siibra 1.0a1__1-py3-none-any.whl

siibra/volumes/volume.py

@@ -0,0 +1,892 @@
+# Copyright 2018-2024
+# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""A specific mesh or 3D array."""
+
+from .providers import provider as _provider
+
+from .. import logger
+from ..retrieval import requests
+from ..core import space as _space, structure
+from ..locations import point, pointcloud, boundingbox
+from ..commons import resample_img_to_img, siibra_tqdm, affine_scaling, connected_components
+from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError, EmptyPointCloudError
+
+from dataclasses import dataclass
+from nibabel import Nifti1Image
+import numpy as np
+from typing import List, Dict, Union, Set, TYPE_CHECKING
+from time import sleep
+import json
+from skimage import feature as skimage_feature, filters
+from functools import lru_cache
+
+if TYPE_CHECKING:
+    from ..retrieval.datasets import EbrainsDataset
+    TypeDataset = EbrainsDataset
+
+
+@dataclass
+class ComponentSpatialProperties:
+    """
+    Centroid and nonzero volume of an image.
+    """
+    centroid: point.Point
+    volume: int
+
+    @staticmethod
+    def compute_from_image(
+        img: Nifti1Image,
+        space: Union[str, "_space.Space"],
+        split_components: bool = True
+
+    ) -> List["ComponentSpatialProperties"]:
+        """
+        Find the center of an image in its (non-zero) voxel space and and its
+        volume.
+
+        Parameters
+        ----------
+        img: Nifti1Image
+        space: str, Space
+        split_components: bool, default: True
+            If True, finds the spatial properties for each connected component
+            found by skimage.measure.label.
+        """
+        scale = affine_scaling(img.affine)
+        if split_components:
+            iter_components = lambda img: connected_components(
+                np.asanyarray(img.dataobj),
+                connectivity=None
+            )
+        else:
+            iter_components = lambda img: [(0, np.asanyarray(img.dataobj))]
+
+        spatial_props: List[ComponentSpatialProperties] = []
+        for _, component in iter_components(img):
+            nonzero: np.ndarray = np.c_[np.nonzero(component)]
+            spatial_props.append(
+                ComponentSpatialProperties(
+                    centroid=point.Point(
+                        np.dot(img.affine, np.r_[nonzero.mean(0), 1])[:3],
+                        space=space
+                    ),
+                    volume=nonzero.shape[0] * scale,
+                )
+            )
+
+        # sort by volume
+        spatial_props.sort(key=lambda cmp: cmp.volume, reverse=True)
+
+        return spatial_props
+
+
+class Volume(structure.BrainStructure):
+    """
+    A volume is a specific mesh or 3D array,
+    which can be accessible via multiple providers in different formats.
+    """
+
+    IMAGE_FORMATS = [
+        "nii",
+        "zip/nii",
+        "neuroglancer/precomputed"
+    ]
+
+    MESH_FORMATS = [
+        "neuroglancer/precompmesh",
+        "neuroglancer/precompmesh/surface",
+        "gii-mesh",
+        "gii-label",
+        "freesurfer-annot",
+        "zip/freesurfer-annot",
+    ]
+
+    SUPPORTED_FORMATS = IMAGE_FORMATS + MESH_FORMATS
+
+    _FORMAT_LOOKUP = {
+        "image": IMAGE_FORMATS,
+        "mesh": MESH_FORMATS,
+        "surface": MESH_FORMATS,
+        "nifti": ["nii", "zip/nii"],
+        "nii": ["nii", "zip/nii"]
+    }
+
+    _FETCH_CACHE = {}  # we keep a cache of the most recently fetched volumes
+    _FETCH_CACHE_MAX_ENTRIES = 3
+
+    def __init__(
+        self,
+        space_spec: dict,
+        providers: List['_provider.VolumeProvider'],
+        name: str = "",
+        variant: str = None,
+        datasets: List['TypeDataset'] = [],
+        bbox: "boundingbox.BoundingBox" = None
+    ):
+        self._name = name
+        self._space_spec = space_spec
+        self.variant = variant
+        self._providers: Dict[str, _provider.VolumeProvider] = {}
+        self.datasets = datasets
+        self._boundingbox = bbox
+        for provider in providers:
+            srctype = provider.srctype
+            assert srctype not in self._providers
+            self._providers[srctype] = provider
+        if len(self._providers) == 0:
+            logger.debug(f"No provider for volume {name}")
+
+    def __hash__(self):
+        return super().__hash__()
+
+    def __eq__(self, other: 'Volume'):
+        return (
+            isinstance(other, Volume)
+            and self.name == other.name
+            and self.space == other.space
+            and self.variant == other.variant
+            and self._providers == other._providers
+        )
+
+    @property
+    def name(self):
+        """Allows derived classes to implement a lazy name specification."""
