabber import DataType
 from ..typing import DataGrabberPatterns
-from ..utils import logger, raise_error, warn_with_log
+from ..utils import raise_error, warn_with_log
+from .base import DataType, logger
 
 
 __all__ = [

junifer/datareader/default.py

@@ -8,15 +8,18 @@ from pathlib import Path
 
 import nibabel as nib
 import pandas as pd
+import structlog
 from pydantic import BaseModel
 
 from ..api.decorators import register_datareader
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
-from ..utils.logging import logger, warn_with_log
+from ..utils.logging import warn_with_log
 
 
 __all__ = ["DefaultDataReader"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="datareader", step="datareader")
 
 # Map each file extension to a type
 _extensions = {

junifer/markers/__init__.pyi

@@ -23,9 +23,10 @@ __all__ = [
     "TemporalSNRParcels",
     "TemporalSNRSpheres",
     "BrainPrint",
+    "logger",
 ]
 
-from .base import BaseMarker
+from .base import BaseMarker, logger
 from .ets_rss import RSSETSMarker
 from .maps_aggregation import MapsAggregation
 from .parcel_aggregation import ParcelAggregation

junifer/markers/base.py

@@ -8,17 +8,21 @@ from abc import ABC, abstractmethod
 from copy import deepcopy
 from typing import Any, ClassVar
 
+import structlog
 from pydantic import BaseModel, ConfigDict
 
 from ..datagrabber import DataType
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..storage import StorageType
 from ..typing import MarkerInOutMappings, StorageLike
-from ..utils import logger, raise_error
+from ..utils import raise_error
 
 
 __all__ = ["BaseMarker"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="markers", step="marker")
+
 
 class BaseMarker(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
     """Abstract base class for marker.
@@ -84,6 +88,9 @@ class BaseMarker(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
         self.validate_marker_params()
         # Set default name if not provided
         self.name = self.__class__.__name__ if self.name is None else self.name
+        logger.info(
+            f"Parameters: {self.model_dump(mode='json')}", component=self.name
+        )
 
     @property
     def valid_inputs(self) -> list[DataType]:

junifer/markers/brainprint.py

@@ -24,8 +24,8 @@ from ..external.BrainPrint.brainprint.surfaces import surf_to_vtk
 from ..pipeline import ExtDep, WorkDirManager
 from ..storage import StorageType
 from ..typing import Dependencies, ExternalDependencies, MarkerInOutMappings
-from ..utils import logger, run_ext_cmd
+from ..utils import run_ext_cmd
-from .base import BaseMarker
+from .base import BaseMarker, logger
 
 
 __all__ = ["BrainPrint"]

junifer/markers/complexity/hurst_exponent.py

@@ -9,7 +9,8 @@ import neurokit2 as nk
 import numpy as np
 
 from ...api.decorators import register_marker
-from ...utils import logger, warn_with_log
+from ...utils import warn_with_log
+from ..base import logger
 from .complexity_base import ComplexityBase
 
 

junifer/markers/complexity/multiscale_entropy_auc.py

@@ -9,7 +9,8 @@ import neurokit2 as nk
 import numpy as np
 
 from ...api.decorators import register_marker
-from ...utils import logger, warn_with_log
+from ...utils import warn_with_log
+from ..base import logger
 from .complexity_base import ComplexityBase
 
 

junifer/markers/complexity/perm_entropy.py

@@ -9,7 +9,8 @@ import neurokit2 as nk
 import numpy as np
 
 from ...api.decorators import register_marker
-from ...utils import logger, warn_with_log
+from ...utils import warn_with_log
+from ..base import logger
 from .complexity_base import ComplexityBase
 
 

junifer/markers/complexity/range_entropy.py

@@ -9,7 +9,8 @@ import neurokit2 as nk
 import numpy as np
 
 from ...api.decorators import register_marker
-from ...utils import logger, warn_with_log
+from ...utils import warn_with_log
+from ..base import logger
 from .complexity_base import ComplexityBase
 
