junifer 0.0.7.dev132__py3-none-any.whl → 0.0.7.dev169__py3-none-any.whl

junifer/data/maps/_maps.py

@@ -0,0 +1,446 @@
+"""Provide a class for centralized maps data registry."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from pathlib import Path
+from typing import TYPE_CHECKING, Any, Optional, Union
+
+import nibabel as nib
+import nilearn.image as nimg
+import numpy as np
+from junifer_data import get
+
+from ...utils import logger, raise_error
+from ..pipeline_data_registry_base import BasePipelineDataRegistry
+from ..utils import (
+    JUNIFER_DATA_PARAMS,
+    closest_resolution,
+    get_dataset_path,
+    get_native_warper,
+)
+from ._ants_maps_warper import ANTsMapsWarper
+from ._fsl_maps_warper import FSLMapsWarper
+
+
+if TYPE_CHECKING:
+    from nibabel.nifti1 import Nifti1Image
+
+
+__all__ = ["MapsRegistry"]
+
+
+class MapsRegistry(BasePipelineDataRegistry):
+    """Class for maps data registry.
+
+    This class is a singleton and is used for managing available maps
+    data in a centralized manner.
+
+    """
+
+    def __init__(self) -> None:
+        """Initialize the class."""
+        super().__init__()
+        # Each entry in registry is a dictionary that must contain at least
+        # the following keys:
+        # * 'family': the maps' family name (e.g., 'Smith')
+        # * 'space': the maps' space (e.g., 'MNI')
+        # and can also have optional key(s):
+        # * 'valid_resolutions': a list of valid resolutions for the
+        # maps (e.g., [1, 2])
+        # The built-in maps are files that are shipped with the
+        # junifer-data dataset.
+        # Make built-in and external dictionaries for validation later
+        self._builtin = {}
+        self._external = {}
+
+        # Add Smith
+        for comp in ["rsn", "bm"]:
+            for dim in [10, 20, 70]:
+                self._builtin.update(
+                    {
+                        f"Smith_{comp}_{dim}": {
+                            "family": "Smith2009",
+                            "components": comp,
+                            "dimension": dim,
+                            "space": "MNI152NLin6Asym",
+                        }
+                    }
+                )
+
+        # Update registry with built-in ones
+        self._registry.update(self._builtin)
+
+    def register(
+        self,
+        name: str,
+        maps_path: Union[str, Path],
+        maps_labels: list[str],
+        space: str,
+        overwrite: bool = False,
+    ) -> None:
+        """Register a custom user map(s).
+
+        Parameters
+        ----------
+        name : str
+            The name of the map(s).
+        maps_path : str or pathlib.Path
+            The path to the map(s) file.
+        maps_labels : list of str
+            The list of labels for the map(s).
+        space : str
+            The template space of the map(s), e.g., "MNI152NLin6Asym".
+        overwrite : bool, optional
+            If True, overwrite an existing maps with the same name.
+            Does not apply to built-in maps (default False).
+
+        Raises
+        ------
+        ValueError
+            If the map(s) ``name`` is a built-in map(s) or
+            if the map(s) ``name`` is already registered and
+            ``overwrite=False``.
+
+        """
+        # Check for attempt of overwriting built-in maps
+        if name in self._builtin:
+            raise_error(
+                f"Map(s): {name} already registered as built-in map(s)."
+            )
+        # Check for attempt of overwriting external maps
+        if name in self._external:
+            if overwrite:
+                logger.info(f"Overwriting map(s): {name}")
+            else:
+                raise_error(
+                    f"Map(s): {name} already registered. Set "
+                    "`overwrite=True` to update its value."
+                )
+        # Convert str to Path
+        if not isinstance(maps_path, Path):
+            maps_path = Path(maps_path)
+        # Registration
+        logger.info(f"Registering map(s): {name}")
+        # Add user maps info
+        self._external[name] = {
+            "path": maps_path,
+            "labels": maps_labels,
+            "family": "CustomUserMaps",
+            "space": space,
+        }
+        # Update registry
+        self._registry[name] = {
+            "path": maps_path,
+            "labels": maps_labels,
+            "family": "CustomUserMaps",
+            "space": space,
+        }
+
+    def deregister(self, name: str) -> None:
+        """De-register a custom user map(s).
