docs/changes/newsfragments/349.change

@@ -0,0 +1 @@
+``fractional`` parameter for ``ALFFBase``, :class:`.ALFFParcels` and :class:`.ALFFSpheres` have been removed in favour of returning both ALFF and fALFF by `Synchon Mandal`_

docs/changes/newsfragments/349.enh

@@ -0,0 +1 @@
+Enable Markers to output multiple features by `Synchon Mandal`_

docs/extending/marker.rst

@@ -5,24 +5,17 @@
 Creating Markers
 ================
 
-Computing a marker (a.k.a. *feature*) is the main goal of ``junifer``. While we
+Computing a marker (a.k.a. *feature(s)*) is the main goal of ``junifer``. While
-aim to provide as many Markers as possible, it might be the case that the Marker
+we aim to provide as many Markers as possible, it might be the case that the
-you are looking for is not available. In this case, you can create your own Marker
+Marker you are looking for is not available. In this case, you can create your
-by following this tutorial.
+own Marker by following this tutorial.
 
 Most of the functionality of a ``junifer`` Marker has been taken care by the
-:class:`.BaseMarker` class. Thus, only a few methods are required:
+:class:`.BaseMarker` class. Thus, only a few methods and class attributes are
+required:
 
-#. ``get_valid_inputs``: The method to obtain the list of valid inputs for the
-   Marker. This is used to check that the inputs provided by the user are
-   valid. This method should return a list of strings, representing
-   :ref:`data types <data_types>`.
-#. ``get_output_type``: The method to obtain the output type of the Marker.
-   This is used to check that the output of the Marker is compatible with the
-   storage. This method should return a string, representing
-   :ref:`storage types <storage_types>`.
-#. ``compute``: The method that given the data, computes the Marker.
 #. ``__init__``: The initialisation method, where the Marker is configured.
+#. ``compute``: The method that given the data, computes the Marker.
 
 As an example, we will develop a ``ParcelMean`` Marker, a Marker that first
 applies a parcellation and then computes the mean of the data in each parcel.
@@ -35,24 +28,26 @@ Step 1: Configure input and output
 
 This step is quite simple: we need to define the input and output of the Marker.
 Based on the current :ref:`data types <data_types>`, we can have ``BOLD``,
-``VBM_WM`` and ``VBM_GM`` as valid inputs.
+``VBM_WM`` and ``VBM_GM`` as valid inputs. The output of the Marker depends on
+the input. For ``BOLD``, it will be ``timeseries``, while for the rest of the
+inputs, it will be ``vector``. Thus, we have a class attribute like so:
 
 .. code-block:: python
 
-    def get_valid_inputs(self) -> list[str]:
+    # NOTE: data type -> feature -> storage type
-        return ["BOLD", "VBM_WM", "VBM_GM"]
+    # You can have multiple features for one data type,
-
+    # each feature having same or different storage type
-The output of the Marker depends on the input. For ``BOLD``, it will be
+    _MARKER_INOUT_MAPPINGS = {
-``timeseries``, while for the rest of the inputs, it will be ``vector``. Thus,
+        "BOLD": {
-we can define the output as:
+            "parcel_mean": "timeseries",
-
+        },
-.. code-block:: python
+        "VBM_WM": {
-
+            "parcel_mean": "vector",
-    def get_output_type(self, input_type: str) -> str:
+        },
-        if input_type == "BOLD":
+        "VBM_GM": {
-            return "timeseries"
+            "parcel_mean": "vector",
-        else:
+        },
-            return "vector"
+    }
 
 .. _extending_markers_init:
 
@@ -119,7 +114,8 @@ arguments:
 Following the example, we will compute the mean of the data in each parcel using
 :class:`nilearn.maskers.NiftiLabelsMasker`. Importantly, the output of the
 compute function must be a dictionary. This dictionary will later be passed onto
-the ``store`` method.
+the ``store`` method. The dictionary's first level of keys would the feature name
+and the values would be a dictionary of storage type specific key-value pairs.
 
 .. hint::
 
@@ -162,11 +158,13 @@ the ``store`` method.
         # mask the data
         out_values = masker.fit_transform([data])
 
-        # Create the output dictionary
+        # Create and return the output dictionary
-        out = {"data": out_values, "col_names": t_labels}
+        return {
-
+            "parcel_mean": {
-        return out
+                "data": out_values,
-
+                "col_names": t_labels,
+            },
+        }
 
 .. _extending_markers_finalize:
 
@@ -193,11 +191,11 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
 
 .. code-block:: python
 
-    from typing import Any
+    from typing import Any, ClassVar
 
     from junifer.api.decorators import register_marker
     from junifer.data import get_parcellation
-    from junifer.markers.base import BaseMarker
+    from junifer.markers import BaseMarker
     from nilearn.maskers import NiftiLabelsMasker
 
 
@@ -206,6 +204,18 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
 
         _DEPENDENCIES = {"nilearn", "numpy"}
 
+        _MARKER_INOUT_MAPPINGS: ClassVar[dict[str, dict[str, str]]] = {
+            "BOLD": {
+                "parcel_mean": "timeseries",
+            },
+            "VBM_WM": {
+                "parcel_mean": "vector",
+            },
+            "VBM_GM": {
+                "parcel_mean": "vector",
+            },
+        }
+
         def __init__(
             self,
             parcellation: str,
@@ -215,15 +225,6 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
             self.parcellation = parcellation
             super().__init__(on=on, name=name)
 
-        def get_valid_inputs(self) -> list[str]:
-            return ["BOLD", "VBM_WM", "VBM_GM"]
-
-        def get_output_type(self, input_type: str) -> str:
-            if input_type == "BOLD":
-                return "timeseries"
-            else:
-                return "vector"
-
         def compute(
             self,
             input: dict[str, Any],
@@ -250,11 +251,13 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
             # mask the data
             out_values = masker.fit_transform([data])
 
-            # Create the output dictionary
+            # Create and return the output dictionary
-            out = {"data": out_values, "col_names": t_labels}
+            return {
-
+                "parcel_mean": {
-            return out
+                    "data": out_values,
-
+                    "col_names": t_labels,
+                },
+            }
 
 .. _extending_markers_template:
 
@@ -269,22 +272,16 @@ Template for a custom Marker
 
     @register_marker
     class TemplateMarker(BaseMarker):
+
+        # TODO: add the dependencies
+        _DEPENDENCIES = {}
+
+        # TODO: add the input-output mappings
+        _MARKER_INOUT_MAPPINGS = {}
+
         def __init__(self, on=None, name=None):
             # TODO: add marker-specific parameters
             super().__init__(on=on, name=name)
 
-        def get_valid_inputs(self):
-            # TODO: Complete with the valid inputs
-            valid = []
-            return valid
-
-        def get_output_type(self, input_type):
-            # TODO: Return the valid output type for each input type
-            pass
-
         def compute(self, input, extra_input):
             # TODO: compute the marker and create the output dictionary
-
-            # Create the output dictionary
-            out = {"data": None, "col_names": None}
-            return out

docs/understanding/marker.rst

@@ -26,7 +26,5 @@ on them outside the context as long as the actual data is in the memory and the
 Python runtime has not garbage-collected it.
 
 If you are interested in using already provided Markers, please go to
-:doc:`../builtin`. And, if you want to implement your own Marker, you need to
+:doc:`../builtin`. And, if you want to implement your own Marker, please check
-provide concrete implementation of :class:`.BaseMarker`. Specifically, you
+out :doc:`../extending/marker`.
-need to override ``get_valid_inputs``, ``get_output_type`` and ``compute``
-methods.

junifer/datagrabber/tests/test_datalad_base.py

@@ -15,13 +15,13 @@ from junifer.datagrabber import DataladDataGrabber
 _testing_dataset = {
     "example_bids": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids",
-        "commit": "522dfb203afcd2cd55799bf347f9b211919a7338",
+        "commit": "b87897cbe51bf0ee5514becaa5c7dd76491db5ad",
-        "id": "fec92475-d9c0-4409-92ba-f041b6a12c40",
+        "id": "8fddff30-6993-420a-9d1e-b5b028c59468",
     },
     "example_bids_ses": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids-ses",
-        "commit": "3d08d55d1faad4f12ab64ac9497544a0d924d47a",
+        "commit": "6b163aa98af76a9eac0272273c27e14127850181",
-        "id": "c83500d0-532f-45be-baf1-0dab703bdc2a",
+        "id": "715c17cf-a1b9-42d6-9af8-9f74c1a4a724",
     },
 }
 

junifer/datagrabber/tests/test_pattern_datalad.py

@@ -15,13 +15,13 @@ from junifer.datagrabber import PatternDataladDataGrabber
 _testing_dataset = {
     "example_bids": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids",
-        "commit": "522dfb203afcd2cd55799bf347f9b211919a7338",
+        "commit": "b87897cbe51bf0ee5514becaa5c7dd76491db5ad",
-        "id": "fec92475-d9c0-4409-92ba-f041b6a12c40",
+        "id": "8fddff30-6993-420a-9d1e-b5b028c59468",
     },
     "example_bids_ses": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids-ses",
-        "commit": "3d08d55d1faad4f12ab64ac9497544a0d924d47a",
+        "commit": "6b163aa98af76a9eac0272273c27e14127850181",
-        "id": "c83500d0-532f-45be-baf1-0dab703bdc2a",
+        "id": "715c17cf-a1b9-42d6-9af8-9f74c1a4a724",
     },
 }
 

junifer/markers/base.py

@@ -5,6 +5,7 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
+from copy import deepcopy
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
 
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
@@ -35,6 +36,8 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
 
     Raises
     ------
+    AttributeError
+        If the marker does not have `_MARKER_INOUT_MAPPINGS` attribute.
     ValueError
         If required input data type(s) is(are) not found.
 
@@ -45,6 +48,12 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
         on: Optional[Union[List[str], str]] = None,
         name: Optional[str] = None,
     ) -> None:
+        # Check for missing mapping attribute
+        if not hasattr(self, "_MARKER_INOUT_MAPPINGS"):
+            raise_error(
+                msg=("Missing `_MARKER_INOUT_MAPPINGS` for the marker"),
+                klass=AttributeError,
+            )
         # Use all data types if not provided
         if on is None:
             on = self.get_valid_inputs()
@@ -88,7 +97,6 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
             )
         return [x for x in self._on if x in input]
 
-    @abstractmethod
     def get_valid_inputs(self) -> List[str]:
         """Get valid data types for input.
 
@@ -98,30 +106,25 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
             The list of data types that can be used as input for this marker.
 
         """
-        raise_error(
+        return list(self._MARKER_INOUT_MAPPINGS.keys())
-            msg="Concrete classes need to implement get_valid_inputs().",
-            klass=NotImplementedError,
-        )
 
-    @abstractmethod
+    def get_output_type(self, input_type: str, output_feature: str) -> str:
-    def get_output_type(self, input_type: str) -> str:
         """Get output type.
 
         Parameters
         ----------
         input_type : str
             The data type input to the marker.
+        output_feature : str
+            The feature output of the marker.
 
         Returns
         -------
         str
-            The storage type output by the marker.
+            The storage type output of the marker.
 
         """
-        raise_error(
+        return self._MARKER_INOUT_MAPPINGS[input_type][output_feature]
-            msg="Concrete classes need to implement get_output_type().",
-            klass=NotImplementedError,
-        )
 
     @abstractmethod
     def compute(self, input: Dict, extra_input: Optional[Dict] = None) -> Dict:
@@ -154,6 +157,7 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
     def store(
         self,
         type_: str,
+        feature: str,
         out: Dict[str, Any],
         storage: "BaseFeatureStorage",
     ) -> None:
@@ -163,13 +167,15 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
         ----------
         type_ : str
             The data type to store.
+        feature : str
+            The feature to store.
         out : dict
             The computed result as a dictionary to store.
         storage : storage-like
             The storage class, for example, SQLiteFeatureStorage.
 
