.pre-commit-config.yaml

@@ -17,17 +17,17 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.15
+    rev: v0.16
     hooks:
       - id: validate-pyproject
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.1.1
     hooks:
       - id: black
         exclude: ^(docs/|examples/|tools/)
         args: [--check]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.0
+    rev: v0.1.15
     hooks:
       - id: ruff
         types_or: [python, jupyter]

docs/api/data.rst

@@ -4,6 +4,7 @@ Parcellations
 .. automodule:: junifer.data.parcellations
    :members:
 
+
 Coordinates
 ===========
 
@@ -16,3 +17,10 @@ Masks
 
 .. automodule:: junifer.data.masks
    :members:
+
+
+Template Spaces
+===============
+
+.. automodule:: junifer.data.template_spaces
+   :members:

docs/changes/newsfragments/297.feature

@@ -0,0 +1 @@
+Introduce :func:`.get_xfm` to fetch transformation files for moving between template spaces by `Synchon Mandal`_

junifer/api/cli.py

@@ -141,6 +141,7 @@ def _validate_verbose(
     -------
     str or int
         The validated value.
+
     """
     if isinstance(value, int):
         return value

junifer/api/functions.py

@@ -575,6 +575,7 @@ def _queue_slurm(
         (default None).
     config : dict
         The configuration to be used for queueing the job.
+
     """
     pass
     # logger.debug("Creating SLURM job")

junifer/api/tests/test_api_utils.py

@@ -32,7 +32,7 @@ def test_get_python_information() -> None:
 def test_get_dependency_information_short() -> None:
     """Test short version of _get_dependency_information()."""
     dependency_information = _get_dependency_information(long_=False)
-    assert list(dependency_information.keys()) == [
+    dependency_list = [
         "click",
         "numpy",
         "scipy",
@@ -42,14 +42,20 @@ def test_get_dependency_information_short() -> None:
         "nilearn",
         "sqlalchemy",
         "ruamel.yaml",
+        "httpx",
     ]
+    if int(pl.python_version_tuple()[1]) < 10:
+        dependency_list.append("importlib_metadata")
+    assert frozenset(dependency_information.keys()) == frozenset(
+        dependency_list
+    )
 
 
 def test_get_dependency_information_long() -> None:
     """Test long version of _get_dependency_information()."""
     dependency_information = _get_dependency_information(long_=True)
     dependency_information_keys = list(dependency_information.keys())
-    for key in [
+    dependency_list = [
         "click",
         "numpy",
         "scipy",
@@ -59,7 +65,9 @@ def test_get_dependency_information_long() -> None:
         "nilearn",
         "sqlalchemy",
         "ruamel.yaml",
-    ]:
+        "httpx",
+    ]
+    for key in dependency_list:
         assert key in dependency_information_keys
 
 

junifer/data/__init__.py

@@ -25,4 +25,6 @@ from .masks import (
     get_mask,
 )
 
+from .template_spaces import get_xfm
+
 from . import utils

junifer/data/template_spaces.py

@@ -0,0 +1,91 @@
+"""Provide functions for template spaces."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from pathlib import Path
+from typing import Union
+
+import httpx
+
+from ..utils import logger, raise_error
+
+
+def get_xfm(
+    src: str, dst: str, xfms_dir: Union[str, Path, None] = None
+) -> Path:  # pragma: no cover
+    """Fetch warp files to convert from ``src`` to ``dst``.
+
+    Parameters
+    ----------
+    src : str
+        The template space to transform from.
+    dst : str
+        The template space to transform to.
+    xfms_dir : str or pathlib.Path, optional
+        Path where the retrieved transformation files are stored.
+        The default location is "$HOME/junifer/data/xfms" (default None).
+
+    Returns
+    -------
+    pathlib.Path
+        The path to the transformation file.
+
+    Raises
+    ------
+    RuntimeError
+        If there is a problem fetching files.
+
+    """
+    if xfms_dir is None:
+        xfms_dir = Path().home() / "junifer" / "data" / "xfms"
+        logger.debug(f"Creating xfm directory at: {xfms_dir.resolve()}")
+        # Create default junifer data directory if not present
+        xfms_dir.mkdir(exist_ok=True, parents=True)
+    # Convert str to Path
+    elif not isinstance(xfms_dir, Path):
+        xfms_dir = Path(xfms_dir)
+
+    # Set local file prefix
+    xfm_file_prefix = f"{src}_to_{dst}"
+    # Set local file dir
+    xfm_file_dir = xfms_dir / xfm_file_prefix
+    # Create local directory if not present
+    xfm_file_dir.mkdir(exist_ok=True, parents=True)
+    # Set file name with extension
+    xfm_file = f"{src}_to_{dst}_Composite.h5"
+    # Set local file path
+    xfm_file_path = xfm_file_dir / xfm_file
+    # Check if the file exists
+    if xfm_file_path.exists():
+        logger.info(
+            f"Found existing xfm file for {src} to {dst} at "
+            f"{xfm_file_path.resolve()}"
+        )
+        return xfm_file_path
+
+    # Set URL
+    url = (
+        "https://gin.g-node.org/juaml/human-template-xfms/raw/main/xfms/"
+        f"{xfm_file_prefix}/{xfm_file}"
+    )
+    # Create the file before proceeding
+    xfm_file_path.touch()
+
+    logger.info(f"Downloading xfm file for {src} to {dst} from {url}")
+    # Steam response
+    with httpx.stream("GET", url) as resp:
+        try:
+            resp.raise_for_status()
+        except httpx.HTTPError as exc:
+            raise_error(
+                f"Error response {exc.response.status_code} while "
+                f"requesting {exc.request.url!r}",
+                klass=RuntimeError,
+            )
+        else:
+            with open(xfm_file_path, "ab") as f:
+                for chunk in resp.iter_bytes():
+                    f.write(chunk)
+
+    return xfm_file_path