+        return self._name
+
+    @property
+    def providers(self):
+        def concat(url: Union[str, Dict[str, str]], concat: str):
+            if isinstance(url, str):
+                return url + concat
+            return {key: url[key] + concat for key in url}
+        return {
+            srctype: concat(prov._url, f" {prov.label}" if hasattr(prov, "label") else "")
+            for srctype, prov in self._providers.items()
+        }
+
+    @lru_cache(2)
+    def get_boundingbox(self, clip: bool = True, background: float = 0.0, **fetch_kwargs) -> "boundingbox.BoundingBox":
+        """
+        Obtain the bounding box in physical coordinates of this volume.
+
+        Parameters
+        ----------
+        clip : bool, default: True
+            Whether to clip the background of the volume.
+        background : float, default: 0.0
+            The background value to clip.
+            Note
+            ----
+            To use it, clip must be True.
+        fetch_kwargs:
+            key word arguments that are used for fetchin volumes,
+            such as voi or resolution_mm. Currently, only possible for
+            Neuroglancer volumes except for `format`.
+
+        Raises
+        ------
+        RuntimeError
+            If the volume provider does not have a bounding box calculator.
+        """
+        if self._boundingbox is not None and len(fetch_kwargs) == 0:
+            return self._boundingbox
+
+        if not self.provides_image:
+            raise NotImplementedError("Bounding box calculation of meshes is not implemented yet.")
+
+        if clip:  # clippin requires fetching the image
+            img = self.fetch(**fetch_kwargs)
+            assert isinstance(img, Nifti1Image)
+            return boundingbox.from_array(
+                array=np.asanyarray(img.dataobj),
+                background=background,
+            ).transform(img.affine, space=self.space)
+
+        # if clipping is not required, providers migth have methods of creating
+        # bounding boxes without fetching the image
+        fmt = fetch_kwargs.get("format")
+        if (fmt is not None) and (fmt not in self.formats):
+            raise ValueError(
+                f"Requested format {fmt} is not available as provider of "
+                "this volume. See `volume.formats` for possible options."
+            )
+        providers = [self._providers[fmt]] if fmt else self._providers.values()
+        for provider in providers:
+            try:
+                assert clip is False
+                bbox = provider.get_boundingbox(
+                    background=background, **fetch_kwargs
+                )
+                if bbox.space is None:  # provider do not know the space!