         """
-        output_type_ = self.get_output_type(type_)
+        output_type_ = self.get_output_type(type_, feature)
         logger.debug(f"Storing {output_type_} in {storage}")
         storage.store(kind=output_type_, **out)
 
@@ -213,15 +219,35 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
                 t_meta["type"] = type_
                 # Compute marker
                 t_out = self.compute(input=t_input, extra_input=extra_input)
-                t_out["meta"] = t_meta
+                # Initialize empty dictionary if no storage object is provided
-                # Update metadata for step
+                if storage is None:
-                self.update_meta(t_out, "marker")
+                    out[type_] = {}
-                # Check storage
+                # Store individual features
+                for feature_name, feature_data in t_out.items():
+                    # Make deep copy of the feature data for manipulation
+                    feature_data_copy = deepcopy(feature_data)
+                    # Make deep copy of metadata and add to feature data
+                    feature_data_copy["meta"] = deepcopy(t_meta)
+                    # Update metadata for the feature,
+                    # feature data is not manipulated, only meta
+                    self.update_meta(feature_data_copy, "marker")
+                    # Update marker feature's metadata name
+                    feature_data_copy["meta"]["marker"][
+                        "name"
+                    ] += f"_{feature_name}"
+
                     if storage is not None:
                         logger.info(f"Storing in {storage}")
-                    self.store(type_=type_, out=t_out, storage=storage)
+                        self.store(
+                            type_=type_,
+                            feature=feature_name,
+                            out=feature_data_copy,
+                            storage=storage,
+                        )
                     else:
-                    logger.info("No storage specified, returning dictionary")
+                        logger.info(
-                    out[type_] = t_out
+                            "No storage specified, returning dictionary"
+                        )
+                        out[type_][feature_name] = feature_data_copy
 
         return out

junifer/markers/brainprint.py

@@ -3,21 +3,9 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import sys
-
-
-if sys.version_info < (3, 11):  # pragma: no cover
-    from importlib_metadata import packages_distributions
-else:
-    from importlib.metadata import packages_distributions
-
 import uuid
-from copy import deepcopy
-from importlib.util import find_spec
-from itertools import chain
 from pathlib import Path
 from typing import (
-    TYPE_CHECKING,
     Any,
     ClassVar,
     Dict,
@@ -37,15 +25,10 @@ from ..external.BrainPrint.brainprint.brainprint import (
 )
 from ..external.BrainPrint.brainprint.surfaces import surf_to_vtk
 from ..pipeline import WorkDirManager
-from ..pipeline.utils import check_ext_dependencies
+from ..utils import logger, run_ext_cmd
-from ..utils import logger, raise_error, run_ext_cmd
 from .base import BaseMarker
 
 
-if TYPE_CHECKING:
-    from junifer.storage import BaseFeatureStorage
-
-
 __all__ = ["BrainPrint"]
 
 
@@ -99,6 +82,15 @@ class BrainPrint(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"lapy", "numpy"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "FreeSurfer": {
+            "eigenvalues": "scalar_table",
+            "areas": "vector",
+            "volumes": "vector",
+            "distances": "vector",
+        }
+    }
+
     def __init__(
         self,
         num: int = 50,
@@ -121,117 +113,6 @@ class BrainPrint(BaseMarker):
         self.use_cholmod = use_cholmod
         super().__init__(name=name, on="FreeSurfer")
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["FreeSurfer"]
-
-    # TODO: kept for making this class concrete; should be removed later
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "vector"
-
-    # TODO: overridden to allow multiple outputs from single data type; should
-    # be removed later
-    def validate(self, input: List[str]) -> List[str]:
-        """Validate the the pipeline step.
-
-        Parameters
-        ----------
-        input : list of str
-            The input to the pipeline step.
-
-        Returns
-        -------
-        list of str
-            The output of the pipeline step.
-
-        """
-
-        def _check_dependencies(obj) -> None:
-            """Check obj._DEPENDENCIES.
-
-            Parameters
-            ----------
-            obj : object
-                Object to check _DEPENDENCIES of.
-
-            Raises
-            ------
-            ImportError
-                If the pipeline step object is missing dependencies required
-                for its working.
-
-            """
-            # Check if _DEPENDENCIES attribute is found;
-            # (markers and preprocessors will have them but not datareaders
-            # as of now)
-            dependencies_not_found = []
-            if hasattr(obj, "_DEPENDENCIES"):
-                # Check if dependencies are importable
-                for dependency in obj._DEPENDENCIES:
-                    # First perform an easy check
-                    if find_spec(dependency) is None:
-                        # Then check mapped names
-                        if dependency not in list(
-                            chain.from_iterable(
-                                packages_distributions().values()
-                            )
-                        ):
-                            dependencies_not_found.append(dependency)
-            # Raise error if any dependency is not found
-            if dependencies_not_found:
-                raise_error(
-                    msg=(
-                        f"{dependencies_not_found} are not installed but are "
-                        f"required for using {obj.__class__.__name__}."
-                    ),
-                    klass=ImportError,
-                )
-
-        def _check_ext_dependencies(obj) -> None:
-            """Check obj._EXT_DEPENDENCIES.
-
-            Parameters
-            ----------
-            obj : object
-                Object to check _EXT_DEPENDENCIES of.
-
-            """
-            # Check if _EXT_DEPENDENCIES attribute is found;
-            # (some markers and preprocessors might have them)
-            if hasattr(obj, "_EXT_DEPENDENCIES"):
-                for dependency in obj._EXT_DEPENDENCIES:
-                    check_ext_dependencies(**dependency)
-
-        # Check dependencies
-        _check_dependencies(self)
-        # Check external dependencies
-        # _check_ext_dependencies(self)
-        # Validate input
-        _ = self.validate_input(input=input)
-        # Validate output type
-        outputs = ["scalar_table", "vector"]
-        return outputs
-
     def _create_aseg_surface(
         self,
         aseg_path: Path,
@@ -426,6 +307,27 @@ class BrainPrint(BaseMarker):
             ),
         }
 
+    def _fix_nan(
+        self,
+        input_data: List[Union[float, str, npt.ArrayLike]],
+    ) -> np.ndarray:
+        """Convert BrainPrint output with string NaN to ``numpy.nan``.
+
+        Parameters
+        ----------
+        input_data : list of str, float or numpy.ndarray-like
+            The data to convert.
+
+        Returns
+        -------
+        np.ndarray
+            The converted data as ``numpy.ndarray``.
+
+        """
+        arr = np.asarray(input_data)
+        arr[arr == "NaN"] = np.nan
+        return arr.astype(np.float64)
+
     def compute(
         self,
         input: Dict[str, Any],
@@ -443,16 +345,32 @@ class BrainPrint(BaseMarker):
         Returns
         -------
         dict
-            The computed result as dictionary. The dictionary has the following
+            The computed result as dictionary. This will be either returned
-            keys:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-            * ``eigenvalues`` : dict of surface labels (str) and eigenvalues
+            * ``eigenvalues`` : dictionary with the following keys:
-                                (``np.ndarray``)
+
-            * ``eigenvectors`` : dict of surface labels (str) and eigenvectors
+                - ``data`` : eigenvalues as ``np.ndarray``
-                                 (``np.ndarray``) if ``keep_eigenvectors=True``
+                - ``col_names`` : surface labels as list of str
-                                 else None
+                - ``row_names`` : eigenvalue count labels as list of str
-            * ``distances`` : dict of ``{left_label}_{right_label}`` (str) and
+                - ``row_header_col_name`` : "eigenvalue"
-                              distance (float) if ``asymmetry=True`` else None
+                                ()
+            * ``areas`` : dictionary with the following keys:
+
+                - ``data`` : areas as ``np.ndarray``
+                - ``col_names`` : surface labels as list of str
+
+            * ``volumes`` : dictionary with the following keys:
+
+                - ``data`` : volumes as ``np.ndarray``
+                - ``col_names`` : surface labels as list of str
+
+            * ``distances`` : dictionary with the following keys
+                              if ``asymmetry = True``:
+
+                - ``data`` : distances as ``np.ndarray``
+                - ``col_names`` : surface labels as list of str
 
         References
         ----------
@@ -539,130 +457,3 @@ class BrainPrint(BaseMarker):
                 "col_names": list(distances.keys()),
             }
         return output
-
-    def _fix_nan(
-        self,
-        input_data: List[Union[float, str, npt.ArrayLike]],
-    ) -> np.ndarray:
-        """Convert BrainPrint output with string NaN to ``numpy.nan``.
-
-        Parameters
-        ----------
-        input_data : list of str, float or numpy.ndarray-like
-            The data to convert.
-
-        Returns
-        -------
-        np.ndarray
-            The converted data as ``numpy.ndarray``.
-
-        """
-        arr = np.asarray(input_data)
-        arr[arr == "NaN"] = np.nan
-        return arr.astype(np.float64)
-
-    # TODO: overridden to allow storing multiple outputs from single input;
-    # should be removed later
-    def store(
-        self,
-        type_: str,
-        feature: str,
-        out: Dict[str, Any],
-        storage: "BaseFeatureStorage",
-    ) -> None:
-        """Store.
-
-        Parameters
-        ----------
-        type_ : str
-            The data type to store.
-        feature : {"eigenvalues", "distances", "areas", "volumes"}
-            The feature name to store.
-        out : dict
-            The computed result as a dictionary to store.
-        storage : storage-like
-            The storage class, for example, SQLiteFeatureStorage.
-
-        Raises
-        ------
-        ValueError
-            If ``feature`` is invalid.
-
-        """
-        if feature == "eigenvalues":
-            output_type = "scalar_table"
-        elif feature in ["distances", "areas", "volumes"]:
-            output_type = "vector"
-        else:
-            raise_error(f"Unknown feature: {feature}")
-
-        logger.debug(f"Storing {output_type} in {storage}")
-        storage.store(kind=output_type, **out)
-
-    # TODO: overridden to allow storing multiple outputs from single input;
-    # should be removed later
-    def _fit_transform(
-        self,
-        input: Dict[str, Dict],
-        storage: Optional["BaseFeatureStorage"] = None,
-    ) -> Dict:
-        """Fit and transform.
-
-        Parameters
-        ----------
-        input : dict
-            The Junifer Data object.
-        storage : storage-like, optional
-            The storage class, for example, SQLiteFeatureStorage.
-
-        Returns
-        -------
-        dict
-            The processed output as a dictionary. If `storage` is provided,
-            empty dictionary is returned.
-
-        """
-        out = {}
-        for type_ in self._on:
-            if type_ in input.keys():
-                logger.info(f"Computing {type_}")
-                t_input = input[type_]
-                extra_input = input.copy()
-                extra_input.pop(type_)
-                t_meta = t_input["meta"].copy()
-                t_meta["type"] = type_
-
-                # Returns multiple features
-                t_out = self.compute(input=t_input, extra_input=extra_input)
-
-                if storage is None:
-                    out[type_] = {}
-
-                for feature_name, feature_data in t_out.items():
-                    # Make deep copy of the feature data for manipulation
-                    feature_data_copy = deepcopy(feature_data)
-                    # Make deep copy of metadata and add to feature data
-                    feature_data_copy["meta"] = deepcopy(t_meta)
-                    # Update metadata for the feature,
-                    # feature data is not manipulated, only meta
-                    self.update_meta(feature_data_copy, "marker")
-                    # Update marker feature's metadata name
-                    feature_data_copy["meta"]["marker"][
-                        "name"
-                    ] += f"_{feature_name}"
-
-                    if storage is not None:
-                        logger.info(f"Storing in {storage}")
-                        self.store(
-                            type_=type_,
-                            feature=feature_name,
-                            out=feature_data_copy,
-                            storage=storage,
-                        )
-                    else:
-                        logger.info(
-                            "No storage specified, returning dictionary"
-                        )
-                        out[type_][feature_name] = feature_data_copy
-
-        return out

