junifer 0.0.7.dev93__tar.gz → 0.0.7.dev103__tar.gz

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/.github/workflows/docker-ci-publish.yml

@@ -45,7 +45,7 @@ jobs:
       # https://github.com/sigstore/cosign-installer
       - name: Install cosign
         if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@3454372f43399081ed03b604cb2d021dabca52bb #v3.8.2
+        uses: sigstore/cosign-installer@398d4b0eeef1380460a10c8013a76f728fb906ac #v3.9.1
         with:
           cosign-release: 'v2.2.4'
 
@@ -53,7 +53,7 @@ jobs:
       # multi-platform images and export cache
       # https://github.com/docker/setup-buildx-action
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2 # v3.10.0
+        uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3.11.1
 
       # Login against a Docker registry except on PR
       # https://github.com/docker/login-action
@@ -77,7 +77,7 @@ jobs:
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@14487ce63c7a62a4a324b0bfb37086795e31c6c1 # v6.16.0
+        uses: docker/build-push-action@263435318d21b8e681c14492fe198d362a7d2c83 # v6.18.0
         with:
           context: .
           file: Dockerfile-ci

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/.github/workflows/docker-docs-publish.yml

@@ -42,7 +42,7 @@ jobs:
       # https://github.com/sigstore/cosign-installer
       - name: Install cosign
         if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@3454372f43399081ed03b604cb2d021dabca52bb #v3.8.2
+        uses: sigstore/cosign-installer@398d4b0eeef1380460a10c8013a76f728fb906ac #v3.9.1
         with:
           cosign-release: 'v2.2.4'
 
@@ -50,7 +50,7 @@ jobs:
       # multi-platform images and export cache
       # https://github.com/docker/setup-buildx-action
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2 # v3.10.0
+        uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3.11.1
 
       # Login against a Docker registry except on PR
       # https://github.com/docker/login-action
@@ -74,7 +74,7 @@ jobs:
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@14487ce63c7a62a4a324b0bfb37086795e31c6c1 # v6.16.0
+        uses: docker/build-push-action@263435318d21b8e681c14492fe198d362a7d2c83 # v6.18.0
         with:
           context: .
           file: Dockerfile-docs

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev93
+Version: 0.0.7.dev103
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/docs/builtin.rst

@@ -167,6 +167,10 @@ Available
      - Slice ``BOLD`` data temporally
      - | Done
      - :gh:`443`
+   * - ``TemporalFilter``
+     - Filter (clean) ``BOLD`` data temporally
+     - | Done
+     - :gh:`432`
 
 
 ..

junifer-0.0.7.dev103/docs/changes/newsfragments/432.feature

@@ -0,0 +1 @@
+Introduce :class:`.TemporalFilter` preprocessor for temporally filtering BOLD data by `Fede Raimondo`_

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/junifer/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.7.dev93'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev93')
+__version__ = version = '0.0.7.dev103'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev103')

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/junifer/pipeline/pipeline_component_registry.py

@@ -76,6 +76,7 @@ class PipelineComponentRegistry(metaclass=Singleton):
                 "SpaceWarper": "SpaceWarper",
                 "fMRIPrepConfoundRemover": "fMRIPrepConfoundRemover",
                 "TemporalSlicer": "TemporalSlicer",
+                "TemporalFilter": "TemporalFilter",
             },
             "marker": {
                 "ALFFParcels": "ALFFParcels",

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/junifer/preprocess/__init__.pyi

@@ -4,6 +4,7 @@ __all__ = [
     "SpaceWarper",
     "Smoothing",
     "TemporalSlicer",
+    "TemporalFilter",
 ]
 
 from .base import BasePreprocessor
@@ -11,3 +12,4 @@ from .confounds import fMRIPrepConfoundRemover
 from .warping import SpaceWarper
 from .smoothing import Smoothing
 from ._temporal_slicer import TemporalSlicer
+from ._temporal_filter import TemporalFilter