+                    bbox._space_cached = self.space
+                    bbox.minpoint._space_cached = self.space
+                    bbox.maxpoint._space_cached = self.space
+            except NotImplementedError:
+                continue
+            return bbox
+        raise RuntimeError(f"No bounding box specified by any volume provider of {str(self)}")
+
+    @property
+    def formats(self) -> Set[str]:
+        return {fmt for fmt in self._providers}
+
+    @property
+    def provides_mesh(self):
+        return any(f in self.MESH_FORMATS for f in self.formats)
+
+    @property
+    def provides_image(self):
+        return any(f in self.IMAGE_FORMATS for f in self.formats)
+
+    @property
+    def fragments(self) -> Dict[str, List[str]]:
+        result = {}
+        for srctype, p in self._providers.items():
+            t = 'mesh' if srctype in self.MESH_FORMATS else 'image'
+            for fragment_name in p.fragments:
+                if t in result:
+                    result[t].append(fragment_name)
+                else:
+                    result[t] = [fragment_name]
+        return result
+
+    @property
+    def space(self):
+        for key in ["@id", "name"]:
+            if key in self._space_spec:
+                return _space.Space.get_instance(self._space_spec[key])
+        return _space.Space(None, "Unspecified space", species=_space.Species.UNSPECIFIED_SPECIES)
+
+    @property
+    def species(self):
+        s = self.space
+        return None if s is None else s.species
+
+    def __str__(self):
+        return (
+            f"{self.__class__.__name__} {f'{self.name}' if self.name else ''}"
+            f"{f' in space {self.space.name}' if self.space else ''}"
+        )
+
+    def __repr__(self):
+        return (
+            f"<{self.__class__.__name__}(space_spec={self._space_spec}, "
+            f"name='{self.name}', providers={self._providers})>"
+        )
+
+    def evaluate_points(
+        self,
+        points: Union['point.Point', 'pointcloud.PointCloud'],
+        outside_value: Union[int, float] = 0,
+        **fetch_kwargs
+    ) -> np.ndarray:
+        """
+        Evaluate the image at the positions of the given points.
+
+        Note
+        ----
+        Uses nearest neighbor interpolation. Other interpolation schemes are not
+        yet implemented.
+
+        Note
+        ----
+        If points are not on the same space as the map, they will be warped to
+        the space of the volume.
+
+        Parameters
+        ----------
+        points: PointCloud
+        outside_value: int, float. Default: 0
+        fetch_kwargs: dict
+            Any additional arguments are passed to the `fetch()` call for
+            retrieving the image data.
+
+        Returns
+        -------
+        values: numpy.ndarray
+            The values of the volume at the voxels points correspond to.
+
+        Raises
+        ------
+        SpaceWarpingFailedError
+            If warping of the points fails.
+        """
+        if not self.provides_image:
+            raise NotImplementedError("Filtering of points by pure mesh volumes not yet implemented.")
+
+        # make sure the points are in the same physical space as this volume
+        as_pointcloud = pointcloud.from_points([points]) if isinstance(points, point.Point) else points
+        warped = as_pointcloud.warp(self.space)
+        assert warped is not None, SpaceWarpingFailedError
+
+        # get the voxel array of this volume
+        img = self.fetch(format='image', **fetch_kwargs)
+        arr = np.asanyarray(img.dataobj)
+
+        # transform the points to the voxel space of the volume for extracting values
+        phys2vox = np.linalg.inv(img.affine)
+        voxels = warped.transform(phys2vox, space=None)
+        XYZ = voxels.coordinates.astype('int')
+
+        # temporarily set all outside voxels to (0,0,0) so that the index access doesn't fail
+        inside = np.all((XYZ < arr.shape) & (XYZ > 0), axis=1)
+        XYZ[~inside, :] = 0
+
+        # read out the values
+        X, Y, Z = XYZ.T
+        values = arr[X, Y, Z]
+
+        # fix the outside voxel values, which might have an inconsistent value now
+        values[~inside] = outside_value
+
+        return values
+
+    def _points_inside(
+        self,
+        points: Union['point.Point', 'pointcloud.PointCloud'],
+        keep_labels: bool = True,
+        outside_value: Union[int, float] = 0,
+        **fetch_kwargs
+    ) -> 'pointcloud.PointCloud':
+        """
+        Reduce a pointcloud to the points which fall inside nonzero pixels of
+        this map.
+
+
+        Paramaters
+        ----------
+        points: PointCloud
+        keep_labels: bool
+            If False, the returned PointCloud will be labeled with their indices
+            in the original PointCloud.