junifer/markers/complexity/complexity_base.py

@@ -53,6 +53,12 @@ class ComplexityBase(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "neurokit2"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "complexity": "vector",
+        },
+    }
+
     def __init__(
         self,
         parcellation: Union[str, List[str]],
@@ -78,33 +84,6 @@ class ComplexityBase(BaseMarker):
             klass=NotImplementedError,
         )
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "vector"
-
     def compute(
         self,
         input: Dict[str, Any],
@@ -124,29 +103,30 @@ class ComplexityBase(BaseMarker):
         Returns
         -------
         dict
-            The computed result as dictionary. The following keys will be
+            The computed result as dictionary. This will be either returned
-            included in the dictionary:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-           * ``data`` : ROI-wise complexity measures as ``numpy.ndarray``
+           *  ``complexity`` : dictionary with the following keys:
-           * ``col_names`` : ROI labels for the complexity measures as list
+
+                - ``data`` : ROI-wise complexity measures as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         """
-        # Initialize a ParcelAggregation
+        # Extract the 2D time series using ParcelAggregation
         parcel_aggregation = ParcelAggregation(
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input=input, extra_input=extra_input)
-        # Extract the 2D time series using parcel aggregation
-        parcel_aggregation_map = parcel_aggregation.compute(
-            input=input, extra_input=extra_input
-        )
-
         # Compute complexity measure
-        parcel_aggregation_map["data"] = self.compute_complexity(
+        return {
-            parcel_aggregation_map["data"]
+            "complexity": {
-        )
+                "data": self.compute_complexity(
-
+                    parcel_aggregation["aggregation"]["data"]
-        return parcel_aggregation_map
+                ),
+                "col_names": parcel_aggregation["aggregation"]["col_names"],
+            }
+        }

junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -40,13 +40,14 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test HurstExponent get_output_type()."""
-    marker = HurstExponent(parcellation=PARCELLATION)
+    assert "vector" == HurstExponent(
-    assert marker.get_output_type("BOLD") == "vector"
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -39,13 +39,14 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test MultiscaleEntropyAUC get_output_type()."""
-    marker = MultiscaleEntropyAUC(parcellation=PARCELLATION)
+    assert "vector" == MultiscaleEntropyAUC(
-    assert marker.get_output_type("BOLD") == "vector"
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_perm_entropy.py

@@ -39,13 +39,14 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test PermEntropy get_output_type()."""
-    marker = PermEntropy(parcellation=PARCELLATION)
+    assert "vector" == PermEntropy(parcellation=PARCELLATION).get_output_type(
-    assert marker.get_output_type("BOLD") == "vector"
+        input_type="BOLD", output_feature="complexity"
+    )
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_range_entropy.py

@@ -40,13 +40,14 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test RangeEntropy get_output_type()."""
-    marker = RangeEntropy(parcellation=PARCELLATION)
+    assert "vector" == RangeEntropy(parcellation=PARCELLATION).get_output_type(
-    assert marker.get_output_type("BOLD") == "vector"
+        input_type="BOLD", output_feature="complexity"
+    )
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -40,13 +40,14 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test RangeEntropyAUC get_output_type()."""
-    marker = RangeEntropyAUC(parcellation=PARCELLATION)
+    assert "vector" == RangeEntropyAUC(
-    assert marker.get_output_type("BOLD") == "vector"
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_sample_entropy.py

@@ -39,13 +39,14 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test SampleEntropy get_output_type()."""
-    marker = SampleEntropy(parcellation=PARCELLATION)
+    assert "vector" == SampleEntropy(
-    assert marker.get_output_type("BOLD") == "vector"
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -39,13 +39,14 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test WeightedPermEntropy get_output_type()."""
-    marker = WeightedPermEntropy(parcellation=PARCELLATION)
+    assert "vector" == WeightedPermEntropy(
-    assert marker.get_output_type("BOLD") == "vector"
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
 @pytest.mark.skipif(

junifer/markers/ets_rss.py

@@ -47,6 +47,12 @@ class RSSETSMarker(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "rss_ets": "timeseries",
+        },
+    }
+
     def __init__(
         self,
         parcellation: Union[str, List[str]],
@@ -61,33 +67,6 @@ class RSSETSMarker(BaseMarker):
         self.masks = masks
         super().__init__(name=name)
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "timeseries"
-
     def compute(
         self,
         input: Dict[str, Any],
@@ -109,8 +88,9 @@ class RSSETSMarker(BaseMarker):
         Returns
         -------
         dict
-            The computed result as dictionary. The dictionary has the following
+            The computed result as dictionary. This will be either returned
-            keys:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
             * ``data`` : the actual computed values as a numpy.ndarray
             * ``col_names`` : the column labels for the computed values as list
@@ -124,20 +104,22 @@ class RSSETSMarker(BaseMarker):
 
         """
         logger.debug("Calculating root sum of squares of edgewise timeseries.")
-        # Initialize a ParcelAggregation
+        # Perform aggregation
-        parcel_aggregation = ParcelAggregation(
+        aggregation = ParcelAggregation(
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
-        )
+        ).compute(input=input, extra_input=extra_input)
-        # Compute the parcel aggregation
+        # Compute edgewise timeseries
-        out = parcel_aggregation.compute(input=input, extra_input=extra_input)
+        edge_ts, _ = _ets(aggregation["aggregation"]["data"])
-        edge_ts, _ = _ets(out["data"])
+        # Compute the RSS of edgewise timeseries
-        # Compute the RSS
+        rss = np.sum(edge_ts**2, 1) ** 0.5
-        out["data"] = np.sum(edge_ts**2, 1) ** 0.5
+
+        return {
+            "rss_ets": {
                 # Make it 2D
-        out["data"] = out["data"][:, np.newaxis]
+                "data": rss[:, np.newaxis],
-        # Set correct column label
+                "col_names": ["root_sum_of_squares_ets"],
-        out["col_names"] = ["root_sum_of_squares_ets"]
+            }
-        return out
+        }

junifer/markers/falff/falff_base.py

@@ -37,8 +37,6 @@ class ALFFBase(BaseMarker):
 
     Parameters
     ----------
-    fractional : bool
-        Whether to compute fractional ALFF.
     highpass : positive float
         Highpass cutoff frequency.
     lowpass : positive float
@@ -85,9 +83,15 @@ class ALFFBase(BaseMarker):
         },
     ]
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "alff": "vector",
+            "falff": "vector",
+        },
+    }
+
     def __init__(
         self,
-        fractional: bool,
         highpass: float,
         lowpass: float,
         using: str,
@@ -110,45 +114,12 @@ class ALFFBase(BaseMarker):
             )
         self.using = using
         self.tr = tr
-        self.fractional = fractional
-
-        # Create a name based on the class name if none is provided
-        if name is None:
-            suffix = "_fractional" if fractional else ""
-            name = f"{self.__class__.__name__}{suffix}"
         super().__init__(on="BOLD", name=name)
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "vector"
-
     def _compute(
         self,
         input_data: Dict[str, Any],
-    ) -> Tuple["Nifti1Image", Path]:
+    ) -> Tuple["Nifti1Image", "Nifti1Image", Path, Path]:
         """Compute ALFF and fALFF.
 
         Parameters
@@ -161,9 +132,13 @@ class ALFFBase(BaseMarker):
         Returns
         -------
         Niimg-like object
-            The ALFF / fALFF as NIfTI.
+            The ALFF as NIfTI.
+        Niimg-like object
+            The fALFF as NIfTI.
         pathlib.Path
-            The path to the ALFF / fALFF as NIfTI.
+            The path to the ALFF as NIfTI.
+        pathlib.Path
+            The path to the fALFF as NIfTI.
 
         """
         logger.debug("Calculating ALFF and fALFF")
@@ -186,11 +161,7 @@ class ALFFBase(BaseMarker):
         # parcellation / coordinates to native space, else the
         # path should be passed for use later if required.
         # TODO(synchon): will be taken care in #292
-        if input_data["space"] == "native" and self.fractional:
+        if input_data["space"] == "native":
-            return falff, input_data["path"]
+            return alff, falff, input_data["path"], input_data["path"]
-        elif input_data["space"] == "native" and not self.fractional:
-            return alff, input_data["path"]
-        elif input_data["space"] != "native" and self.fractional:
-            return falff, falff_path
         else:
-            return alff, alff_path
+            return alff, falff, alff_path, falff_path

junifer/markers/falff/falff_parcels.py

@@ -26,8 +26,6 @@ class ALFFParcels(ALFFBase):
     parcellation : str or list of str
         The name(s) of the parcellation(s). Check valid options by calling
         :func:`.list_parcellations`.
-    fractional : bool
-        Whether to compute fractional ALFF.
     using : {"junifer", "afni"}
         Implementation to use for computing ALFF:
 
@@ -73,7 +71,6 @@ class ALFFParcels(ALFFBase):
     def __init__(
         self,
         parcellation: Union[str, List[str]],
-        fractional: bool,
         using: str,
         highpass: float = 0.01,
         lowpass: float = 0.1,
@@ -85,7 +82,6 @@ class ALFFParcels(ALFFBase):
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(
-            fractional=fractional,
             highpass=highpass,
             lowpass=lowpass,
             using=using,
@@ -114,33 +110,63 @@ class ALFFParcels(ALFFBase):
         Returns
         -------
         dict
-            The computed result as dictionary. The dictionary has the following
+            The computed result as dictionary. This will be either returned
-            keys:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``alff`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+              - ``data`` : ROI values as ``numpy.ndarray``
+              - ``col_names`` : ROI labels as list of str
+
+            * ``falff`` : dictionary with the following keys:
+
+              - ``data`` : ROI values as ``numpy.ndarray``
+              - ``col_names`` : ROI labels as list of str
 
         """
         logger.info("Calculating ALFF / fALFF for parcels")
 
-        # Compute ALFF / fALFF
+        # Compute ALFF + fALFF
-        output_data, output_file_path = self._compute(input_data=input)
+        alff_output, falff_output, alff_output_path, falff_output_path = (
+            self._compute(input_data=input)
+        )
 
-        # Initialize parcel aggregation
+        # Perform aggregation on ALFF + fALFF
-        parcel_aggregation = ParcelAggregation(
+        aggregation_alff_input = dict(input.items())
+        aggregation_falff_input = dict(input.items())
+        aggregation_alff_input["data"] = alff_output
+        aggregation_falff_input["data"] = falff_output
+        aggregation_alff_input["path"] = alff_output_path
+        aggregation_falff_input["path"] = falff_output_path
+
+        return {
+            "alff": {
+                **ParcelAggregation(
                     parcellation=self.parcellation,
                     method=self.agg_method,
                     method_params=self.agg_method_params,
                     masks=self.masks,
                     on="BOLD",
-        )
+                ).compute(
-        # Perform aggregation on ALFF / fALFF
+                    input=aggregation_alff_input,
-        parcel_aggregation_input = dict(input.items())
-        parcel_aggregation_input["data"] = output_data
-        parcel_aggregation_input["path"] = output_file_path
-        output = parcel_aggregation.compute(
-            input=parcel_aggregation_input,
                     extra_input=extra_input,
-        )
+                )[
-
+                    "aggregation"
-        return output
+                ],
+            },
+            "falff": {
+                **ParcelAggregation(
+                    parcellation=self.parcellation,
+                    method=self.agg_method,
+                    method_params=self.agg_method_params,
+                    masks=self.masks,
+                    on="BOLD",
+                ).compute(
+                    input=aggregation_falff_input,
+                    extra_input=extra_input,
+                )[
+                    "aggregation"
+                ],
+            },
+        }

junifer/markers/falff/falff_spheres.py

@@ -26,8 +26,6 @@ class ALFFSpheres(ALFFBase):
     coords : str
         The name of the coordinates list to use. See
         :func:`.list_coordinates` for options.
-    fractional : bool
-        Whether to compute fractional ALFF.
     using : {"junifer", "afni"}
         Implementation to use for computing ALFF:
 