+
+        Parameters
+        ----------
+        name : str
+            The name of the map(s).
+
+        """
+        logger.info(f"De-registering map(s): {name}")
+        # Remove maps info
+        _ = self._external.pop(name)
+        # Update registry
+        _ = self._registry.pop(name)
+
+    def load(
+        self,
+        name: str,
+        target_space: str,
+        resolution: Optional[float] = None,
+        path_only: bool = False,
+    ) -> tuple[Optional["Nifti1Image"], list[str], Path, str]:
+        """Load map(s) and labels.
+
+        Parameters
+        ----------
+        name : str
+            The name of the map(s).
+        target_space : str
+            The desired space of the map(s).
+        resolution : float, optional
+            The desired resolution of the map(s) to load. If it is not
+            available, the closest resolution will be loaded. Preferably, use a
+            resolution higher than the desired one. By default, will load the
+            highest one (default None).
+        path_only : bool, optional
+            If True, the map(s) image will not be loaded (default False).
+
+        Returns
+        -------
+        Nifti1Image or None
+            Loaded map(s) image.
+        list of str
+            Map(s) labels.
+        pathlib.Path
+            File path to the map(s) image.
+        str
+            The space of the map(s).
+
+        Raises
+        ------
+        ValueError
+            If ``name`` is invalid or
+            if the map(s) family is invalid or
+            if the map(s) values and labels
+            don't have equal dimension or if the value range is invalid.
+
+        """
+        # Check for valid maps name
+        if name not in self._registry:
+            raise_error(
+                f"Map(s): {name} not found. Valid options are: {self.list}"
+            )
+
+        # Copy maps definition to avoid edits in original object
+        maps_def = self._registry[name].copy()
+        t_family = maps_def.pop("family")
+        space = maps_def.pop("space")
+
+        # Check and get highest resolution
+        if space != target_space:
+            logger.info(
+                f"Map(s) will be warped from {space} to {target_space} "
+                "using highest resolution"
+            )
+            resolution = None
+
+        # Check if the maps family is custom or built-in
+        if t_family == "CustomUserMaps":
+            maps_fname = maps_def["path"]
+            maps_labels = maps_def["labels"]
+        elif t_family in [
+            "Smith2009",
+        ]:
+            # Load maps and labels
+            if t_family == "Smith2009":
+                maps_fname, maps_labels = _retrieve_smith(
+                    resolution=resolution,
+                    **maps_def,
+                )
+        else:  # pragma: no cover
+            raise_error(f"Unknown map(s) family: {t_family}")
+
+        # Load maps image and values
+        logger.info(f"Loading map(s): {maps_fname.absolute()!s}")
+        maps_img = None
+        if not path_only:
+            # Load image via nibabel
+            maps_img = nib.load(maps_fname)
+            # Get regions
+            maps_regions = maps_img.get_fdata().shape[-1]
+            # Check for dimension
+            if maps_regions != len(maps_labels):
+                raise_error(
+                    f"Map(s) {name} has {maps_regions} "
+                    f"regions but {len(maps_labels)} labels."
+                )
+
+        return maps_img, maps_labels, maps_fname, space
+
+    def get(
+        self,
+        maps: str,
+        target_data: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple["Nifti1Image", list[str]]:
+        """Get map(s), tailored for the target image.
+
+        Parameters
+        ----------
+        maps : str
+            The name of the map(s).
+        target_data : dict
+            The corresponding item of the data object to which the map(s)
+            will be applied.
+        extra_input : dict, optional
+            The other fields in the data object. Useful for accessing other
+            data kinds that needs to be used in the computation of
+            map(s) (default None).
+
+        Returns
+        -------
+        Nifti1Image
+            The map(s) image.
+        list of str
+            Map(s) labels.
+
+        Raises
+        ------
+        ValueError
+            If ``extra_input`` is None when ``target_data``'s space is native.
+
+        """
+        # Check pre-requirements for space manipulation
+        target_space = target_data["space"]
+        logger.debug(f"Getting {maps} in {target_space} space.")