+        fetch_kwargs: dict
+            Any additional arguments are passed to the `fetch()` call for
+            retrieving the image data.
+
+        Returns
+        -------
+        PointCloud
+            A new PointCloud containing only the points inside the volume.
+            Labels reflect the indices of the original points if `keep_labels`
+            is False.
+        """
+        ptset = pointcloud.from_points([points]) if isinstance(points, point.Point) else points
+        values = self.evaluate_points(ptset, outside_value=outside_value, **fetch_kwargs)
+        inside = list(np.where(values != outside_value)[0])
+        return pointcloud.from_points(
+            [ptset[i] for i in inside],
+            newlabels=None if keep_labels else inside
+        )
+
+    def intersection(self, other: structure.BrainStructure, **fetch_kwargs) -> structure.BrainStructure:
+        """
+        Compute the intersection of a location with this volume. This will
+        fetch actual image data. Any additional arguments are passed to fetch.
+        """
+        if isinstance(other, (pointcloud.PointCloud, point.Point)):
+            try:
+                points_inside = self._points_inside(other, keep_labels=False, **fetch_kwargs)
+            except EmptyPointCloudError:
+                return None  # BrainStructure.intersects checks for not None
+            if isinstance(other, point.Point):  # preserve the type
+                return points_inside[0]
+            return points_inside
+        elif isinstance(other, boundingbox.BoundingBox):
+            return self.get_boundingbox(clip=True, background=0.0, **fetch_kwargs).intersection(other)
+        elif isinstance(other, Volume):
+            if self.space != other.space:
+                raise NotImplementedError("Cannot intersect volumes from different spaces. Try comparing their boudning boxes.")
+            format = fetch_kwargs.pop('format', 'image')
+            v1 = self.fetch(format=format, **fetch_kwargs)
+            v2 = other.fetch(format=format, **fetch_kwargs)
+            arr1 = np.asanyarray(v1.dataobj)
+            arr2 = np.asanyarray(resample_img_to_img(v2, v1).dataobj)
+            pointwise_min = np.minimum(arr1, arr2)
+            if np.any(pointwise_min):
+                return from_array(
+                    data=pointwise_min,
+                    affine=v1.affine,
+                    space=self.space,
+                    name=f"Intersection between {self} and {other} computed as their pointwise minimum"
+                )
+            else:
+                return None
+        else:  # other BrainStructures should have intersection with locations implemented.
+            try:
+                return other.intersection(self)
+            except NoMapAvailableError:
+                return None
+
+    def fetch(
+        self,
+        format: str = None,
+        **kwargs
+    ):
+        """
+        Fetch a volumetric or surface representation from one of the providers.
+
+        Parameters
+        ----------
+        format: str, default=None
+            Requested format. If `None`, the first supported format matching in
+            `self.formats` is tried, starting with volumetric formats.
+            It can be explicitly specified as:
+                - 'surface' or 'mesh' to fetch a surface format
+                - 'volumetric' or 'voxel' to fetch a volumetric format
+                - supported format types, see SUPPORTED_FORMATS. This includes
+                'nii', 'zip/nii', 'neuroglancer/precomputed', 'gii-mesh',
+                'neuroglancer/precompmesh', 'gii-label'
+
+        Returns
+        -------
+        An image (Nifti1Image) or mesh (Dict['verts': ndarray, 'faces': ndarray, 'labels': ndarray])
+        """
+        kwargs_serialized = json.dumps({k: hash(v) for k, v in kwargs.items()}, sort_keys=True)
+
+        if "resolution_mm" in kwargs and format is None:
+            if 'neuroglancer/precomputed' not in self.formats:
+                raise ValueError("'resolution_mm' is only available for volumes with 'neuroglancer/precomputed' formats.")