@@ -80,7 +78,6 @@ class ALFFSpheres(ALFFBase):
     def __init__(
         self,
         coords: str,
-        fractional: bool,
         using: str,
         radius: Optional[float] = None,
         allow_overlap: bool = False,
@@ -94,7 +91,6 @@ class ALFFSpheres(ALFFBase):
     ) -> None:
         # Superclass init first to validate `using` parameter
         super().__init__(
-            fractional=fractional,
             highpass=highpass,
             lowpass=lowpass,
             using=using,
@@ -125,20 +121,39 @@ class ALFFSpheres(ALFFBase):
         Returns
         -------
         dict
-            The computed result as dictionary. The dictionary has the following
+            The computed result as dictionary. This will be either returned
-            keys:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``alff`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+              - ``data`` : ROI values as ``numpy.ndarray``
+              - ``col_names`` : ROI labels as list of str
+
+            * ``falff`` : dictionary with the following keys:
+
+              - ``data`` : ROI values as ``numpy.ndarray``
+              - ``col_names`` : ROI labels as list of str
 
         """
         logger.info("Calculating ALFF / fALFF for spheres")
 
-        # Compute ALFF / fALFF
+        # Compute ALFF + fALFF
-        output_data, output_file_path = self._compute(input_data=input)
+        alff_output, falff_output, alff_output_path, falff_output_path = (
+            self._compute(input_data=input)
+        )
 
-        # Initialize sphere aggregation
+        # Perform aggregation on ALFF / fALFF
-        sphere_aggregation = SphereAggregation(
+        aggregation_alff_input = dict(input.items())
+        aggregation_falff_input = dict(input.items())
+        aggregation_alff_input["data"] = alff_output
+        aggregation_falff_input["data"] = falff_output
+        aggregation_alff_input["path"] = alff_output_path
+        aggregation_falff_input["path"] = falff_output_path
+
+        return {
+            "alff": {
+                **SphereAggregation(
                     coords=self.coords,
                     radius=self.radius,
                     allow_overlap=self.allow_overlap,
@@ -146,14 +161,27 @@ class ALFFSpheres(ALFFBase):
                     method_params=self.agg_method_params,
                     masks=self.masks,
                     on="BOLD",
-        )
+                ).compute(
-        # Perform aggregation on ALFF / fALFF
+                    input=aggregation_alff_input,
-        sphere_aggregation_input = dict(input.items())
-        sphere_aggregation_input["data"] = output_data
-        sphere_aggregation_input["path"] = output_file_path
-        output = sphere_aggregation.compute(
-            input=sphere_aggregation_input,
                     extra_input=extra_input,
-        )
+                )[
-
+                    "aggregation"
-        return output
+                ],
+            },
+            "falff": {
+                **SphereAggregation(
+                    coords=self.coords,
+                    radius=self.radius,
+                    allow_overlap=self.allow_overlap,
+                    method=self.agg_method,
+                    method_params=self.agg_method_params,
+                    masks=self.masks,
+                    on="BOLD",
+                ).compute(
+                    input=aggregation_falff_input,
+                    extra_input=extra_input,
+                )[
+                    "aggregation"
+                ],
+            },
+        }

junifer/markers/falff/tests/test_falff_parcels.py

@@ -21,6 +21,28 @@ from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 PARCELLATION = "TianxS1x3TxMNInonlinear2009cAsym"
 
 
+@pytest.mark.parametrize(
+    "feature",
+    [
+        "alff",
+        "falff",
+    ],
+)
+def test_ALFFParcels_get_output_type(feature: str) -> None:
+    """Test ALFFParcels get_output_type().
+
+    Parameters
+    ----------
+    feature : str
+        The parametrized feature name.
+
+    """
+    assert "vector" == ALFFParcels(
+        parcellation=PARCELLATION,
+        using="junifer",
+    ).get_output_type(input_type="BOLD", output_feature=feature)
+
+
 def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
     """Test ALFFParcels.
 
@@ -41,7 +63,6 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Initialize marker
             marker = ALFFParcels(
                 parcellation=PARCELLATION,
-                fractional=False,
                 using="junifer",
             )
             # Fit transform marker on data
@@ -51,7 +72,8 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 
             # Get BOLD output
             assert "BOLD" in output
-            output_bold = output["BOLD"]
+            for feature in output["BOLD"].keys():
+                output_bold = output["BOLD"][feature]
                 # Assert BOLD output keys
                 assert "data" in output_bold
                 assert "col_names" in output_bold
@@ -77,18 +99,13 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires AFNI to be in PATH"
 )
-@pytest.mark.parametrize(
+def test_ALFFParcels_comparison(tmp_path: Path) -> None:
-    "fractional", [True, False], ids=["fractional", "non-fractional"]
-)
-def test_ALFFParcels_comparison(tmp_path: Path, fractional: bool) -> None:
     """Test ALFFParcels implementation comparison.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
-    fractional : bool
-        Whether to compute fractional ALFF or not.
 
     """
     with PartlyCloudyTestingDataGrabber() as dg:
@@ -99,7 +116,6 @@ def test_ALFFParcels_comparison(tmp_path: Path, fractional: bool) -> None:
         # Initialize marker
         junifer_marker = ALFFParcels(
             parcellation=PARCELLATION,
-            fractional=fractional,
             using="junifer",
         )
         # Fit transform marker on data
@@ -110,7 +126,6 @@ def test_ALFFParcels_comparison(tmp_path: Path, fractional: bool) -> None:
         # Initialize marker
         afni_marker = ALFFParcels(
             parcellation=PARCELLATION,
-            fractional=fractional,
             using="afni",
         )
         # Fit transform marker on data
@@ -118,9 +133,10 @@ def test_ALFFParcels_comparison(tmp_path: Path, fractional: bool) -> None:
         # Get BOLD output
         afni_output_bold = afni_output["BOLD"]
 
+        for feature in afni_output_bold.keys():
             # Check for Pearson correlation coefficient
             r, _ = sp.stats.pearsonr(
-            junifer_output_bold["data"][0],
+                junifer_output_bold[feature]["data"][0],
-            afni_output_bold["data"][0],
+                afni_output_bold[feature]["data"][0],
             )
             assert r > 0.97

junifer/markers/falff/tests/test_falff_spheres.py

@@ -21,6 +21,28 @@ from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 COORDINATES = "DMNBuckner"
 
 
+@pytest.mark.parametrize(
+    "feature",
+    [
+        "alff",
+        "falff",
+    ],
+)
+def test_ALFFSpheres_get_output_type(feature: str) -> None:
+    """Test ALFFSpheres get_output_type().
+
+    Parameters
+    ----------
+    feature : str
+        The parametrized feature name.
+
+    """
+    assert "vector" == ALFFSpheres(
+        coords=COORDINATES,
+        using="junifer",
+    ).get_output_type(input_type="BOLD", output_feature=feature)
+
+
 def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
     """Test ALFFSpheres.
 
@@ -41,7 +63,6 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Initialize marker
             marker = ALFFSpheres(
                 coords=COORDINATES,
-                fractional=False,
                 using="junifer",
                 radius=5.0,
             )
@@ -52,7 +73,8 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 
             # Get BOLD output
             assert "BOLD" in output
-            output_bold = output["BOLD"]
+            for feature in output["BOLD"].keys():
+                output_bold = output["BOLD"][feature]
                 # Assert BOLD output keys
                 assert "data" in output_bold
                 assert "col_names" in output_bold
@@ -78,18 +100,13 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires AFNI to be in PATH"
 )
-@pytest.mark.parametrize(
+def test_ALFFSpheres_comparison(tmp_path: Path) -> None:
-    "fractional", [True, False], ids=["fractional", "non-fractional"]
-)
-def test_ALFFSpheres_comparison(tmp_path: Path, fractional: bool) -> None:
     """Test ALFFSpheres implementation comparison.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
-    fractional : bool
-        Whether to compute fractional ALFF or not.
 
     """
     with PartlyCloudyTestingDataGrabber() as dg:
@@ -100,7 +117,6 @@ def test_ALFFSpheres_comparison(tmp_path: Path, fractional: bool) -> None:
         # Initialize marker
         junifer_marker = ALFFSpheres(
             coords=COORDINATES,
-            fractional=fractional,
             using="junifer",
             radius=5.0,
         )
@@ -112,7 +128,6 @@ def test_ALFFSpheres_comparison(tmp_path: Path, fractional: bool) -> None:
         # Initialize marker
         afni_marker = ALFFSpheres(
             coords=COORDINATES,
-            fractional=fractional,
             using="afni",
             radius=5.0,
         )
@@ -121,9 +136,10 @@ def test_ALFFSpheres_comparison(tmp_path: Path, fractional: bool) -> None:
         # Get BOLD output
         afni_output_bold = afni_output["BOLD"]
 
+        for feature in afni_output_bold.keys():
             # Check for Pearson correlation coefficient
             r, _ = sp.stats.pearsonr(
-            junifer_output_bold["data"][0],
+                junifer_output_bold[feature]["data"][0],
-            afni_output_bold["data"][0],
+                afni_output_bold[feature]["data"][0],
             )
             assert r > 0.99

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -45,6 +45,12 @@ class CrossParcellationFC(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "functional_connectivity": "matrix",
+        },
+    }
+
     def __init__(
         self,
         parcellation_one: str,
@@ -65,33 +71,6 @@ class CrossParcellationFC(BaseMarker):
         self.masks = masks
         super().__init__(on=["BOLD"], name=name)
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "matrix"
-
     def compute(
         self,
         input: Dict[str, Any],
@@ -118,10 +97,14 @@ class CrossParcellationFC(BaseMarker):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the correlation values between the two parcellations
+            * ``functional_connectivity`` : dictionary with the following keys:
-              as a numpy.ndarray
+
-            * ``col_names`` : the ROIs for first parcellation as a list
+              - ``data`` : correlation between the two parcellations as
-            * ``row_names`` : the ROIs for second parcellation as a list
+                           ``numpy.ndarray``
+              - ``col_names`` : ROI labels for first parcellation as list of
+                                str
+              - ``row_names`` : ROI labels for second parcellation as list of
+                                str
 
         """
         logger.debug(
@@ -129,31 +112,32 @@ class CrossParcellationFC(BaseMarker):
             f" {self.parcellation_one} and "
             f"{self.parcellation_two} parcellations."
         )
-        # Initialize a ParcelAggregation
+        # Perform aggregation using two parcellations
-        parcellation_one_dict = ParcelAggregation(
+        aggregation_parcellation_one = ParcelAggregation(
             parcellation=self.parcellation_one,
             method=self.aggregation_method,
             masks=self.masks,
         ).compute(input, extra_input=extra_input)
-        parcellation_two_dict = ParcelAggregation(
+        aggregation_parcellation_two = ParcelAggregation(
             parcellation=self.parcellation_two,
             method=self.aggregation_method,
             masks=self.masks,
         ).compute(input, extra_input=extra_input)
 