+        # Extra data type requirement check if target space is native
+        if target_space == "native":  # pragma: no cover
+            # Check for extra inputs
+            if extra_input is None:
+                raise_error(
+                    "No extra input provided, requires `Warp` and `T1w` "
+                    "data types in particular for transformation to "
+                    f"{target_data['space']} space for further computation."
+                )
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
+            # Set target standard space to warp file space source
+            target_std_space = warper_spec["src"]
+            logger.debug(
+                f"Target space is native. Will warp from {target_std_space}"
+            )
+        else:
+            # Set target standard space to target space
+            target_std_space = target_space
+
+        # Get the min of the voxels sizes and use it as the resolution
+        target_img = target_data["data"]
+        resolution = np.min(target_img.header.get_zooms()[:3])
+
+        # Load maps
+        logger.debug(f"Loading map(s) {maps}")
+        img, labels, _, space = self.load(
+            name=maps,
+            resolution=resolution,
+            target_space=target_space,
+        )
+
+        # Convert maps spaces if required;
+        # cannot be "native" due to earlier check
+        if space != target_std_space:
+            logger.debug(
+                f"Warping {maps} to {target_std_space} space using ANTs."
+            )
+            raw_img = ANTsMapsWarper().warp(
+                maps_name=maps,
+                maps_img=img,
+                src=space,
+                dst=target_std_space,
+                target_data=target_data,
+                warp_data=None,
+            )
+            # Remove extra dimension added by ANTs
+            img = nimg.math_img("np.squeeze(img)", img=raw_img)
+
+        if target_space != "native":
+            # No warping is going to happen, just resampling, because
+            # we are in the correct space
+            logger.debug(f"Resampling {maps} to target image.")
+            # Resample maps to target image
+            img = nimg.resample_to_img(
+                source_img=img,
+                target_img=target_img,
+                interpolation="continuous",
+                copy=True,
+            )
+        else:  # pragma: no cover
+            # Warp maps if target space is native as either
+            # the image is in the right non-native space or it's
+            # warped from one non-native space to another non-native space
+            logger.debug(
+                "Warping map(s) to native space using "
+                f"{warper_spec['warper']}."
+            )
+            # extra_input check done earlier and warper_spec exists
+            if warper_spec["warper"] == "fsl":
+                img = FSLMapsWarper().warp(
+                    maps_name="native",
+                    maps_img=img,
+                    target_data=target_data,
+                    warp_data=warper_spec,
+                )
+            elif warper_spec["warper"] == "ants":
+                img = ANTsMapsWarper().warp(
+                    maps_name="native",
+                    maps_img=img,
+                    src="",
+                    dst="native",
+                    target_data=target_data,
+                    warp_data=warper_spec,
+                )
+
+        return img, labels
+
+
+def _retrieve_smith(
+    resolution: Optional[float] = None,
+    components: Optional[str] = None,
+    dimension: Optional[int] = None,
+) -> tuple[Path, list[str]]:
+    """Retrieve Smith maps.
+
+    Parameters
+    ----------
+    resolution : 2.0, optional
+        The desired resolution of the maps to load. If it is not
+        available, the closest resolution will be loaded. Preferably, use a
+        resolution higher than the desired one. By default, will load the
+        highest one (default None). Available resolution for these
+        maps are 2mm.
+    components : {"rsn", "bm"}, optional
+        The components to load. "rsn" loads the resting-fMRI components and
+        "bm" loads the BrainMap components (default None).
+    dimension : {10, 20, 70}, optional
+        The number of dimensions to load (default None).
+
+    Returns
+    -------
+    pathlib.Path
+        File path to the maps image.
+    list of str
+        Maps labels.
+
+    Raises
+    ------
+    ValueError
+        If invalid value is provided for ``components`` or ``dimension``.