junifer-0.0.7.dev103/junifer/preprocess/_temporal_filter.py

@@ -0,0 +1,240 @@
+"""Provide class for temporal filtering."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Optional,
+    Union,
+)
+
+import nibabel as nib
+from nilearn import image as nimg
+from nilearn._utils.niimg_conversions import check_niimg_4d
+
+from ..api.decorators import register_preprocessor
+from ..data import get_data
+from ..pipeline import WorkDirManager
+from ..typing import Dependencies
+from ..utils import logger
+from .base import BasePreprocessor
+
+
+__all__ = ["TemporalFilter"]
+
+
+@register_preprocessor
+class TemporalFilter(BasePreprocessor):
+    """Class for temporal filtering.
+
+    Temporal filtering is based on :func:`nilearn.image.clean_img`.
+
+    Parameters
+    ----------
+    detrend : bool, optional
+        If True, detrending will be applied on timeseries (default True).
+    standardize : bool, optional
+        If True, returned signals are set to unit variance (default True).
+    low_pass : float, optional
+        Low cutoff frequencies, in Hertz. If None, no filtering is applied
+        (default None).
+    high_pass : float, optional
+        High cutoff frequencies, in Hertz. If None, no filtering is
+        applied (default None).
+    t_r : float, optional
+        Repetition time, in second (sampling period).
+        If None, it will use t_r from nifti header (default None).
+    masks : str, dict or list of dict or str, optional
+        The specification of the masks to apply to regions before extracting
+        signals. Check :ref:`Using Masks <using_masks>` for more details.
+        If None, will not apply any mask (default None).
+
+    """
+
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nilearn"}
+
+    def __init__(
+        self,
+        detrend: bool = True,
+        standardize: bool = True,
+        low_pass: Optional[float] = None,
+        high_pass: Optional[float] = None,
+        t_r: Optional[float] = None,
+        masks: Union[str, dict, list[Union[dict, str]], None] = None,
+    ) -> None:
+        """Initialize the class."""
+        self.detrend = detrend
+        self.standardize = standardize
+        self.low_pass = low_pass
+        self.high_pass = high_pass
+        self.t_r = t_r
+        self.masks = masks
+
+        super().__init__(on="BOLD", required_data_types=["BOLD"])
+
+    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
+            preprocessor.
+
+        """
+        return ["BOLD"]
+
+    def get_output_type(self, input_type: str) -> str:
+        """Get output type.
+
+        Parameters
+        ----------
+        input_type : str
+            The input to the preprocessor.
+
+        Returns
+        -------
+        str
+            The data type output by the preprocessor.
+
+        """
+        # Does not add any new keys
+        return input_type
+
+    def _validate_data(
+        self,
+        input: dict[str, Any],
+    ) -> None:
+        """Validate input data.
+
+        Parameters
+        ----------
+        input : dict
+            Dictionary containing the ``BOLD`` data from the
+            Junifer Data object.
+
+        Raises
+        ------
+        ValueError
+            If ``"data"`` is not 4D
+
+        """
+        # BOLD must be 4D niimg
+        check_niimg_4d(input["data"])
+
+    def preprocess(
+        self,
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[dict[str, Any], Optional[dict[str, dict[str, Any]]]]:
+        """Preprocess.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object to preprocess.
+        extra_input : dict, optional
+            The other fields in the Junifer Data object.
+
+        Returns
+        -------
+        dict
+            The computed result as dictionary. If `self.masks` is not None,
+            then the target data computed mask is updated for further steps.
+        None
+            Extra "helper" data types as dictionary to add to the Junifer Data
+            object.
+
+        """
+        # Validate data
+        self._validate_data(input)
+
+        # Get BOLD data
+        bold_img = input["data"]
+        # Set t_r
+        t_r = self.t_r
+        if t_r is None:
+            logger.info("No `t_r` specified, using t_r from NIfTI header")
+            t_r = bold_img.header.get_zooms()[3]  # type: ignore
+            logger.info(
+                f"Read t_r from NIfTI header: {t_r}",
+            )
+
+        # Create element-specific tempdir for storing generated data
+        # and / or mask
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="temporal_filter"
+        )
+
+        # Set mask data
+        mask_img = None
+        if self.masks is not None:
+            # Generate mask
+            logger.debug(f"Masking with {self.masks}")
+            mask_img = get_data(
+                kind="mask",
+                names=self.masks,
+                target_data=input,
+                extra_input=extra_input,
+            )
+            # Save generated mask for use later
+            generated_mask_img_path = element_tempdir / "generated_mask.nii.gz"
+            nib.save(mask_img, generated_mask_img_path)
+
+            # Save BOLD mask and link it to the BOLD data type dict;
+            # this allows to use "inherit" down the pipeline
+            logger.debug("Setting `BOLD.mask`")
+            input.update(
+                {
+                    "mask": {
+                        # Update path to sync with "data"
+                        "path": generated_mask_img_path,
+                        # Update data
+                        "data": mask_img,
+                        # Should be in the same space as target data
+                        "space": input["space"],
+                    }
+                }
+            )
+
+        signal_clean_kwargs = {}
+
+        # Clean image
+        logger.info("Temporal filter image using nilearn")
+        logger.debug(f"\tdetrend: {self.detrend}")
+        logger.debug(f"\tstandardize: {self.standardize}")
+        logger.debug(f"\tlow_pass: {self.low_pass}")
+        logger.debug(f"\thigh_pass: {self.high_pass}")
+        logger.debug(f"\tt_r: {self.t_r}")
+
+        cleaned_img = nimg.clean_img(
+            imgs=bold_img,
+            detrend=self.detrend,
+            standardize=self.standardize,
+            low_pass=self.low_pass,
+            high_pass=self.high_pass,
+            t_r=t_r,
+            mask_img=mask_img,
+            **signal_clean_kwargs,
+        )
+        # Fix t_r as nilearn messes it up
+        cleaned_img.header["pixdim"][4] = t_r
+        # Save filtered data
+        filtered_data_path = element_tempdir / "filtered_data.nii.gz"
+        nib.save(cleaned_img, filtered_data_path)
+
+        logger.debug("Updating `BOLD`")
+        input.update(
+            {
+                # Update path to sync with "data"
+                "path": filtered_data_path,
+                # Update data
+                "data": cleaned_img,
+            }
+        )
+
+        return input, None