junifer/data/tests/test_data_utils.py

@@ -36,6 +36,7 @@ def test_closest_resolution(
         The valid resolutions.
     expected: float
         The expected result.
+
     """
     assert closest_resolution(resolution, valid_resolutions) == expected
     assert (

junifer/data/tests/test_masks.py

@@ -343,6 +343,7 @@ def test_nilearn_compute_masks(
         Parameters to pass to the function.
     resample : bool
         Whether to resample the mask to the target data.
+
     """
     reader = DefaultDataReader()
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -423,6 +424,7 @@ def test_get_mask_multiple(
         Masks to get, junifer style.
     params : dict
         Parameters to pass to the intersect_masks function.
+
     """
     reader = DefaultDataReader()
     with SPMAuditoryTestingDataGrabber() as dg:

junifer/data/tests/test_template_spaces.py

@@ -0,0 +1,30 @@
+"""Provide tests for template spaces."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import socket
+from pathlib import Path
+
+import pytest
+
+from junifer.data import get_xfm
+
+
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+def test_get_xfm(tmp_path: Path) -> None:
+    """Test warp file fetching.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    xfm_path = get_xfm(
+        src="MNI152NLin6Asym", dst="MNI152NLin2009cAsym", xfms_dir=tmp_path
+    )
+    assert isinstance(xfm_path, Path)

junifer/data/utils.py

@@ -1,4 +1,5 @@
 """Provide utilities for data module."""
+
 from typing import List, Optional, Union
 
 import numpy as np
@@ -24,6 +25,7 @@ def closest_resolution(
     -------
     float or int
         The closest valid resolution.
+
     """
     # Convert list of int to numpy.ndarray
     if not isinstance(valid_resolution, np.ndarray):

junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -98,6 +98,7 @@ def _apply_mask_and_get_affinity(
     A : scipy.sparse.lil_matrix
         Contains the boolean indices for each sphere.
         shape: (number of seeds, number of voxels)
+
     """
     seeds = list(seeds)
 
@@ -204,6 +205,7 @@ def _iter_signals_from_spheres(
     mask_img : Niimg-like object, optional
         See :ref:`extracting_data`.
         Mask to apply to regions before extracting signals.
+
     """
     X, A = _apply_mask_and_get_affinity(
         seeds, niimg, radius, allow_overlap, mask_img=mask_img

junifer/markers/falff/falff_base.py

@@ -184,6 +184,7 @@ class ALFFBase(BaseMarker):
             other data kind that needs to be used in the computation. For
             example, the functional connectivity markers can make use of the
             confounds if available (default None).
+
         """
         raise_error(
             "_postprocess must be implemented", klass=NotImplementedError

junifer/markers/falff/falff_parcels.py

@@ -59,6 +59,7 @@ class ALFFParcels(ALFFBase):
     ALFF/fALFF are computed using a bandpass butterworth filter. See
     :func:`scipy.signal.butter` and :func:`scipy.signal.filtfilt` for more
     details.
+
     """
 
     def __init__(

junifer/markers/falff/falff_spheres.py

@@ -66,6 +66,7 @@ class ALFFSpheres(ALFFBase):
     ALFF/fALFF are computed using a bandpass butterworth filter. See
     :func:`scipy.signal.butter` and :func:`scipy.signal.filtfilt` for more
     details.
+
     """
 
     def __init__(

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -37,6 +37,7 @@ class CrossParcellationFC(BaseMarker):
     name : str, optional
         The name of the marker. If None, will use the class name
         (default None).
+
     """
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -97,6 +97,7 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
 