+
+    """
+    logger.info("Maps parameters:")
+    logger.info(f"\tresolution: {resolution}")
+    logger.info(f"\tcomponents: {components}")
+    logger.info(f"\tdimension: {dimension}")
+
+    # Check resolution
+    _valid_resolutions = [2.0]
+    resolution = closest_resolution(resolution, _valid_resolutions)
+
+    # Check components value
+    _valid_components = ["rsn", "bm"]
+    if components not in _valid_components:
+        raise_error(
+            f"The parameter `components` ({components}) needs to be one of "
+            f"the following: {_valid_components}"
+        )
+
+    # Check dimension value
+    _valid_dimension = [10, 20, 70]
+    if dimension not in _valid_dimension:
+        raise_error(
+            f"The parameter `dimension` ({dimension}) needs to be one of the "
+            f"following: {_valid_dimension}"
+        )
+
+    # Fetch file path
+    maps_img_path = get(
+        file_path=Path(
+            f"parcellations/Smith2009/{components}{dimension}.nii.gz"
+        ),
+        dataset_path=get_dataset_path(),
+        **JUNIFER_DATA_PARAMS,
+    )
+
+    return maps_img_path, [f"Map_{i}" for i in range(dimension)]

junifer/data/maps/tests/test_maps.py

@@ -0,0 +1,255 @@
+"""Provide tests for maps."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import pytest
+from numpy.testing import assert_array_equal
+
+from junifer.data import (
+    deregister_data,
+    get_data,
+    list_data,
+    load_data,
+    register_data,
+)
+from junifer.data.maps._maps import _retrieve_smith
+from junifer.datagrabber import PatternDataladDataGrabber
+from junifer.datareader import DefaultDataReader
+from junifer.pipeline.utils import _check_ants
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
+
+
+def test_register_built_in_check() -> None:
+    """Test maps registration check for built-in maps."""
+    with pytest.raises(ValueError, match=r"built-in"):
+        register_data(
+            kind="maps",
+            name="Smith_rsn_10",
+            maps_path="testmaps.nii.gz",
+            maps_labels=["1", "2"],
+            space="MNI",
+        )
+
+
+def test_list_incorrect() -> None:
+    """Test incorrect information check for list mapss."""
+    assert "testmaps" not in list_data(kind="maps")
+
+
+def test_register_overwrite() -> None:
+    """Test maps registration check for overwriting."""
+    register_data(
+        kind="maps",
+        name="testmaps",
+        maps_path="testmaps.nii.gz",
+        maps_labels=["1", "2"],
+        space="MNI152NLin6Sym",
+    )
+    with pytest.raises(ValueError, match=r"already registered"):
+        register_data(
+            kind="maps",
+            name="testmaps",
+            maps_path="testmaps.nii.gz",
+            maps_labels=["1", "2"],
+            space="MNI152NLin6Sym",
+            overwrite=False,
+        )
+
+    register_data(
+        kind="maps",
+        name="testmaps",
+        maps_path="testmaps.nii.gz",
+        maps_labels=["1", "2"],
+        space="MNI152NLin6Sym",
+        overwrite=True,
+    )
+
+    assert (
+        load_data(
+            kind="maps",
+            name="testmaps",
+            target_space="MNI152NLin6Sym",
+            path_only=True,
+        )[2].name
+        == "testmaps.nii.gz"
+    )
+
+
+def test_register_valid_input() -> None:
+    """Test maps registration check for valid input."""
+    maps, labels, maps_path, _ = load_data(
+        kind="maps",
+        name="Smith_rsn_10",
+        target_space="MNI152NLin6Asym",
+    )
+    assert maps is not None
+
+    # Test wrong number of labels
+    register_data(
+        kind="maps",
+        name="WrongLabels",
+        maps_path=maps_path,
+        maps_labels=labels[:5],
+        space="MNI152NLin6Asym",
+    )
+    with pytest.raises(ValueError, match=r"has 10 regions but 5"):
+        load_data(
+            kind="maps",
+            name="WrongLabels",
+            target_space="MNI152NLin6Asym",
+        )
+
+
+def test_list() -> None:
+    """Test listing of available coordinates."""
+    assert {"Smith_rsn_10", "Smith_bm_70"}.issubset(
+        set(list_data(kind="maps"))
+    )
+
+
+def test_load_nonexisting() -> None:
+    """Test loading maps that not exist."""
+    with pytest.raises(ValueError, match=r"not found"):
+        load_data(kind="maps", name="nomaps", target_space="MNI152NLin6Sym")
+
+
+def test_get() -> None:
+    """Test tailored maps fetch."""