-        parcellated_ts_one = parcellation_one_dict["data"]
-        parcellated_ts_two = parcellation_two_dict["data"]
-        # columns should be named after parcellation 1
-        # rows should be named after parcellation 2
-
-        result = _correlate_dataframes(
-            pd.DataFrame(parcellated_ts_one),
-            pd.DataFrame(parcellated_ts_two),
-            method=self.correlation_method,
-        ).values
-
         return {
-            "data": result,
+            "functional_connectivity": {
-            "col_names": parcellation_one_dict["col_names"],
+                "data": _correlate_dataframes(
-            "row_names": parcellation_two_dict["col_names"],
+                    pd.DataFrame(
+                        aggregation_parcellation_one["aggregation"]["data"]
+                    ),
+                    pd.DataFrame(
+                        aggregation_parcellation_two["aggregation"]["data"]
+                    ),
+                    method=self.correlation_method,
+                ).values,
+                # Columns should be named after parcellation 1
+                "col_names": aggregation_parcellation_one["col_names"],
+                # Rows should be named after parcellation 2
+                "row_names": aggregation_parcellation_two["col_names"],
+            },
         }

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -98,23 +98,29 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+                - ``data`` : ROI values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         """
-        parcel_aggregation = ParcelAggregation(
+        # Perform aggregation
+        aggregation = ParcelAggregation(
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input, extra_input=extra_input)
-
+        # Compute edgewise timeseries
-        bold_aggregated = parcel_aggregation.compute(
-            input, extra_input=extra_input
-        )
         ets, edge_names = _ets(
-            bold_aggregated["data"], bold_aggregated["col_names"]
+            bold_ts=aggregation["aggregation"]["data"],
+            roi_names=aggregation["aggregation"]["col_names"],
         )
 
-        return {"data": ets, "col_names": edge_names}
+        return {
+            "aggregation": {
+                "data": ets,
+                "col_names": edge_names,
+            },
+        }

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -110,11 +110,14 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+                - ``data`` : ROI values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         """
-        sphere_aggregation = SphereAggregation(
+        # Perform aggregation
+        aggregation = SphereAggregation(
             coords=self.coords,
             radius=self.radius,
             allow_overlap=self.allow_overlap,
@@ -122,12 +125,13 @@ class EdgeCentricFCSpheres(FunctionalConnectivityBase):
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input, extra_input=extra_input)
-        bold_aggregated = sphere_aggregation.compute(
+        # Compute edgewise timeseries
-            input, extra_input=extra_input
-        )
         ets, edge_names = _ets(
-            bold_aggregated["data"], bold_aggregated["col_names"]
+            bold_ts=aggregation["aggregation"]["data"],
+            roi_names=aggregation["aggregation"]["col_names"],
         )
 
-        return {"data": ets, "col_names": edge_names}
+        return {
+            "aggregation": {"data": ets, "col_names": edge_names},
+        }

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -47,6 +47,12 @@ class FunctionalConnectivityBase(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "scikit-learn"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "functional_connectivity": "matrix",
+        },
+    }
+
     def __init__(
         self,
         agg_method: str = "mean",
@@ -80,33 +86,6 @@ class FunctionalConnectivityBase(BaseMarker):
             klass=NotImplementedError,
         )
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "matrix"
-
     def compute(
         self,
         input: Dict[str, Any],
@@ -128,13 +107,16 @@ class FunctionalConnectivityBase(BaseMarker):
         Returns
         -------
         dict
-            The computed result as dictionary. The following keys will be
+            The computed result as dictionary. This will be either returned
-            included in the dictionary:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : functional connectivity matrix as a ``numpy.ndarray``.
+            * ``functional_connectivity`` : dictionary with the following keys:
-            * ``row_names`` : row names as a list
+
-            * ``col_names`` : column names as a list
+              - ``data`` : functional connectivity matrix as ``numpy.ndarray``
-            * ``matrix_kind`` : the kind of matrix (tril, triu or full)
+              - ``row_names`` : ROI labels as list of str
+              - ``col_names`` : ROI labels as list of str
+              - ``matrix_kind`` : the kind of matrix (tril, triu or full)
 
         """
         # Perform necessary aggregation
@@ -148,10 +130,14 @@ class FunctionalConnectivityBase(BaseMarker):
         else:
             connectivity = ConnectivityMeasure(kind=self.cor_method)
         # Create dictionary for output
-        out = {}
+        return {
-        out["data"] = connectivity.fit_transform([aggregation["data"]])[0]
+            "functional_connectivity": {
+                "data": connectivity.fit_transform(
+                    [aggregation["aggregation"]["data"]]
+                )[0],
                 # Create column names
-        out["row_names"] = aggregation["col_names"]
+                "row_names": aggregation["aggregation"]["col_names"],
-        out["col_names"] = aggregation["col_names"]
+                "col_names": aggregation["aggregation"]["col_names"],
-        out["matrix_kind"] = "tril"
+                "matrix_kind": "tril",
-        return out
+            },
+        }

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -90,16 +90,16 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+                - ``data`` : ROI values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         """
-        parcel_aggregation = ParcelAggregation(
+        return ParcelAggregation(
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input=input, extra_input=extra_input)
-        # Return the 2D timeseries after parcel aggregation
-        return parcel_aggregation.compute(input, extra_input=extra_input)

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -104,11 +104,13 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+                - ``data`` : ROI values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         """
-        sphere_aggregation = SphereAggregation(
+        return SphereAggregation(
             coords=self.coords,
             radius=self.radius,
             allow_overlap=self.allow_overlap,
@@ -116,6 +118,4 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input=input, extra_input=extra_input)
-        # Return the 2D timeseries after sphere aggregation
-        return sphere_aggregation.compute(input, extra_input=extra_input)

junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -33,10 +33,11 @@ def test_init() -> None:
 
 def test_get_output_type() -> None:
     """Test CrossParcellationFC get_output_type()."""
-    crossparcellation = CrossParcellationFC(
+    assert "matrix" == CrossParcellationFC(
         parcellation_one=parcellation_one, parcellation_two=parcellation_two
+    ).get_output_type(
+        input_type="BOLD", output_feature="functional_connectivity"
     )
-    assert "matrix" == crossparcellation.get_output_type("BOLD")
 
 
 @pytest.mark.skipif(
@@ -59,7 +60,9 @@ def test_compute(tmp_path: Path) -> None:
             parcellation_two=parcellation_two,
             correlation_method="spearman",
         )
-        out = crossparcellation.compute(element_data["BOLD"])
+        out = crossparcellation.compute(element_data["BOLD"])[
+            "functional_connectivity"
+        ]
         assert out["data"].shape == (200, 100)
         assert len(out["col_names"]) == 100
         assert len(out["row_names"]) == 200
@@ -92,5 +95,6 @@ def test_store(tmp_path: Path) -> None:
         crossparcellation.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_CrossParcellationFC" for x in features.values()
+            x["name"] == "BOLD_CrossParcellationFC_functional_connectivity"
+            for x in features.values()
         )

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -28,11 +28,13 @@ def test_EdgeCentricFCParcels(tmp_path: Path) -> None:
             cor_method_params={"empirical": True},
         )
         # Check correct output
-        assert marker.get_output_type("BOLD") == "matrix"
+        assert "matrix" == marker.get_output_type(
+            input_type="BOLD", output_feature="functional_connectivity"
+        )
 
         # Fit-transform the data
         edge_fc = marker.fit_transform(element_data)
-        edge_fc_bold = edge_fc["BOLD"]
+        edge_fc_bold = edge_fc["BOLD"]["functional_connectivity"]
 
         # For 16 ROIs we should get (16 * (16 -1) / 2) edges in the ETS
         n_edges = int(16 * (16 - 1) / 2)
@@ -51,5 +53,6 @@ def test_EdgeCentricFCParcels(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_EdgeCentricFCParcels" for x in features.values()
+            x["name"] == "BOLD_EdgeCentricFCParcels_functional_connectivity"
+            for x in features.values()
         )

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -27,11 +27,13 @@ def test_EdgeCentricFCSpheres(tmp_path: Path) -> None:
             coords="DMNBuckner", radius=5.0, cor_method="correlation"
         )
         # Check correct output
-        assert marker.get_output_type("BOLD") == "matrix"
+        assert "matrix" == marker.get_output_type(
+            input_type="BOLD", output_feature="functional_connectivity"
+        )
 
         # Fit-transform the data
         edge_fc = marker.fit_transform(element_data)
-        edge_fc_bold = edge_fc["BOLD"]
+        edge_fc_bold = edge_fc["BOLD"]["functional_connectivity"]
 
         # There are six DMNBuckner coordinates, so
         # for 6 ROIs we should get (6 * (6 -1) / 2) edges in the ETS
@@ -57,5 +59,6 @@ def test_EdgeCentricFCSpheres(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_EdgeCentricFCSpheres" for x in features.values()
+            x["name"] == "BOLD_EdgeCentricFCSpheres_functional_connectivity"
+            for x in features.values()
         )

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -35,11 +35,13 @@ def test_FunctionalConnectivityParcels(tmp_path: Path) -> None:
             parcellation="TianxS1x3TxMNInonlinear2009cAsym"
         )
         # Check correct output
-        assert marker.get_output_type("BOLD") == "matrix"
+        assert "matrix" == marker.get_output_type(
+            input_type="BOLD", output_feature="functional_connectivity"
+        )
 
         # Fit-transform the data
         fc = marker.fit_transform(element_data)
-        fc_bold = fc["BOLD"]
+        fc_bold = fc["BOLD"]["functional_connectivity"]
 
         assert "data" in fc_bold
         assert "row_names" in fc_bold
@@ -83,6 +85,7 @@ def test_FunctionalConnectivityParcels(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_FunctionalConnectivityParcels"
+            x["name"]
+            == "BOLD_FunctionalConnectivityParcels_functional_connectivity"
             for x in features.values()
         )

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -38,11 +38,13 @@ def test_FunctionalConnectivitySpheres(tmp_path: Path) -> None:
             coords="DMNBuckner", radius=5.0, cor_method="correlation"
         )
         # Check correct output
-        assert marker.get_output_type("BOLD") == "matrix"
+        assert "matrix" == marker.get_output_type(
+            input_type="BOLD", output_feature="functional_connectivity"
+        )
 
         # Fit-transform the data
         fc = marker.fit_transform(element_data)
-        fc_bold = fc["BOLD"]
+        fc_bold = fc["BOLD"]["functional_connectivity"]
 
         assert "data" in fc_bold
         assert "row_names" in fc_bold
@@ -80,7 +82,8 @@ def test_FunctionalConnectivitySpheres(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_FunctionalConnectivitySpheres"
+            x["name"]
+            == "BOLD_FunctionalConnectivitySpheres_functional_connectivity"
             for x in features.values()
         )
 
@@ -103,11 +106,13 @@ def test_FunctionalConnectivitySpheres_empirical(tmp_path: Path) -> None:
             cor_method_params={"empirical": True},
         )
         # Check correct output
-        assert marker.get_output_type("BOLD") == "matrix"
+        assert "matrix" == marker.get_output_type(
+            input_type="BOLD", output_feature="functional_connectivity"
+        )
 