+            format = 'neuroglancer/precomputed'
+
+        if format is None:
+            # preseve fetch order in SUPPORTED_FORMATS
+            possible_formats = [f for f in self.SUPPORTED_FORMATS if f in self.formats]
+        elif format in self._FORMAT_LOOKUP:  # allow use of aliases
+            possible_formats = [f for f in self._FORMAT_LOOKUP[format] if f in self.formats]
+        elif format in self.SUPPORTED_FORMATS:
+            possible_formats = [format] if format in self.formats else []
+        else:
+            possible_formats = []
+        if len(possible_formats) == 0:
+            raise ValueError(
+                f"Invalid format requested: {format}. Possible values for this "
+                f"volume are: {self.formats}"
+            )
+
+        # ensure the voi is inside the template
+        voi = kwargs.get("voi", None)
+        if voi is not None and voi.space is not None:
+            assert isinstance(voi, boundingbox.BoundingBox)
+            tmplt_bbox = voi.space.get_template().get_boundingbox(clip=False)
+            intersection_bbox = voi.intersection(tmplt_bbox)
+            if intersection_bbox is None:
+                raise RuntimeError(f"voi provided ({voi}) lies out side the voxel space of the {voi.space.name} template.")
+            if intersection_bbox != voi:
+                logger.info(
+                    f"Since provided voi lies outside the template ({voi.space}) it is clipped as: {intersection_bbox}"
+                )
+                kwargs["voi"] = intersection_bbox
+
+        result = None
+        # try each possible format
+        for fmt in possible_formats:
+            fetch_hash = hash((hash(self), hash(fmt), hash(kwargs_serialized)))
+            # cached
+            if fetch_hash in self._FETCH_CACHE:
+                break
+            # Repeat in case of too many requests only
+            fwd_args = {k: v for k, v in kwargs.items() if k != "format"}
+            for try_count in range(6):
+                try:
+                    if fmt in ["gii-label", "freesurfer-annot", "zip/freesurfer-annot"]:
+                        tpl = self.space.get_template(variant=kwargs.get('variant'))
+                        mesh = tpl.fetch(**kwargs)
+                        labels = self._providers[fmt].fetch(**fwd_args)
+                        result = dict(**mesh, **labels)
+                    else:
+                        result = self._providers[fmt].fetch(**fwd_args)
+                except requests.SiibraHttpRequestError as e:
+                    if e.status_code == 429:  # too many requests
+                        sleep(0.1)
+                        logger.error(f"Cannot access {self._providers[fmt]}", exc_info=(try_count == 5))
+                        continue
+                    else:
+                        break
+                except Exception as e:
+                    logger.info(e, exc_info=1)
+                    break
+                else:
+                    break
+            # udpate the cache if fetch is successful
+            if result is not None:
+                self._FETCH_CACHE[fetch_hash] = result
+                while len(self._FETCH_CACHE) >= self._FETCH_CACHE_MAX_ENTRIES:
+                    # remove oldest entry
+                    self._FETCH_CACHE.pop(next(iter(self._FETCH_CACHE)))
+                break
+        else:
+            # unsuccessful: do not poison the cache if none fetched
+            logger.error(f"Could not fetch any formats from {possible_formats}.")
+            return None
+
+        return self._FETCH_CACHE[fetch_hash]
+
+    def fetch_connected_components(self, **fetch_kwargs):
+        """
+        Provide an generator over masks of connected components in the volume
+        """
+        img = self.fetch(**fetch_kwargs)
+        assert isinstance(img, Nifti1Image), NotImplementedError(
+            f"Connected components for type {type(img)} is not yet implemeneted."
+        )
+        for label, component in connected_components(np.asanyarray(img.dataobj)):
+            yield (
+                label,
+                Nifti1Image(component, img.affine)
+            )
+
+    def compute_spatial_props(self, split_components: bool = True, **fetch_kwargs) -> List[ComponentSpatialProperties]:
+        """
+        Find the center of this volume in its (non-zero) voxel space and and its
+        volume.