+    with PatternDataladDataGrabber(
+        uri="https://github.com/OpenNeuroDatasets/ds005226.git",
+        types=["BOLD"],
+        patterns={
+            "BOLD": {
+                "pattern": (
+                    "derivatives/pre-processed_data/space-MNI/{subject}/"
+                    "{subject-padded}_task-{task}_run-{run}_space-MNI152NLin6Asym"
+                    "_res-2_desc-preproc_bold.nii.gz"
+                ),
+                "space": "MNI152NLin6Asym",
+            },
+        },
+        replacements=["subject", "subject-padded", "task", "run"],
+    ) as dg:
+        element = dg[("sub-01", "sub-001", "rest", "1")]
+        element_data = DefaultDataReader().fit_transform(element)
+        bold = element_data["BOLD"]
+        bold_img = bold["data"]
+        # Get tailored coordinates
+        tailored_maps, tailored_labels = get_data(
+            kind="maps", names="Smith_rsn_10", target_data=bold
+        )
+
+        # Check shape with original element data
+        assert tailored_maps.shape[:3] == bold_img.shape[:3]
+
+        # Get raw maps
+        raw_maps, raw_labels, _, _ = load_data(
+            kind="maps", name="Smith_rsn_10", target_space="MNI152NLin6Asym"
+        )
+        # Tailored and raw shape should be same
+        assert tailored_maps.shape[:3] == raw_maps.shape[:3]
+        assert tailored_labels == raw_labels
+
+
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+def test_get_different_space() -> None:
+    """Test tailored maps fetch in different space."""
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(element)
+        bold = element_data["BOLD"]
+        bold_img = bold["data"]
+        # Get tailored coordinates
+        tailored_maps, tailored_labels = get_data(
+            kind="maps", names="Smith_rsn_10", target_data=bold
+        )
+
+        # Check shape with original element data
+        assert tailored_maps.shape[:3] == bold_img.shape[:3]
+
+        # Get raw maps
+        raw_maps, raw_labels, _, _ = load_data(
+            kind="maps",
+            name="Smith_rsn_10",
+            target_space="MNI152NLin2009cAsym",
+        )
+        # Tailored and raw should not be same
+        assert tailored_maps.shape[:3] != raw_maps.shape[:3]
+        assert tailored_labels == raw_labels
+
+
+def test_deregister() -> None:
+    """Test maps deregistration."""
+    deregister_data(kind="maps", name="testmaps")
+    assert "testmaps" not in list_data(kind="maps")
+
+
+@pytest.mark.parametrize(
+    "resolution, components, dimension",
+    [
+        (2.0, "rsn", 10),
+        (2.0, "rsn", 20),
+        (2.0, "rsn", 70),
+        (2.0, "bm", 10),
+        (2.0, "bm", 20),
+        (2.0, "bm", 70),
+    ],
+)
+def test_smith(
+    resolution: float,
+    components: str,
+    dimension: int,
+) -> None:
+    """Test Smith maps.
+
+    Parameters
+    ----------
+    resolution : float
+        The parametrized resolution values.
+    components : str
+        The parametrized components values.
+    dimension : int
+        The parametrized dimension values.
+
+    """
+    maps = list_data(kind="maps")
+    maps_name = f"Smith_{components}_{dimension}"
+    assert maps_name in maps
+
+    maps_file = f"{components}{dimension}.nii.gz"
+    # Load maps
+    img, label, img_path, space = load_data(
+        kind="maps",
+        name=maps_name,
+        target_space="MNI152NLin6Asym",
+        resolution=resolution,
+    )
+    assert img is not None
+    assert img_path.name == maps_file
+    assert space == "MNI152NLin6Asym"
+    assert len(label) == dimension
+    assert_array_equal(
+        img.header["pixdim"][1:4],
+        3 * [2.0],
+    )
+
+
+def test_retrieve_smith_incorrect_components() -> None:
+    """Test retrieve Smith with incorrect components."""
+    with pytest.raises(ValueError, match="The parameter `components`"):
+        _retrieve_smith(
+            components="abc",
+            dimension=10,
+        )
+
+
+def test_retrieve_smith_incorrect_dimension() -> None:
+    """Test retrieve Smith with incorrect dimension."""
+    with pytest.raises(ValueError, match="The parameter `dimension`"):
+        _retrieve_smith(
+            components="rsn",
+            dimension=100,
+        )