         # Fit-transform the data
         fc = marker.fit_transform(element_data)
-        fc_bold = fc["BOLD"]
+        fc_bold = fc["BOLD"]["functional_connectivity"]
 
         assert "data" in fc_bold
         assert "row_names" in fc_bold

junifer/markers/parcel_aggregation.py

@@ -63,6 +63,36 @@ class ParcelAggregation(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "T1w": {
+            "aggregation": "vector",
+        },
+        "T2w": {
+            "aggregation": "vector",
+        },
+        "BOLD": {
+            "aggregation": "timeseries",
+        },
+        "VBM_GM": {
+            "aggregation": "vector",
+        },
+        "VBM_WM": {
+            "aggregation": "vector",
+        },
+        "VBM_CSF": {
+            "aggregation": "vector",
+        },
+        "fALFF": {
+            "aggregation": "vector",
+        },
+        "GCOR": {
+            "aggregation": "vector",
+        },
+        "LCOR": {
+            "aggregation": "vector",
+        },
+    }
+
     def __init__(
         self,
         parcellation: Union[str, List[str]],
@@ -96,61 +126,6 @@ class ParcelAggregation(BaseMarker):
         self.time_method = time_method
         self.time_method_params = time_method_params or {}
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return [
-            "T1w",
-            "T2w",
-            "BOLD",
-            "VBM_GM",
-            "VBM_WM",
-            "VBM_CSF",
-            "fALFF",
-            "GCOR",
-            "LCOR",
-        ]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        Raises
-        ------
-        ValueError
-            If the ``input_type`` is invalid.
-
-        """
-
-        if input_type in [
-            "VBM_GM",
-            "VBM_WM",
-            "VBM_CSF",
-            "fALFF",
-            "GCOR",
-            "LCOR",
-        ]:
-            return "vector"
-        elif input_type == "BOLD":
-            return "timeseries"
-        else:
-            raise_error(f"Unknown input kind for {input_type}")
-
     def compute(
         self, input: Dict[str, Any], extra_input: Optional[Dict] = None
     ) -> Dict:
@@ -174,8 +149,10 @@ class ParcelAggregation(BaseMarker):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+                - ``data`` : ROI values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         Warns
         -----
@@ -253,5 +230,9 @@ class ParcelAggregation(BaseMarker):
                     "available."
                 )
         # Format the output
-        out = {"data": out_values, "col_names": labels}
+        return {
-        return out
+            "aggregation": {
+                "data": out_values,
+                "col_names": labels,
+            },
+        }

junifer/markers/reho/reho_base.py

@@ -62,6 +62,12 @@ class ReHoBase(BaseMarker):
         },
     ]
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "reho": "vector",
+        },
+    }
+
     def __init__(
         self,
         using: str,
@@ -76,33 +82,6 @@ class ReHoBase(BaseMarker):
         self.using = using
         super().__init__(on="BOLD", name=name)
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "vector"
-
     def _compute(
         self,
         input_data: Dict[str, Any],

junifer/markers/reho/reho_parcels.py

@@ -125,11 +125,14 @@ class ReHoParcels(ReHoBase):
         Returns
         -------
         dict
-            The computed result as dictionary. The dictionary has the following
+            The computed result as dictionary. This will be either returned
-            keys:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a 1D numpy.ndarray
+            * ``reho`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the parcels as a list
+
+              - ``data`` : ROI values as ``numpy.ndarray``
+              - ``col_names`` : ROI labels as list of str
 
         """
         logger.info("Calculating ReHo for parcels")
@@ -145,22 +148,27 @@ class ReHoParcels(ReHoBase):
         else:
             reho_map, reho_file_path = self._compute(input_data=input)
 
-        # Initialize parcel aggregation
+        # Perform aggregation on reho map
+        aggregation_input = dict(input.items())
+        aggregation_input["data"] = reho_map
+        aggregation_input["path"] = reho_file_path
         parcel_aggregation = ParcelAggregation(
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(
-        # Perform aggregation on reho map
+            input=aggregation_input,
-        parcel_aggregation_input = dict(input.items())
-        parcel_aggregation_input["data"] = reho_map
-        parcel_aggregation_input["path"] = reho_file_path
-        output = parcel_aggregation.compute(
-            input=parcel_aggregation_input,
             extra_input=extra_input,
         )
+
+        return {
+            "reho": {
                 # Only use the first row and expand row dimension
-        output["data"] = output["data"][0][np.newaxis, :]
+                "data": parcel_aggregation["aggregation"]["data"][0][
-        return output
+                    np.newaxis, :
+                ],
+                "col_names": parcel_aggregation["aggregation"]["col_names"],
+            }
+        }

junifer/markers/reho/reho_spheres.py

@@ -140,11 +140,14 @@ class ReHoSpheres(ReHoBase):
         Returns
         -------
         dict
-            The computed result as dictionary. The dictionary has the following
+            The computed result as dictionary. This will be either returned
-            keys:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a 1D numpy.ndarray
+            * ``reho`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the spheres as a list
+
+              - ``data`` : ROI values as ``numpy.ndarray``
+              - ``col_names`` : ROI labels as list of str
 
         """
         logger.info("Calculating ReHo for spheres")
@@ -160,7 +163,10 @@ class ReHoSpheres(ReHoBase):
         else:
             reho_map, reho_file_path = self._compute(input_data=input)
 
-        # Initialize sphere aggregation
+        # Perform aggregation on reho map
+        aggregation_input = dict(input.items())
+        aggregation_input["data"] = reho_map
+        aggregation_input["path"] = reho_file_path
         sphere_aggregation = SphereAggregation(
             coords=self.coords,
             radius=self.radius,
@@ -169,14 +175,14 @@ class ReHoSpheres(ReHoBase):
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input=aggregation_input, extra_input=extra_input)
-        # Perform aggregation on reho map
+
-        sphere_aggregation_input = dict(input.items())
+        return {
-        sphere_aggregation_input["data"] = reho_map
+            "reho": {
-        sphere_aggregation_input["path"] = reho_file_path
-        output = sphere_aggregation.compute(
-            input=sphere_aggregation_input, extra_input=extra_input
-        )
                 # Only use the first row and expand row dimension
-        output["data"] = output["data"][0][np.newaxis, :]
+                "data": sphere_aggregation["aggregation"]["data"][0][
-        return output
+                    np.newaxis, :
+                ],
+                "col_names": sphere_aggregation["aggregation"]["col_names"],
+            }
+        }

junifer/markers/reho/tests/test_reho_parcels.py

@@ -42,6 +42,11 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
                 parcellation="TianxS1x3TxMNInonlinear2009cAsym",
                 using="junifer",
             )
+            # Check correct output
+            assert "vector" == marker.get_output_type(
+                input_type="BOLD", output_feature="reho"
+            )
+
             # Fit transform marker on data
             output = marker.fit_transform(element_data)
 
@@ -49,7 +54,7 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 
             # Get BOLD output
             assert "BOLD" in output
-            output_bold = output["BOLD"]
+            output_bold = output["BOLD"]["reho"]
             # Assert BOLD output keys
             assert "data" in output_bold
             assert "col_names" in output_bold
@@ -102,14 +107,14 @@ def test_ReHoParcels_comparison(tmp_path: Path) -> None:
         # Fit transform marker on data
         junifer_output = junifer_marker.fit_transform(element_data)
         # Get BOLD output
-        junifer_output_bold = junifer_output["BOLD"]
+        junifer_output_bold = junifer_output["BOLD"]["reho"]
 
         # Initialize marker
         afni_marker = ReHoParcels(parcellation="Schaefer100x7", using="afni")
         # Fit transform marker on data
         afni_output = afni_marker.fit_transform(element_data)
         # Get BOLD output
-        afni_output_bold = afni_output["BOLD"]
+        afni_output_bold = afni_output["BOLD"]["reho"]
 
         # Check for Pearson correlation coefficient
         r, _ = sp.stats.pearsonr(

junifer/markers/reho/tests/test_reho_spheres.py

@@ -40,6 +40,11 @@ def test_ReHoSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             marker = ReHoSpheres(
                 coords=COORDINATES, using="junifer", radius=10.0
             )
+            # Check correct output
+            assert "vector" == marker.get_output_type(
+                input_type="BOLD", output_feature="reho"
+            )
+
             # Fit transform marker on data
             output = marker.fit_transform(element_data)
 
@@ -47,7 +52,7 @@ def test_ReHoSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 
             # Get BOLD output
             assert "BOLD" in output
-            output_bold = output["BOLD"]
+            output_bold = output["BOLD"]["reho"]
             # Assert BOLD output keys
             assert "data" in output_bold
             assert "col_names" in output_bold
@@ -99,7 +104,7 @@ def test_ReHoSpheres_comparison(tmp_path: Path) -> None:
         # Fit transform marker on data
         junifer_output = junifer_marker.fit_transform(element_data)
         # Get BOLD output
-        junifer_output_bold = junifer_output["BOLD"]
+        junifer_output_bold = junifer_output["BOLD"]["reho"]
 
         # Initialize marker
         afni_marker = ReHoSpheres(
@@ -110,7 +115,7 @@ def test_ReHoSpheres_comparison(tmp_path: Path) -> None:
         # Fit transform marker on data
         afni_output = afni_marker.fit_transform(element_data)
         # Get BOLD output
-        afni_output_bold = afni_output["BOLD"]
+        afni_output_bold = afni_output["BOLD"]["reho"]
 
         # Check for Pearson correlation coefficient
         r, _ = sp.stats.pearsonr(

junifer/markers/sphere_aggregation.py

@@ -68,6 +68,36 @@ class SphereAggregation(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn", "numpy"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "T1w": {
+            "aggregation": "vector",
+        },
+        "T2w": {
+            "aggregation": "vector",
+        },
+        "BOLD": {
+            "aggregation": "timeseries",
+        },
+        "VBM_GM": {
+            "aggregation": "vector",
+        },
+        "VBM_WM": {
+            "aggregation": "vector",
+        },
+        "VBM_CSF": {
+            "aggregation": "vector",
+        },
+        "fALFF": {
+            "aggregation": "vector",
+        },
+        "GCOR": {
+            "aggregation": "vector",
+        },
+        "LCOR": {
+            "aggregation": "vector",
+        },
+    }
+
     def __init__(
         self,
         coords: str,
@@ -103,61 +133,6 @@ class SphereAggregation(BaseMarker):
         self.time_method = time_method
         self.time_method_params = time_method_params or {}
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return [
-            "T1w",
-            "T2w",
-            "BOLD",
-            "VBM_GM",
-            "VBM_WM",
-            "VBM_CSF",
-            "fALFF",
-            "GCOR",
-            "LCOR",
-        ]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        Raises
-        ------
-        ValueError
-            If the ``input_type`` is invalid.
-
-        """
-
-        if input_type in [
-            "VBM_GM",
-            "VBM_WM",
-            "VBM_CSF",
-            "fALFF",
-            "GCOR",
-            "LCOR",
-        ]:
-            return "vector"
-        elif input_type == "BOLD":
-            return "timeseries"
-        else:
-            raise_error(f"Unknown input kind for {input_type}")
-
     def compute(
         self,
         input: Dict[str, Any],
@@ -183,8 +158,10 @@ class SphereAggregation(BaseMarker):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the actual computed values as a numpy.ndarray
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+                - ``data`` : ROI values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         Warns
         -----
@@ -241,5 +218,9 @@ class SphereAggregation(BaseMarker):
                     "available."
                 )
         # Format the output
-        out = {"data": out_values, "col_names": labels}
+        return {
-        return out
+            "aggregation": {
+                "data": out_values,
+                "col_names": labels,
+            },
+        }

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -39,6 +39,12 @@ class TemporalSNRBase(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "tsnr": "vector",
+        },
+    }
+
     def __init__(
         self,
         agg_method: str = "mean",
@@ -61,33 +67,6 @@ class TemporalSNRBase(BaseMarker):
             klass=NotImplementedError,
         )
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "vector"
-
     def compute(
         self,
         input: Dict[str, Any],
@@ -107,11 +86,14 @@ class TemporalSNRBase(BaseMarker):
         Returns
         -------
         dict
-            The computed result as dictionary. The following keys will be
+            The computed result as dictionary. This will be either returned
-            included in the dictionary:
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : the computed values as a ``numpy.ndarray``
+            * ``tsnr`` : dictionary with the following keys:
-            * ``col_names`` : the column labels for the computed values as list
+
+              - ``data`` : computed tSNR as ``numpy.ndarray``
+              - ``col_names`` : ROI labels as list of str
 