 

junifer/markers/complexity/range_entropy_auc.py

@@ -9,7 +9,8 @@ import neurokit2 as nk
 import numpy as np
 
 from ...api.decorators import register_marker
-from ...utils import logger, warn_with_log
+from ...utils import warn_with_log
+from ..base import logger
 from .complexity_base import ComplexityBase
 
 

junifer/markers/complexity/sample_entropy.py

@@ -9,7 +9,8 @@ import neurokit2 as nk
 import numpy as np
 
 from ...api.decorators import register_marker
-from ...utils import logger, warn_with_log
+from ...utils import warn_with_log
+from ..base import logger
 from .complexity_base import ComplexityBase
 
 

junifer/markers/complexity/weighted_perm_entropy.py

@@ -9,7 +9,8 @@ import neurokit2 as nk
 import numpy as np
 
 from ...api.decorators import register_marker
-from ...utils import logger, warn_with_log
+from ...utils import warn_with_log
+from ..base import logger
 from .complexity_base import ComplexityBase
 
 

junifer/markers/ets_rss.py

@@ -15,8 +15,8 @@ from ..api.decorators import register_marker
 from ..datagrabber import DataType
 from ..storage import StorageType
 from ..typing import Dependencies, MarkerInOutMappings
-from ..utils import ensure_list, ensure_list_or_none, logger
+from ..utils import ensure_list, ensure_list_or_none
-from .base import BaseMarker
+from .base import BaseMarker, logger
 from .parcel_aggregation import ParcelAggregation
 from .utils import _ets
 

junifer/markers/falff/_afni_falff.py

@@ -15,8 +15,9 @@ import nibabel as nib
 
 from ...pipeline import ExtDep, WorkDirManager
 from ...typing import ExternalDependencies
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 from ...utils.singleton import Singleton
+from ..base import logger
 
 
 if TYPE_CHECKING:

junifer/markers/falff/_junifer_falff.py

@@ -17,8 +17,8 @@ from nilearn import image as nimg
 
 from ...pipeline import WorkDirManager
 from ...typing import Dependencies
-from ...utils import logger
 from ...utils.singleton import Singleton
+from ..base import logger
 
 
 if TYPE_CHECKING:

junifer/markers/falff/falff_base.py

@@ -20,8 +20,8 @@ from pydantic import BeforeValidator, PositiveFloat
 from ...datagrabber import DataType
 from ...storage import StorageType
 from ...typing import ConditionalDependencies, MarkerInOutMappings
-from ...utils import ensure_list_or_none, logger
+from ...utils import ensure_list_or_none
-from ..base import BaseMarker
+from ..base import BaseMarker, logger
 from ._afni_falff import AFNIALFF
 from ._junifer_falff import JuniferALFF
 

junifer/markers/falff/falff_maps.py

@@ -7,7 +7,7 @@ from typing import Any
 
 from ...api.decorators import register_marker
 from ...datagrabber import DataType
-from ...utils import logger
+from ..base import logger
 from ..maps_aggregation import MapsAggregation
 from .falff_base import ALFFBase
 

junifer/markers/falff/falff_parcels.py

@@ -12,7 +12,8 @@ from pydantic import BeforeValidator
 
 from ...api.decorators import register_marker
 from ...datagrabber import DataType
-from ...utils import ensure_list, logger
+from ...utils import ensure_list
+from ..base import logger
 from ..parcel_aggregation import ParcelAggregation
 from .falff_base import ALFFBase
 

junifer/markers/falff/falff_spheres.py

@@ -12,7 +12,7 @@ from pydantic import PositiveFloat
 
 from ...api.decorators import register_marker
 from ...datagrabber import DataType
-from ...utils import logger
+from ..base import logger
 from ..sphere_aggregation import SphereAggregation
 from .falff_base import ALFFBase
 