             * ``data`` : the actual computed values as a numpy.ndarray
             * ``col_names`` : the column labels for the computed values as list
+
         """
         parcel_aggregation = ParcelAggregation(
             parcellation=self.parcellation,

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -84,6 +84,7 @@ class FunctionalConnectivityBase(BaseMarker):
         -------
         list of str
             The list of data types that can be used as input for this marker.
+
         """
         return ["BOLD"]
 

junifer/markers/reho/reho_estimator.py

@@ -500,9 +500,7 @@ def _kendall_w_reho(
     numerator = (12 * np.sum(np.square(np.sum(timeseries_ranks, axis=0)))) - (
         3 * m**2 * n * (n + 1) ** 2
     )
-    denominator = (m**2 * n * (n**2 - 1)) - (
+    denominator = (m**2 * n * (n**2 - 1)) - (m * np.sum(tied_rank_corrections))
-        m * np.sum(tied_rank_corrections)
-    )
 
     if denominator == 0:
         kcc = 1.0

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -65,6 +65,7 @@ class TemporalSNRBase(BaseMarker):
         -------
         list of str
             The list of data types that can be used as input for this marker.
+
         """
         return ["BOLD"]
 

junifer/pipeline/tests/test_update_meta_mixin.py

@@ -38,6 +38,7 @@ def test_UpdateMetaMixin(
         The dependencies of the pipeline step.
     expected : set
         The expected dependencies.
+
     """
 
     class TestUpdateMetaMixin(UpdateMetaMixin):

junifer/storage/base.py

@@ -177,6 +177,7 @@ class BaseFeatureStorage(ABC):
             The element as a dictionary.
         meta : dict
             The metadata as a dictionary.
+
         """
         raise_error(
             msg="Concrete classes need to implement store_metadata().",

junifer/storage/hdf5.py

@@ -57,6 +57,7 @@ def _create_chunk(
     ------
     ValueError
         If `kind` is not one of ['vector', 'matrix', 'timeseries'].
+
     """
     if kind in ["vector", "matrix"]:
         features_data = np.concatenate(chunk_data, axis=-1)
@@ -678,9 +679,13 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         elif isinstance(data, list):
             if self.force_float32:
                 data = [
-                    x.astype(dtype=np.dtype("float32"), casting="same_kind")
+                    (
-                    if x.dtype == np.dtype("float64")
+                        x.astype(
-                    else x
+                            dtype=np.dtype("float32"), casting="same_kind"
+                        )
+                        if x.dtype == np.dtype("float64")
+                        else x
+                    )
                     for x in data
                 ]
         # Handle cases for existing and new entry

junifer/storage/sqlite.py

@@ -366,6 +366,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
             The element as a dictionary.
         meta : dict
             The metadata as a dictionary.
+
         """
         # Get sqlalchemy engine
         engine = self.get_engine(element=element)

junifer/storage/tests/test_hdf5.py

@@ -838,6 +838,7 @@ def _create_data_to_store(n_elements: int, kind: str) -> Tuple[str, Dict]:
         The meta md5.
     dict
         The data to store.
+
     """
     all_data = []
     t_md5 = None

junifer/storage/utils.py

@@ -131,6 +131,7 @@ def element_to_prefix(element: Dict) -> str:
     -------
     str
         The element converted to prefix.
+
     """
     logger.debug(f"Converting element {element} to prefix.")
     prefix = "element"

junifer/testing/utils.py

@@ -18,6 +18,7 @@ def get_testing_data(fname: str) -> Path:
     -------
     pathlib.Path
         The absolute path to the file.
+
     """
     t_path = Path(__file__).parent / "data" / fname
     if not t_path.exists():

pyproject.toml

@@ -41,11 +41,12 @@ dependencies = [
     "datalad>=0.15.4,<0.20",
     "pandas>=1.4.0,<2.2",
     "nibabel>=3.2.0,<5.11",
-    "nilearn>=0.9.0,<=0.11.0",
+    "nilearn>=0.9.0,<=0.10.2",
     "sqlalchemy>=1.4.27,<=2.1.0",
     "ruamel.yaml>=0.17,<0.18",
     "importlib_metadata; python_version<'3.10'",
     "h5py>=3.8.0,<3.10",
+    "httpx[http2]==0.26.0",
 ]
 dynamic = ["version"]
 
@@ -185,6 +186,7 @@ known-third-party =[
     "nilearn",
     "sqlalchemy",
     "yaml",
+    "httpx",
     "bct",
     "neurokit2",
     "pytest",