         """
         # Calculate voxelwise temporal signal-to-noise ratio in an image
@@ -129,4 +111,10 @@ class TemporalSNRBase(BaseMarker):
             mask_img=mask_img,
         )
         # Perform necessary aggregation and return
-        return self.aggregate(input=input, extra_input=extra_input)
+        return {
+            "tsnr": {
+                **self.aggregate(input=input, extra_input=extra_input)[
+                    "aggregation"
+                ]
+            }
+        }

junifer/markers/temporal_snr/temporal_snr_parcels.py

@@ -77,16 +77,16 @@ class TemporalSNRParcels(TemporalSNRBase):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : ROI-wise temporal SNR as a ``numpy.ndarray``
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the ROI labels for the computed values as list
+
+                - ``data`` : ROI-wise tSNR values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         """
-        parcel_aggregation = ParcelAggregation(
+        return ParcelAggregation(
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input=input, extra_input=extra_input)
-        # Return the 2D timeseries after parcel aggregation
-        return parcel_aggregation.compute(input=input, extra_input=extra_input)

junifer/markers/temporal_snr/temporal_snr_spheres.py

@@ -92,11 +92,13 @@ class TemporalSNRSpheres(TemporalSNRBase):
             to the user or stored in the storage by calling the store method
             with this as a parameter. The dictionary has the following keys:
 
-            * ``data`` : VOI-wise temporal SNR as a ``numpy.ndarray``
+            * ``aggregation`` : dictionary with the following keys:
-            * ``col_names`` : the VOI labels for the computed values as list
+
+                - ``data`` : ROI-wise tSNR values as ``numpy.ndarray``
+                - ``col_names`` : ROI labels as list of str
 
         """
-        sphere_aggregation = SphereAggregation(
+        return SphereAggregation(
             coords=self.coords,
             radius=self.radius,
             allow_overlap=self.allow_overlap,
@@ -104,6 +106,4 @@ class TemporalSNRSpheres(TemporalSNRBase):
             method_params=self.agg_method_params,
             masks=self.masks,
             on="BOLD",
-        )
+        ).compute(input=input, extra_input=extra_input)
-        # Return the 2D timeseries after sphere aggregation
-        return sphere_aggregation.compute(input=input, extra_input=extra_input)

junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py

@@ -20,11 +20,13 @@ def test_TemporalSNRParcels_computation() -> None:
             parcellation="TianxS1x3TxMNInonlinear2009cAsym"
         )
         # Check correct output
-        assert marker.get_output_type("BOLD") == "vector"
+        assert "vector" == marker.get_output_type(
+            input_type="BOLD", output_feature="tsnr"
+        )
 
         # Fit-transform the data
         tsnr_parcels = marker.fit_transform(element_data)
-        tsnr_parcels_bold = tsnr_parcels["BOLD"]
+        tsnr_parcels_bold = tsnr_parcels["BOLD"]["tsnr"]
 
         assert "data" in tsnr_parcels_bold
         assert "col_names" in tsnr_parcels_bold
@@ -51,5 +53,6 @@ def test_TemporalSNRParcels_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_TemporalSNRParcels" for x in features.values()
+            x["name"] == "BOLD_TemporalSNRParcels_tsnr"
+            for x in features.values()
         )

junifer/markers/temporal_snr/tests/test_temporal_snr_spheres.py

@@ -20,11 +20,13 @@ def test_TemporalSNRSpheres_computation() -> None:
         element_data = DefaultDataReader().fit_transform(dg["sub001"])
         marker = TemporalSNRSpheres(coords="DMNBuckner", radius=5.0)
         # Check correct output
-        assert marker.get_output_type("BOLD") == "vector"
+        assert "vector" == marker.get_output_type(
+            input_type="BOLD", output_feature="tsnr"
+        )
 
         # Fit-transform the data
         tsnr_spheres = marker.fit_transform(element_data)
-        tsnr_spheres_bold = tsnr_spheres["BOLD"]
+        tsnr_spheres_bold = tsnr_spheres["BOLD"]["tsnr"]
 
         assert "data" in tsnr_spheres_bold
         assert "col_names" in tsnr_spheres_bold
@@ -49,7 +51,8 @@ def test_TemporalSNRSpheres_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_TemporalSNRSpheres" for x in features.values()
+            x["name"] == "BOLD_TemporalSNRSpheres_tsnr"
+            for x in features.values()
         )
 
 

junifer/markers/tests/test_brainprint.py

@@ -13,16 +13,29 @@ from junifer.markers import BrainPrint
 from junifer.pipeline.utils import _check_freesurfer
 
 
-def test_get_output_type() -> None:
+@pytest.mark.parametrize(
-    """Test BrainPrint get_output_type()."""
+    "feature, storage_type",
-    marker = BrainPrint()
+    [
-    assert marker.get_output_type("FreeSurfer") == "vector"
+        ("eigenvalues", "scalar_table"),
+        ("areas", "vector"),
+        ("volumes", "vector"),
+        ("distances", "vector"),
+    ],
+)
+def test_get_output_type(feature: str, storage_type: str) -> None:
+    """Test BrainPrint get_output_type().
 
+    Parameters
+    ----------
+    feature : str
+        The parametrized feature name.
+    storage_type : str
+        The parametrized storage type.
 
-def test_validate() -> None:
+    """
-    """Test BrainPrint validate()."""
+    assert storage_type == BrainPrint().get_output_type(
-    marker = BrainPrint()
+        input_type="FreeSurfer", output_feature=feature
-    assert set(marker.validate(["FreeSurfer"])) == {"scalar_table", "vector"}
+    )
 
 
 @pytest.mark.skipif(
@@ -39,9 +52,7 @@ def test_compute() -> None:
         element = dg["sub-0001"]
         # Fetch element data
         element_data = DefaultDataReader().fit_transform(element)
-        # Initialize the marker
+        # Compute marker
-        marker = BrainPrint()
+        feature_map = BrainPrint().fit_transform(element_data)
-        # Compute the marker
-        feature_map = marker.fit_transform(element_data)
         # Assert the output keys
         assert {"eigenvalues", "areas", "volumes"} == set(feature_map.keys())

junifer/markers/tests/test_collection.py

@@ -84,7 +84,7 @@ def test_marker_collection() -> None:
         for t_marker in markers:
             t_name = t_marker.name
             assert "BOLD" in out[t_name]
-            t_bold = out[t_name]["BOLD"]
+            t_bold = out[t_name]["BOLD"]["aggregation"]
             assert "data" in t_bold
             assert "col_names" in t_bold
             assert "meta" in t_bold
@@ -107,7 +107,8 @@ def test_marker_collection() -> None:
         for t_marker in markers:
             t_name = t_marker.name
             assert_array_equal(
-                out[t_name]["BOLD"]["data"], out2[t_name]["BOLD"]["data"]
+                out[t_name]["BOLD"]["aggregation"]["data"],
+                out2[t_name]["BOLD"]["aggregation"]["data"],
             )
 
 
@@ -201,20 +202,20 @@ def test_marker_collection_storage(tmp_path: Path) -> None:
     feature_md5 = next(iter(features.keys()))
     t_feature = storage.read_df(feature_md5=feature_md5)
     fname = "tian_mean"
-    t_data = out[fname]["BOLD"]["data"]  # type: ignore
+    t_data = out[fname]["BOLD"]["aggregation"]["data"]  # type: ignore
-    cols = out[fname]["BOLD"]["col_names"]  # type: ignore
+    cols = out[fname]["BOLD"]["aggregation"]["col_names"]  # type: ignore
     assert_array_equal(t_feature[cols].values, t_data)  # type: ignore
 
     feature_md5 = list(features.keys())[1]
     t_feature = storage.read_df(feature_md5=feature_md5)
     fname = "tian_std"
-    t_data = out[fname]["BOLD"]["data"]  # type: ignore
+    t_data = out[fname]["BOLD"]["aggregation"]["data"]  # type: ignore
-    cols = out[fname]["BOLD"]["col_names"]  # type: ignore
+    cols = out[fname]["BOLD"]["aggregation"]["col_names"]  # type: ignore
     assert_array_equal(t_feature[cols].values, t_data)  # type: ignore
 
     feature_md5 = list(features.keys())[2]
     t_feature = storage.read_df(feature_md5=feature_md5)
     fname = "tian_trim_mean90"
-    t_data = out[fname]["BOLD"]["data"]  # type: ignore
+    t_data = out[fname]["BOLD"]["aggregation"]["data"]  # type: ignore
-    cols = out[fname]["BOLD"]["col_names"]  # type: ignore
+    cols = out[fname]["BOLD"]["aggregation"]["col_names"]  # type: ignore
     assert_array_equal(t_feature[cols].values, t_data)  # type: ignore

junifer/markers/tests/test_ets_rss.py

@@ -26,8 +26,9 @@ def test_compute() -> None:
     with PartlyCloudyTestingDataGrabber() as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         # Compute the RSSETSMarker
-        marker = RSSETSMarker(parcellation=PARCELLATION)
+        rss_ets = RSSETSMarker(parcellation=PARCELLATION).compute(
-        rss_ets = marker.compute(element_data["BOLD"])
+            element_data["BOLD"]
+        )
 
         # Compare with nilearn
         # Load testing parcellation
@@ -41,14 +42,14 @@ def test_compute() -> None:
             element_data["BOLD"]["data"]
         )
         # Assert the dimension of timeseries
-        assert extacted_timeseries.shape[0] == len(rss_ets["data"])
+        assert extacted_timeseries.shape[0] == len(rss_ets["rss_ets"]["data"])
 
 
 def test_get_output_type() -> None:
     """Test RSS ETS get_output_type()."""
     assert "timeseries" == RSSETSMarker(
         parcellation=PARCELLATION
-    ).get_output_type("BOLD")
+    ).get_output_type(input_type="BOLD", output_feature="rss_ets")
 
 
 def test_store(tmp_path: Path) -> None:
@@ -61,12 +62,17 @@ def test_store(tmp_path: Path) -> None:
 
     """
     with PartlyCloudyTestingDataGrabber() as dg:
+        # Get element data
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        # Compute the RSSETSMarker
-        marker = RSSETSMarker(parcellation=PARCELLATION)
         # Create storage
         storage = SQLiteFeatureStorage(tmp_path / "test_rss_ets.sqlite")
-        # Store
+        # Compute the RSSETSMarker and store
-        marker.fit_transform(input=element_data, storage=storage)
+        _ = RSSETSMarker(parcellation=PARCELLATION).fit_transform(
+            input=element_data, storage=storage
+        )
+        # Retrieve features
         features = storage.list_features()
-        assert any(x["name"] == "BOLD_RSSETSMarker" for x in features.values())
+        # Check marker name
+        assert any(
+            x["name"] == "BOLD_RSSETSMarker_rss_ets" for x in features.values()
+        )

junifer/markers/tests/test_markers_base.py

@@ -20,27 +20,27 @@ def test_base_marker_subclassing() -> None:
 
     # Create concrete class
     class MyBaseMarker(BaseMarker):
+
+        _MARKER_INOUT_MAPPINGS = {  # noqa: RUF012
+            "BOLD": {
+                "feat_1": "timeseries",
+            },
+        }
+
         def __init__(self, on, name=None) -> None:
             self.parameter = 1
             super().__init__(on, name)
 
-        def get_valid_inputs(self):
-            return ["BOLD", "T1w"]
-
-        def get_output_type(self, input):
-            if input == "BOLD":
-                return "timeseries"
-            raise ValueError(f"Cannot compute output type for {input}")
-
         def compute(self, input, extra_input):
             return {
+                "feat_1": {
                     "data": "data",
-                "columns": "columns",
+                    "col_names": ["columns"],
-                "row_names": "row_names",
+                },
             }
 