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -13,8 +13,8 @@ from ...api.decorators import register_marker
 from ...datagrabber import DataType
 from ...storage import StorageType
 from ...typing import Dependencies, MarkerInOutMappings
-from ...utils import ensure_list_or_none, logger, raise_error
+from ...utils import ensure_list_or_none, raise_error
-from ..base import BaseMarker
+from ..base import BaseMarker, logger
 from ..parcel_aggregation import ParcelAggregation
 from ..utils import _correlate_dataframes
 

junifer/markers/maps_aggregation.py

@@ -14,8 +14,8 @@ from ..datagrabber import DataType
 from ..stats import get_aggfunc_by_name
 from ..storage import StorageType
 from ..typing import Dependencies, MarkerInOutMappings
-from ..utils import ensure_list_or_none, logger, raise_error, warn_with_log
+from ..utils import ensure_list_or_none, raise_error, warn_with_log
-from .base import BaseMarker
+from .base import BaseMarker, logger
 
 
 __all__ = ["MapsAggregation"]

junifer/markers/parcel_aggregation.py

@@ -20,11 +20,10 @@ from ..typing import Dependencies, MarkerInOutMappings
 from ..utils import (
     ensure_list,
     ensure_list_or_none,
-    logger,
     raise_error,
     warn_with_log,
 )
-from .base import BaseMarker
+from .base import BaseMarker, logger
 
 
 __all__ = ["ParcelAggregation"]

junifer/markers/reho/_afni_reho.py

@@ -15,8 +15,9 @@ import nibabel as nib
 
 from ...pipeline import ExtDep, WorkDirManager
 from ...typing import ExternalDependencies
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 from ...utils.singleton import Singleton
+from ..base import logger
 
 
 if TYPE_CHECKING:

junifer/markers/reho/_junifer_reho.py

@@ -19,8 +19,9 @@ from nilearn import masking as nmask
 
 from ...pipeline import WorkDirManager
 from ...typing import Dependencies
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ...utils.singleton import Singleton
+from ..base import logger
 
 
 if TYPE_CHECKING:

junifer/markers/reho/reho_base.py

@@ -17,8 +17,8 @@ from pydantic import BeforeValidator
 from ...datagrabber import DataType
 from ...storage import StorageType
 from ...typing import ConditionalDependencies, MarkerInOutMappings
-from ...utils import ensure_list_or_none, logger
+from ...utils import ensure_list_or_none
-from ..base import BaseMarker
+from ..base import BaseMarker, logger
 from ._afni_reho import AFNIReHo
 from ._junifer_reho import JuniferReHo
 

junifer/markers/reho/reho_maps.py

@@ -9,7 +9,7 @@ import numpy as np
 
 from ...api.decorators import register_marker
 from ...datagrabber import DataType
-from ...utils import logger
+from ..base import logger
 from ..maps_aggregation import MapsAggregation
 from .reho_base import ReHoBase
 

junifer/markers/reho/reho_parcels.py

@@ -10,7 +10,8 @@ from pydantic import BeforeValidator
 
 from ...api.decorators import register_marker
 from ...datagrabber import DataType
-from ...utils import ensure_list, logger
+from ...utils import ensure_list
+from ..base import logger
 from ..parcel_aggregation import ParcelAggregation
 from .reho_base import ReHoBase
 

junifer/markers/reho/reho_spheres.py

@@ -10,7 +10,7 @@ from pydantic import PositiveFloat
 
 from ...api.decorators import register_marker
 from ...datagrabber import DataType
-from ...utils import logger
+from ..base import logger
 from ..sphere_aggregation import SphereAggregation
 from .reho_base import ReHoBase
 

junifer/markers/sphere_aggregation.py

@@ -15,8 +15,8 @@ from ..external.nilearn import JuniferNiftiSpheresMasker
 from ..stats import get_aggfunc_by_name
 from ..storage import StorageType
 from ..typing import Dependencies, MarkerInOutMappings
-from ..utils import ensure_list_or_none, logger, raise_error, warn_with_log
+from ..utils import ensure_list_or_none, raise_error, warn_with_log
-from .base import BaseMarker
+from .base import BaseMarker, logger
 