+
+        Parameters
+        ----------
+        split_components: bool, default: True
+            If True, finds the spatial properties for each connected component
+            found by skimage.measure.label.
+        """
+        assert self.provides_image, NotImplementedError("Spatial properties can currently on be calculated for images.")
+        img = self.fetch(format=fetch_kwargs.pop("format", "image"), **fetch_kwargs)
+        return ComponentSpatialProperties.compute_from_image(
+            img=img,
+            space=self.space,
+            split_components=split_components
+        )
+
+    def draw_samples(self, N: int, sample_size: int = 100, e: float = 1, sigma_mm=None, invert=False, **kwargs):
+        """
+        Draw samples from the volume, by interpreting its values as an
+        unnormalized empirical probability distribtution.
+        Any keyword arguments are passed over to fetch()
+        """
+        if not self.provides_image:
+            raise NotImplementedError(
+                "Drawing samples is so far only implemented for image-type volumes, "
+                f"not {self.__class__.__name__}."
+            )
+        img = self.fetch(**kwargs)
+        array = np.asanyarray(img.dataobj)
+        samples = []
+        P = (array - array.min()) / (array.max() - array.min())
+        if invert:
+            P = 1 - P
+        P = P**e
+        while True:
+            pts = (np.random.rand(sample_size, 3) * max(P.shape))
+            inside = np.all(pts < P.shape, axis=1)
+            Y, X, Z = np.split(pts[inside, :].astype('int'), 3, axis=1)
+            T = np.random.rand(1)
+            choice = np.where(P[Y, X, Z] >= T)[0]
+            samples.extend(list(pts[inside, :][choice, :]))
+            if len(samples) > N:
+                break
+        voxels = pointcloud.PointCloud(
+            np.random.permutation(samples)[:N, :],
+            space=None
+        )
+        result = voxels.transform(img.affine, space='mni152')
+        result.sigma_mm = [sigma_mm for _ in result]
+        return result
+
+    def find_peaks(self, mindist=5, sigma_mm=0, **kwargs):
+        """
+        Find local peaks in the volume.
+        Additional keyword arguments are passed over to fetch()
+        """
+        if not self.provides_image:
+            raise NotImplementedError(
+                "Finding peaks is so far only implemented for image-type volumes, "
+                f"not {self.__class__.__name__}."
+            )
+        img = self.fetch(**kwargs)
+        array = np.asanyarray(img.dataobj)
+        voxels = skimage_feature.peak_local_max(array, min_distance=mindist)
+        points = pointcloud.PointCloud(voxels, space=None, labels=list(range(len(voxels)))).transform(img.affine, space=self.space)
+        points.sigma_mm = [sigma_mm for _ in points]
+        return points
+
+
+class FilteredVolume(Volume):
+
+    def __init__(
+        self,
+        parent_volume: Volume,
+        label: int = None,
+        fragment: str = None,
+        threshold: float = None,
+    ):
+        """
+        A prescribed Volume to fetch specified label and fragment.
+        If threshold is defined, a mask of the values above the threshold.
+
+        Parameters
+        ----------
+        parent_volume : Volume
+        label : int, default: None
+            Get the mask of value equal to label.
+        fragment : str, default None
+            If a volume is fragmented, get a specified one.
+        threshold : float, default None
+            Provide a float value to threshold the image.
+        """
+        name = parent_volume.name
+        if label:
+            name += f" - label: {label}"
+        if fragment:
+            name += f" - fragment: {fragment}"
+        if threshold:
+            name += f" - threshold: {threshold}"
+        Volume.__init__(
+            self,
+            space_spec=parent_volume._space_spec,
+            providers=list(parent_volume._providers.values()),
+            name=name
+        )
+        self.fragment = fragment
+        self.label = label
+        self.threshold = threshold
+
+    def fetch(
+        self,
+        format: str = None,
+        **kwargs
+    ):
+        if "fragment" in kwargs:
+            assert kwargs.get("fragment") == self.fragment, f"This is a filtered volume that can only fetch fragment '{self.fragment}'."