-    with pytest.raises(ValueError, match=r"cannot be computed on \['T2w'\]"):
+    with pytest.raises(ValueError, match=r"cannot be computed on \['T1w'\]"):
-        MyBaseMarker(on=["BOLD", "T2w"])
+        MyBaseMarker(on=["BOLD", "T1w"])
 
     # Create input for marker
     input_ = {
@@ -64,12 +64,11 @@ def test_base_marker_subclassing() -> None:
     output = marker.fit_transform(input=input_)  # process
     # Check output
     assert "BOLD" in output
-    assert "data" in output["BOLD"]
+    assert "data" in output["BOLD"]["feat_1"]
-    assert "columns" in output["BOLD"]
+    assert "col_names" in output["BOLD"]["feat_1"]
-    assert "row_names" in output["BOLD"]
 
-    assert "meta" in output["BOLD"]
+    assert "meta" in output["BOLD"]["feat_1"]
-    meta = output["BOLD"]["meta"]
+    meta = output["BOLD"]["feat_1"]["meta"]
     assert "datagrabber" in meta
     assert "element" in meta
     assert "datareader" in meta

junifer/markers/tests/test_parcel_aggregation.py

@@ -23,16 +23,63 @@ from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
-def test_ParcelAggregation_input_output() -> None:
+@pytest.mark.parametrize(
-    """Test ParcelAggregation input and output types."""
+    "input_type, storage_type",
-    marker = ParcelAggregation(
+    [
-        parcellation="Schaefer100x7", method="mean", on="VBM_GM"
+        (
+            "T1w",
+            "vector",
+        ),
+        (
+            "T2w",
+            "vector",
+        ),
+        (
+            "BOLD",
+            "timeseries",
+        ),
+        (
+            "VBM_GM",
+            "vector",
+        ),
+        (
+            "VBM_WM",
+            "vector",
+        ),
+        (
+            "VBM_CSF",
+            "vector",
+        ),
+        (
+            "fALFF",
+            "vector",
+        ),
+        (
+            "GCOR",
+            "vector",
+        ),
+        (
+            "LCOR",
+            "vector",
+        ),
+    ],
 )
-    for in_, out_ in [("VBM_GM", "vector"), ("BOLD", "timeseries")]:
+def test_ParcelAggregation_input_output(
-        assert marker.get_output_type(in_) == out_
+    input_type: str, storage_type: str
+) -> None:
+    """Test ParcelAggregation input and output types.
 
-    with pytest.raises(ValueError, match="Unknown input"):
+    Parameters
-        marker.get_output_type("unknown")
+    ----------
+    input_type : str
+        The parametrized input type.
+    storage_type : str
+        The parametrized storage type.
+
+    """
+    assert storage_type == ParcelAggregation(
+        parcellation="Schaefer100x7", method="mean", on=input_type
+    ).get_output_type(input_type=input_type, output_feature="aggregation")
 
 
 def test_ParcelAggregation_3D() -> None:
@@ -85,8 +132,8 @@ def test_ParcelAggregation_3D() -> None:
         )
 
         parcel_agg_mean_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
         # Check that arrays are almost equal
         assert_array_equal(parcel_agg_mean_bold_data, manual)
         assert_array_almost_equal(nifti_labels_masked_bold, manual)
@@ -113,8 +160,8 @@ def test_ParcelAggregation_3D() -> None:
             on="BOLD",
         )
         parcel_agg_std_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
         assert parcel_agg_std_bold_data.ndim == 2
         assert parcel_agg_std_bold_data.shape[0] == 1
         assert_array_equal(parcel_agg_std_bold_data, manual)
@@ -139,7 +186,7 @@ def test_ParcelAggregation_3D() -> None:
         )
         parcel_agg_trim_mean_bold_data = marker.fit_transform(element_data)[
             "BOLD"
-        ]["data"]
+        ]["aggregation"]["data"]
         assert parcel_agg_trim_mean_bold_data.ndim == 2
         assert parcel_agg_trim_mean_bold_data.shape[0] == 1
         assert_array_equal(parcel_agg_trim_mean_bold_data, manual)
@@ -154,8 +201,8 @@ def test_ParcelAggregation_4D():
             parcellation="TianxS1x3TxMNInonlinear2009cAsym", method="mean"
         )
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         # Compare with nilearn
         # Load testing parcellation
@@ -204,7 +251,8 @@ def test_ParcelAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_ParcelAggregation" for x in features.values()
+            x["name"] == "BOLD_ParcelAggregation_aggregation"
+            for x in features.values()
         )
 
     # Store 4D
@@ -221,7 +269,8 @@ def test_ParcelAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_ParcelAggregation" for x in features.values()
+            x["name"] == "BOLD_ParcelAggregation_aggregation"
+            for x in features.values()
         )
 
 
@@ -241,8 +290,8 @@ def test_ParcelAggregation_3D_mask() -> None:
             ..., 0:1
         ]
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         # Compare with nilearn
         # Load testing parcellation
@@ -316,8 +365,8 @@ def test_ParcelAggregation_3D_mask_computed() -> None:
             on="BOLD",
         )
         parcel_agg_mean_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         assert parcel_agg_mean_bold_data.ndim == 2
         assert parcel_agg_mean_bold_data.shape[0] == 1
@@ -397,7 +446,9 @@ def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
             name="tian_mean",
             on="BOLD",
         )
-        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"][
+            "aggregation"
+        ]
 
         orig_mean_data = orig_mean["data"]
         assert orig_mean_data.ndim == 2
@@ -417,7 +468,9 @@ def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
         # No warnings should be raised
         with warnings.catch_warnings():
             warnings.simplefilter("error", category=UserWarning)
-            split_mean = marker_split.fit_transform(element_data)["BOLD"]
+            split_mean = marker_split.fit_transform(element_data)["BOLD"][
+                "aggregation"
+            ]
 
         split_mean_data = split_mean["data"]
 
@@ -497,7 +550,9 @@ def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
             name="tian_mean",
             on="BOLD",
         )
-        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"][
+            "aggregation"
+        ]
 
         orig_mean_data = orig_mean["data"]
         assert orig_mean_data.ndim == 2
@@ -515,7 +570,9 @@ def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
         )
         # Warning should be raised
         with pytest.warns(RuntimeWarning, match="overlapping voxels"):
-            split_mean = marker_split.fit_transform(element_data)["BOLD"]
+            split_mean = marker_split.fit_transform(element_data)["BOLD"][
+                "aggregation"
+            ]
 
         split_mean_data = split_mean["data"]
 
@@ -602,7 +659,9 @@ def test_ParcelAggregation_3D_multiple_duplicated_labels(
             name="tian_mean",
             on="BOLD",
         )
-        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"][
+            "aggregation"
+        ]
 
         orig_mean_data = orig_mean["data"]
         assert orig_mean_data.ndim == 2
@@ -621,7 +680,9 @@ def test_ParcelAggregation_3D_multiple_duplicated_labels(
 
         # Warning should be raised
         with pytest.warns(RuntimeWarning, match="duplicated labels."):
-            split_mean = marker_split.fit_transform(element_data)["BOLD"]
+            split_mean = marker_split.fit_transform(element_data)["BOLD"][
+                "aggregation"
+            ]
 
         split_mean_data = split_mean["data"]
 
@@ -653,8 +714,8 @@ def test_ParcelAggregation_4D_agg_time():
             on="BOLD",
         )
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         # Compare with nilearn
         # Loading testing parcellation
@@ -689,8 +750,8 @@ def test_ParcelAggregation_4D_agg_time():
             on="BOLD",
         )
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         assert parcel_agg_bold_data.ndim == 2
         assert_array_equal(

junifer/markers/tests/test_sphere_aggregation.py

@@ -25,14 +25,65 @@ COORDS = "DMNBuckner"
 RADIUS = 8
 
 
-def test_SphereAggregation_input_output() -> None:
+@pytest.mark.parametrize(
-    """Test SphereAggregation input and output types."""
+    "input_type, storage_type",
-    marker = SphereAggregation(coords="DMNBuckner", method="mean", on="VBM_GM")
+    [
-    for in_, out_ in [("VBM_GM", "vector"), ("BOLD", "timeseries")]:
+        (
-        assert marker.get_output_type(in_) == out_
+            "T1w",
+            "vector",
+        ),
+        (
+            "T2w",
+            "vector",
+        ),
+        (
+            "BOLD",
+            "timeseries",
+        ),
+        (
+            "VBM_GM",
+            "vector",
+        ),
+        (
+            "VBM_WM",
+            "vector",
+        ),
+        (
+            "VBM_CSF",
+            "vector",
+        ),
+        (
+            "fALFF",
+            "vector",
+        ),
+        (
+            "GCOR",
+            "vector",
+        ),
+        (
+            "LCOR",
+            "vector",
+        ),
+    ],
+)
+def test_SphereAggregation_input_output(
+    input_type: str, storage_type: str
+) -> None:
+    """Test SphereAggregation input and output types.
 
-    with pytest.raises(ValueError, match="Unknown input"):
+    Parameters
-        marker.get_output_type("unknown")
+    ----------
+    input_type : str
+        The parametrized input type.
+    storage_type : str
+        The parametrized storage type.
+
+    """
+    assert storage_type == SphereAggregation(
+        coords="DMNBuckner",
+        method="mean",
+        on=input_type,
+    ).get_output_type(input_type=input_type, output_feature="aggregation")
 
 
 def test_SphereAggregation_3D() -> None:
@@ -44,8 +95,8 @@ def test_SphereAggregation_3D() -> None:
             coords=COORDS, method="mean", radius=RADIUS, on="VBM_GM"
         )
         sphere_agg_vbm_gm_data = marker.fit_transform(element_data)["VBM_GM"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -76,8 +127,8 @@ def test_SphereAggregation_4D() -> None:
             coords=COORDS, method="mean", radius=RADIUS, on="BOLD"
         )
         sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -120,7 +171,8 @@ def test_SphereAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "VBM_GM_SphereAggregation" for x in features.values()
+            x["name"] == "VBM_GM_SphereAggregation_aggregation"
+            for x in features.values()
         )
 
     # Store 4D
@@ -135,7 +187,8 @@ def test_SphereAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_SphereAggregation" for x in features.values()
+            x["name"] == "BOLD_SphereAggregation_aggregation"
+            for x in features.values()
         )
 
 
@@ -152,8 +205,8 @@ def test_SphereAggregation_3D_mask() -> None:
             masks="compute_brain_mask",
         )
         sphere_agg_vbm_gm_data = marker.fit_transform(element_data)["VBM_GM"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -195,8 +248,8 @@ def test_SphereAggregation_4D_agg_time() -> None:
             on="BOLD",
         )
         sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -231,8 +284,8 @@ def test_SphereAggregation_4D_agg_time() -> None:
             on="BOLD",
         )
         sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "data"
+            "aggregation"
-        ]
+        ]["data"]
 
         assert sphere_agg_bold_data.ndim == 2
         assert_array_equal(

junifer/pipeline/pipeline_step_mixin.py

@@ -210,6 +210,16 @@ class PipelineStepMixin:
         # Validate input
         fit_input = self.validate_input(input=input)
         # Validate output type
+        # Nested output type for marker
+        if hasattr(self, "_MARKER_INOUT_MAPPINGS"):
+            outputs = list(
+                {
+                    val
+                    for t_input in fit_input
+                    for val in self._MARKER_INOUT_MAPPINGS[t_input].values()
+                }
+            )
+        else:
             outputs = [self.get_output_type(t_input) for t_input in fit_input]
         return outputs
 

junifer/pipeline/tests/test_registry.py

@@ -101,7 +101,7 @@ def test_get_class():
     register(step="datagrabber", name="bar", klass=str)
     # Get class
     obj = get_class(step="datagrabber", name="bar")
-    assert obj == str
+    assert isinstance(obj, type(str))
 
 
 # TODO: possible parametrization?