 
 __all__ = ["SphereAggregation"]

junifer/onthefly/read_transform.py

@@ -5,13 +5,17 @@
 
 import numpy as np
 import pandas as pd
+import structlog
 
 from ..typing import StorageLike
-from ..utils import logger, raise_error, warn_with_log
+from ..utils import raise_error, warn_with_log
 
 
 __all__ = ["read_transform"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="onthefly")
+
 
 def read_transform(
     storage: StorageLike,

junifer/pipeline/marker_collection.py

@@ -7,14 +7,19 @@
 from collections import Counter
 from pathlib import Path
 
+import structlog
+
 from ..datareader import DefaultDataReader
 from ..pipeline import DataObjectDumper, PipelineStepMixin, WorkDirManager
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
-from ..utils import config, logger, raise_error
+from ..utils import config, raise_error
 
 
 __all__ = ["MarkerCollection"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="pipeline")
+
 
 class MarkerCollection:
     """Class for marker collection.

junifer/pipeline/pipeline_component_registry.py

@@ -8,13 +8,18 @@
 import importlib
 from collections.abc import Mapping
 
+import structlog
+
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
-from ..utils import logger, raise_error
+from ..utils import raise_error
 from ..utils.singleton import Singleton
 
 
 __all__ = ["PipelineComponentRegistry"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="pipeline")
+
 
 class PipelineComponentRegistry(metaclass=Singleton):
     """Class for pipeline component registry.

junifer/pipeline/utils.py

@@ -10,7 +10,7 @@ from typing import Any
 
 from pydantic import validate_call
 
-from ..utils.logging import raise_error, warn_with_log
+from ..utils import raise_error, warn_with_log
 
 
 __all__ = ["ExtDep", "check_ext_dependencies"]

junifer/pipeline/workdir_manager.py

@@ -8,12 +8,16 @@ import shutil
 import tempfile
 from pathlib import Path
 
-from ..utils import logger
+import structlog
+
 from ..utils.singleton import Singleton
 
 
 __all__ = ["WorkDirManager"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="pipeline")
+
 
 class WorkDirManager(metaclass=Singleton):
     """Class for working directory manager.

junifer/preprocess/__init__.pyi

@@ -9,9 +9,10 @@ __all__ = [
     "SmoothingImpl",
     "TemporalSlicer",
     "TemporalFilter",
+    "logger",
 ]
 
-from .base import BasePreprocessor
+from .base import BasePreprocessor, logger
 from .confounds import fMRIPrepConfoundRemover, Confounds, Strategy
 from .warping import SpaceWarper, SpaceWarpingImpl
 from .smoothing import Smoothing, SmoothingImpl

junifer/preprocess/_temporal_filter.py

@@ -22,8 +22,8 @@ from ..data import get_data
 from ..datagrabber import DataType
 from ..pipeline import WorkDirManager
 from ..typing import Dependencies
-from ..utils import ensure_list_or_none, logger
+from ..utils import ensure_list_or_none
-from .base import BasePreprocessor
+from .base import BasePreprocessor, logger
 
 
 __all__ = ["TemporalFilter"]

junifer/preprocess/_temporal_slicer.py

@@ -14,8 +14,8 @@ from ..api.decorators import register_preprocessor
 from ..datagrabber import DataType
 from ..pipeline import WorkDirManager
 from ..typing import Dependencies
-from ..utils import logger, raise_error
+from ..utils import raise_error
-from .base import BasePreprocessor
+from .base import BasePreprocessor, logger
 
 
 __all__ = ["TemporalSlicer"]

junifer/preprocess/base.py

@@ -8,15 +8,19 @@ from abc import ABC, abstractmethod
 from collections.abc import Sequence
 from typing import Annotated, Any, ClassVar
 