+        else:
+            kwargs["fragment"] = self.fragment
+        if "label" in kwargs:
+            assert kwargs.get("label") == self.label, f"This is a filtered volume that can only fetch label '{self.label}' only."
+        else:
+            kwargs["label"] = self.label
+
+        result = super().fetch(format=format, **kwargs)
+
+        if self.threshold is not None:
+            assert self.label is None
+            if not isinstance(result, Nifti1Image):
+                raise NotImplementedError("Cannot threshold meshes.")
+            imgdata = np.asanyarray(result.dataobj)
+            return Nifti1Image(
+                dataobj=(imgdata > self.threshold).astype("uint8"),
+                affine=result.affine,
+                dtype="uint8"
+            )
+
+        return result
+
+    def get_boundingbox(
+        self,
+        clip: bool = True,
+        background: float = 0.0,
+        **fetch_kwargs
+    ) -> "boundingbox.BoundingBox":
+        # NOTE: since some providers enable different simpllified ways to create a
+        # bounding box without fetching the image, the correct kwargs must be
+        # forwarded since FilteredVolumes enforce their specs to be fetched.
+        return super().get_boundingbox(
+            clip=clip,
+            background=background,
+            **fetch_kwargs
+        )
+
+
+class Subvolume(Volume):
+    """
+    Wrapper class for exposing a z level of a 4D volume to be used like a 3D volume.
+    """
+
+    def __init__(self, parent_volume: Volume, z: int):
+        Volume.__init__(
+            self,
+            space_spec=parent_volume._space_spec,
+            providers=[
+                _provider.SubvolumeProvider(p, z=z)
+                for p in parent_volume._providers.values()
+            ],
+            name=parent_volume.name + f" - z: {z}"
+        )
+
+
+def from_file(filename: str, space: str, name: str) -> Volume:
+    """ Builds a nifti volume from a filename. """
+    from ..core.concept import get_registry
+    from .providers.nifti import NiftiProvider
+    spaceobj = get_registry("Space").get(space)
+    return Volume(
+        space_spec={"@id": spaceobj.id},
+        providers=[NiftiProvider(filename)],
+        name=filename if name is None else name,
+    )
+
+
+def from_nifti(nifti: Nifti1Image, space: str, name: str) -> Volume:
+    """Builds a nifti volume from a Nifti image."""
+    from ..core.concept import get_registry
+    from .providers.nifti import NiftiProvider
+    spaceobj = get_registry("Space").get(space)
+    return Volume(
+        space_spec={"@id": spaceobj.id},
+        providers=[NiftiProvider((np.asanyarray(nifti.dataobj), nifti.affine))],
+        name=name
+    )
+
+
+def from_array(
+    data: np.ndarray,
+    affine: np.ndarray,
+    space: Union[str, Dict[str, str]],
+    name: str
+) -> Volume:
+    """Builds a siibra volume from an array and an affine matrix."""
+    if len(name) == 0:
+        raise ValueError("Please provide a non-empty string for `name`")
+    from ..core.concept import get_registry
+    from .providers.nifti import NiftiProvider
+    spacespec = next(iter(space.values())) if isinstance(space, dict) else space
+    spaceobj = get_registry("Space").get(spacespec)
+    return Volume(
+        space_spec={"@id": spaceobj.id},
+        providers=[NiftiProvider((data, affine))],
+        name=name,
+    )
+
+
+def from_pointcloud(
+    points: pointcloud.PointCloud,
+    label: int = None,
+    target: Volume = None,
+    normalize=True,
+    **kwargs
+) -> Volume:
+    """
+    Get the kernel density estimate as a volume from the points using their
+    average uncertainty on target volume.