junifer-0.0.7.dev103/junifer/preprocess/tests/test_temporal_filter.py

@@ -0,0 +1,99 @@
+"""Provide tests for TemporalFilter."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import Optional
+
+import pytest
+
+from junifer.datareader import DefaultDataReader
+from junifer.preprocess import TemporalFilter
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
+
+
+@pytest.mark.parametrize(
+    "detrend, standardize, low_pass, high_pass, t_r, masks",
+    (
+        [
+            True,
+            True,
+            None,
+            None,
+            None,
+            None,
+        ],
+        [
+            False,
+            True,
+            0.1,
+            None,
+            None,
+            "compute_brain_mask",
+        ],
+        [
+            True,
+            False,
+            None,
+            0.08,
+            None,
+            "compute_background_mask",
+        ],
+        [
+            False,
+            False,
+            None,
+            None,
+            2,
+            None,
+        ],
+        [
+            True,
+            True,
+            0.1,
+            0.08,
+            2,
+            "compute_brain_mask",
+        ],
+    ),
+)
+def test_TemporalFilter(
+    detrend: bool,
+    standardize: bool,
+    low_pass: Optional[float],
+    high_pass: Optional[float],
+    t_r: Optional[float],
+    masks: Optional[str],
+) -> None:
+    """Test TemporalFilter.
+
+    Parameters
+    ----------
+    detrend : bool
+        The parametrized detrending flag.
+    standardize : bool
+        The parametrized standardization flag.
+    low_pass : float or None
+        The parametrized low pass value.
+    high_pass : float or None
+        The parametrized high pass value.
+    t_r : float or None
+        The parametrized repetition time.
+    masks : str or None
+        The parametrized mask.
+
+    """
+    with PartlyCloudyTestingDataGrabber() as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Preprocess data
+        output = TemporalFilter(
+            detrend=detrend,
+            standardize=standardize,
+            low_pass=low_pass,
+            high_pass=high_pass,
+            t_r=t_r,
+            masks=masks,
+        ).fit_transform(element_data)
+
+        assert isinstance(output, dict)

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev93
+Version: 0.0.7.dev103
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.7.dev93 → junifer-0.0.7.dev103}/junifer.egg-info/SOURCES.txt

@@ -64,6 +64,7 @@ docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
 docs/changes/newsfragments/333.enh
+docs/changes/newsfragments/432.feature
 docs/changes/newsfragments/441.misc
 docs/changes/newsfragments/443.feature
 docs/changes/newsfragments/444.bugfix
@@ -372,6 +373,7 @@ junifer/pipeline/tests/test_update_meta_mixin.py
 junifer/pipeline/tests/test_workdir_manager.py
 junifer/preprocess/__init__.py
 junifer/preprocess/__init__.pyi
+junifer/preprocess/_temporal_filter.py
 junifer/preprocess/_temporal_slicer.py
 junifer/preprocess/base.py
 junifer/preprocess/py.typed
@@ -389,6 +391,7 @@ junifer/preprocess/smoothing/py.typed
 junifer/preprocess/smoothing/smoothing.py
 junifer/preprocess/smoothing/tests/test_smoothing.py
 junifer/preprocess/tests/test_preprocess_base.py
+junifer/preprocess/tests/test_temporal_filter.py
 junifer/preprocess/tests/test_temporal_slicer.py
 junifer/preprocess/warping/__init__.py
 junifer/preprocess/warping/__init__.pyi