+import structlog
 from pydantic import BaseModel, BeforeValidator, ConfigDict
 
 from ..datagrabber import DataType
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
-from ..utils import ensure_list_or_none, logger, raise_error
+from ..utils import ensure_list_or_none, raise_error
 
 
 __all__ = ["BasePreprocessor"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="preprocess", step="preprocessing")
+
 
 class BasePreprocessor(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
     """Abstract base class for preprocessor.
@@ -97,6 +101,10 @@ class BasePreprocessor(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
                 DataType(t) if isinstance(t, str) else t
                 for t in self.required_data_types
             ]
+        logger.info(
+            f"Parameters: {self.model_dump(mode='json')}",
+            component=self.__class__.__name__,
+        )
 
     @property
     def valid_inputs(self) -> list[DataType]:

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -35,8 +35,8 @@ from ...data import get_data
 from ...datagrabber import DataType
 from ...pipeline import WorkDirManager
 from ...typing import Dependencies
-from ...utils import ensure_list_or_none, logger, raise_error
+from ...utils import ensure_list_or_none, raise_error
-from ..base import BasePreprocessor
+from ..base import BasePreprocessor, logger
 
 
 __all__ = ["Confounds", "Strategy", "fMRIPrepConfoundRemover"]

junifer/preprocess/smoothing/_afni_smoothing.py

@@ -12,7 +12,8 @@ import nibabel as nib
 
 from ...pipeline import ExtDep, WorkDirManager
 from ...typing import Dependencies, ExternalDependencies
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
+from ..base import logger
 
 
 __all__ = ["AFNISmoothing"]

junifer/preprocess/smoothing/_fsl_smoothing.py

@@ -12,7 +12,8 @@ import nibabel as nib
 
 from ...pipeline import ExtDep, WorkDirManager
 from ...typing import Dependencies, ExternalDependencies
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
+from ..base import logger
 
 
 __all__ = ["FSLSmoothing"]

junifer/preprocess/smoothing/_nilearn_smoothing.py

@@ -15,7 +15,7 @@ from numpy.typing import ArrayLike
 
 from ...pipeline import WorkDirManager
 from ...typing import Dependencies
-from ...utils import logger
+from ..base import logger
 
 
 __all__ = ["NilearnSmoothing"]

junifer/preprocess/smoothing/smoothing.py

@@ -17,8 +17,8 @@ from pydantic import BeforeValidator
 from ...api.decorators import register_preprocessor
 from ...datagrabber import DataType
 from ...typing import ConditionalDependencies
-from ...utils import ensure_list_or_none, logger
+from ...utils import ensure_list_or_none
-from ..base import BasePreprocessor
+from ..base import BasePreprocessor, logger
 from ._afni_smoothing import AFNISmoothing
 from ._fsl_smoothing import FSLSmoothing
 from ._nilearn_smoothing import NilearnSmoothing

junifer/preprocess/warping/_ants_warper.py

@@ -14,7 +14,8 @@ import numpy as np
 from ...data import get_template, get_xfm
 from ...pipeline import ExtDep, WorkDirManager
 from ...typing import Dependencies, ExternalDependencies
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
+from ..base import logger
 
 
 __all__ = ["ANTsWarper"]

junifer/preprocess/warping/_fsl_warper.py

@@ -13,7 +13,8 @@ import numpy as np
 
 from ...pipeline import ExtDep, WorkDirManager
 from ...typing import Dependencies, ExternalDependencies
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
+from ..base import logger
 
 
 __all__ = ["FSLWarper"]

junifer/preprocess/warping/space_warper.py

@@ -13,8 +13,8 @@ from templateflow import api as tflow
 from ...api.decorators import register_preprocessor
 from ...datagrabber import DataType
 from ...typing import ConditionalDependencies
-from ...utils import ensure_list_or_none, logger, raise_error
+from ...utils import ensure_list_or_none, raise_error
-from ..base import BasePreprocessor
+from ..base import BasePreprocessor, logger
 from ._ants_warper import ANTsWarper
 from ._fsl_warper import FSLWarper
 

junifer/stats.py

@@ -9,11 +9,12 @@ from enum import Enum
 from typing import Any
 
 import numpy as np
+import structlog
 from pydantic import validate_call
 from scipy.stats import mode, trim_mean
 from scipy.stats.mstats import winsorize
 