+
+    Parameters
+    ----------
+    points: pointcloud.PointCloud
+    label: int, default: None
+        If None, finds the KDE for all points. Otherwise, selects the points
+        labelled with this integer value.
+    target: Volume, default: None
+        If None, the template of the space points are defined on will be used.
+    normalize: bool, default: True
+
+    Raises
+    ------
+    RuntimeError
+        If no points with labels found
+    """
+    if target is None:
+        target = points.space.get_template()
+    targetimg = target.fetch(**kwargs)
+    voxels = points.transform(np.linalg.inv(targetimg.affine), space=None)
+
+    if (label is None) or (points.labels is None):
+        selection = [True for _ in points]
+    else:
+        assert label in points.labels, f"No points with the label {label} in the set: {set(points.labels)}"
+        selection = points.labels == label
+
+    voxelcount_img = np.zeros_like(targetimg.get_fdata())
+    unique_coords, counts = np.unique(
+        np.array(voxels.as_list(), dtype='int')[selection, :],
+        axis=0,
+        return_counts=True
+    )
+    voxelcount_img[tuple(unique_coords.T)] = counts
+
+    # TODO: consider how to handle pointclouds with varied sigma_mm
+    sigmas = np.array(points.sigma_mm)[selection]
+    bandwidth = np.mean(sigmas)
+    if len(np.unique(sigmas)) > 1:
+        logger.warning(f"KDE of pointcloud uses average bandwith {bandwidth} instead of the points' individual sigmas.")
+
+    filtered_arr = filters.gaussian(voxelcount_img, bandwidth)
+    if normalize:
+        filtered_arr /= filtered_arr.sum()
+
+    return from_array(
+        data=filtered_arr,
+        affine=targetimg.affine,
+        space=target.space,
+        name=f'KDE map of {points}{f"labelled {label}" if label else ""}'
+    )
+
+
+def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volume:
+    """
+    Merge a list of nifti volumes in the same space into a single volume.
+
+    Note
+    ----
+    In case of voxel conflicts, the volumes will be override the previous values
+    in the given order.
+
+    Parameters
+    ----------
+    volumes : List[Volume]
+    labels : List[int], optional
+        Supply new labels to replace exisiting values per volume.
+
+    Returns
+    -------
+    Volume
+    """
+    if len(volumes) == 1:
+        logger.debug("Only one volume supplied returning as is (kwargs are ignored).")
+        return volumes[0]
+
+    assert len(volumes) > 1, "Need to supply at least two volumes to merge."
+    if labels:
+        assert len(volumes) == len(labels), "Need to supply as many labels as volumes."
+
+    space = volumes[0].space
+    assert all(v.space == space for v in volumes), "Cannot merge volumes from different spaces."
+
+    if len(labels) > 0:
+        dtype = 'int32'
+    elif FilteredVolume in {type(v) for v in volumes}:
+        dtype = 'uint8'
+    else:
+        dtype = volumes[0].fetch().dataobj.dtype
+    template_img = space.get_template().fetch(**fetch_kwargs)
+    merged_array = np.zeros(template_img.shape, dtype=dtype)
+
+    for i, vol in siibra_tqdm(
+        enumerate(volumes),
+        unit=" volume",
+        desc=f"Resampling volumes to {space.name} and merging",
+        total=len(volumes),
+        disable=len(volumes) < 3
+    ):
+        img = vol.fetch(**fetch_kwargs)
+        resampled_arr = np.asanyarray(
+            resample_img_to_img(img, template_img).dataobj
+        )
+        nonzero_voxels = resampled_arr > 0
+        if labels:
+            merged_array[nonzero_voxels] = labels[i]
+        else:
+            merged_array[nonzero_voxels] = resampled_arr[nonzero_voxels]
+
+    return from_array(
+        data=merged_array,
+        affine=template_img.affine,
+        space=space,
+        name=f"Resampled and merged volumes: {','.join([v.name for v in volumes])}"
+    )