-from .utils import logger, raise_error
+from .utils import raise_error
 
 
 __all__ = [
@@ -24,6 +25,9 @@ __all__ = [
     "winsorized_mean",
 ]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="stats")
+
 
 class AggFunc(str, Enum):
     """Accepted aggregation function names.

junifer/storage/__init__.pyi

@@ -6,9 +6,10 @@ __all__ = [
     "PandasBaseFeatureStorage",
     "SQLiteFeatureStorage",
     "Upsert",
+    "logger",
 ]
 
-from .base import BaseFeatureStorage, MatrixKind, StorageType
+from .base import BaseFeatureStorage, MatrixKind, StorageType, logger
 from .hdf5 import HDF5FeatureStorage
 from .pandas_base import PandasBaseFeatureStorage
 from .sqlite import SQLiteFeatureStorage, Upsert

junifer/storage/base.py

@@ -12,9 +12,10 @@ from typing import Any, ClassVar
 
 import numpy as np
 import pandas as pd
+import structlog
 from pydantic import BaseModel, ConfigDict
 
-from ..utils import logger, raise_error
+from ..utils import raise_error
 
 
 __all__ = ["BaseFeatureStorage", "MatrixKind", "StorageType"]
@@ -28,6 +29,10 @@ class MatrixKind(str, Enum):
     Full = "full"
 
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="storage", step="storage")
+
+
 class StorageType(str, Enum):
     """Accepted storage type."""
 
@@ -79,6 +84,10 @@ class BaseFeatureStorage(BaseModel, ABC):
                 "does not exist, creating now"
             )
             self.uri.parent.mkdir(parents=True, exist_ok=True)
+        logger.info(
+            f"Parameters: {self.model_dump(mode='json')}",
+            component=self.__class__.__name__,
+        )
 
     def validate_input(self, input_: list[str]) -> None:
         """Validate the input to the pipeline step.

junifer/storage/hdf5.py

@@ -22,8 +22,8 @@ from ..external.h5io.h5io import (
     read_hdf5,
     write_hdf5,
 )
-from ..utils import logger, raise_error
+from ..utils import raise_error
-from .base import BaseFeatureStorage, MatrixKind, StorageType
+from .base import BaseFeatureStorage, MatrixKind, StorageType, logger
 from .utils import (
     element_to_prefix,
     matrix_to_vector,

junifer/storage/sqlite.py

@@ -16,8 +16,8 @@ from sqlalchemy import create_engine, inspect
 from tqdm import tqdm
 
 from ..api.decorators import register_storage
-from ..utils import logger, raise_error, warn_with_log
+from ..utils import raise_error, warn_with_log
-from .base import MatrixKind
+from .base import MatrixKind, logger
 from .pandas_base import PandasBaseFeatureStorage
 from .utils import (
     element_to_prefix,

junifer/storage/utils.py

@@ -12,8 +12,8 @@ from importlib.metadata import PackageNotFoundError, version
 import numpy as np
 from pydantic import validate_call
 
-from ..utils import logger, raise_error
+from ..utils import raise_error
-from .base import MatrixKind
+from .base import MatrixKind, logger
 
 
 __all__ = [

junifer/utils/logging.py

@@ -111,7 +111,8 @@ structlog.configure(
     cache_logger_on_first_use=True,
 )
 
-logger = logging.getLogger("junifer")
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="utils")
 
 # Remove datalad logger handlers to avoid duplicate logging
 _datalad_lgr_hdlrs = datalad.log.lgr.handlers