siibra 1.0a19__py3-none-any.whl → 1.0.1a1__py3-none-any.whl

siibra/volumes/volume.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,9 +19,9 @@ from .providers import provider as _provider
 from .. import logger
 from ..retrieval import requests
 from ..core import space as _space, structure
-from ..locations import location, point, pointset, boundingbox
+from ..locations import point, pointcloud, boundingbox
 from ..commons import resample_img_to_img, siibra_tqdm, affine_scaling, connected_components
-from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError
+from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError, EmptyPointCloudError
 
 from dataclasses import dataclass
 from nibabel import Nifti1Image
@@ -92,7 +92,7 @@ class ComponentSpatialProperties:
         return spatial_props
 
 
-class Volume(location.Location):
+class Volume(structure.BrainStructure):
     """
     A volume is a specific mesh or 3D array,
     which can be accessible via multiple providers in different formats.
@@ -191,7 +191,7 @@ class Volume(location.Location):
             ----
             To use it, clip must be True.
         fetch_kwargs:
-            key word arguments that are used for fetchin volumes,
+            key word arguments that are used for fetching volumes,
             such as voi or resolution_mm. Currently, only possible for
             Neuroglancer volumes except for `format`.
 
@@ -203,6 +203,19 @@ class Volume(location.Location):
         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:  # clipping 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 might 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(
@@ -212,15 +225,15 @@ class Volume(location.Location):
         providers = [self._providers[fmt]] if fmt else self._providers.values()
         for provider in providers:
             try:
+                assert clip is False
                 bbox = provider.get_boundingbox(
-                    clip=clip, background=background, **fetch_kwargs
+                    background=background, **fetch_kwargs
                 )
-                if bbox.space is None:  # provider does usually not know the space!
+                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 as e:
-                logger.info(e)
+            except NotImplementedError:
                 continue
             return bbox
         raise RuntimeError(f"No bounding box specified by any volume provider of {str(self)}")
@@ -275,7 +288,7 @@ class Volume(location.Location):
 
     def evaluate_points(
         self,
-        points: Union['point.Point', 'pointset.PointSet'],
+        points: Union['point.Point', 'pointcloud.PointCloud'],
         outside_value: Union[int, float] = 0,
         **fetch_kwargs
     ) -> np.ndarray:
@@ -294,7 +307,7 @@ class Volume(location.Location):
 
         Parameters
         ----------
-        points: PointSet
+        points: PointCloud
         outside_value: int, float. Default: 0
         fetch_kwargs: dict
             Any additional arguments are passed to the `fetch()` call for
@@ -314,8 +327,8 @@ class Volume(location.Location):
             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_pointset = pointset.from_points([points]) if isinstance(points, point.Point) else points
-        warped = as_pointset.warp(self.space)
+        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
@@ -342,57 +355,50 @@ class Volume(location.Location):
 
     def _points_inside(
         self,
-        points: Union['point.Point', 'pointset.PointSet'],
+        points: Union['point.Point', 'pointcloud.PointCloud'],
         keep_labels: bool = True,
         outside_value: Union[int, float] = 0,
         **fetch_kwargs
-    ) -> 'pointset.PointSet':
+    ) -> 'pointcloud.PointCloud':
         """
-        Reduce a pointset to the points which fall inside nonzero pixels of
+        Reduce a pointcloud to the points which fall inside nonzero pixels of
         this map.
 
 
-        Paramaters
+        Parameters
         ----------
-        points: PointSet
+        points: PointCloud
         keep_labels: bool
-            If False, the returned PointSet will be labeled with their indices
-            in the original PointSet.
+            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
         -------
-        PointSet
-            A new PointSet containing only the points inside the volume.
+        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 = pointset.from_points([points]) if isinstance(points, point.Point) else points
+        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 pointset.from_points(
+        return pointcloud.from_points(
             [ptset[i] for i in inside],
             newlabels=None if keep_labels else inside
         )
 
-    def union(self, other: location.Location):
-        if isinstance(other, Volume):
-            return merge([self, other])
-        else:
-            raise NotImplementedError(
-                f"There are no union method for {(self.__class__.__name__, other.__class__.__name__)}"
-            )
-
     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, (pointset.PointSet, point.Point)):
-            points_inside = self._points_inside(other, keep_labels=False, **fetch_kwargs)
-            if len(points_inside) == 0:
+        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]
@@ -401,7 +407,7 @@ class Volume(location.Location):
             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.")
+                raise NotImplementedError("Cannot intersect volumes from different spaces. Try comparing their bounding boxes.")
             format = fetch_kwargs.pop('format', 'image')
             v1 = self.fetch(format=format, **fetch_kwargs)
             v2 = other.fetch(format=format, **fetch_kwargs)
@@ -423,15 +429,6 @@ class Volume(location.Location):
             except NoMapAvailableError:
                 return None
 
-    def transform(self, affine: np.ndarray, space=None):
-        raise NotImplementedError("Volume transformation is not yet implemented.")
-
-    def warp(self, space):
-        if self.space.matches(space):
-            return self
-        else:
-            raise SpaceWarpingFailedError('Warping of full volumes is not yet supported.')
-
     def fetch(
         self,
         format: str = None,
@@ -464,7 +461,7 @@ class Volume(location.Location):
             format = 'neuroglancer/precomputed'
 
         if format is None:
-            # preseve fetch order in SUPPORTED_FORMATS
+            # preserve 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]
@@ -522,7 +519,7 @@ class Volume(location.Location):
                     break
                 else:
                     break
-            # udpate the cache if fetch is successful
+            # update 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:
@@ -542,7 +539,7 @@ class Volume(location.Location):
         """
         img = self.fetch(**fetch_kwargs)
         assert isinstance(img, Nifti1Image), NotImplementedError(
-            f"Connected components for type {type(img)} is not yet implemeneted."
+            f"Connected components for type {type(img)} is not yet implemented."
         )
         for label, component in connected_components(np.asanyarray(img.dataobj)):
             yield (
@@ -562,7 +559,7 @@ class Volume(location.Location):
             found by skimage.measure.label.
         """
         assert self.provides_image, NotImplementedError("Spatial properties can currently on be calculated for images.")
-        img = self.fetch(format="image", **fetch_kwargs)
+        img = self.fetch(format=fetch_kwargs.pop("format", "image"), **fetch_kwargs)
         return ComponentSpatialProperties.compute_from_image(
             img=img,
             space=self.space,
@@ -572,7 +569,7 @@ class Volume(location.Location):
     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.
+        unnormalized empirical probability distributions.
         Any keyword arguments are passed over to fetch()
         """
         if not self.provides_image:
@@ -596,7 +593,7 @@ class Volume(location.Location):
             samples.extend(list(pts[inside, :][choice, :]))
             if len(samples) > N:
                 break
-        voxels = pointset.PointSet(
+        voxels = pointcloud.PointCloud(
             np.random.permutation(samples)[:N, :],
             space=None
         )
@@ -617,11 +614,96 @@ class Volume(location.Location):
         img = self.fetch(**kwargs)
         array = np.asanyarray(img.dataobj)
         voxels = skimage_feature.peak_local_max(array, min_distance=mindist)
-        points = pointset.PointSet(voxels, space=None, labels=list(range(len(voxels)))).transform(img.affine, space=self.space)
+        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.
@@ -634,7 +716,8 @@ class Subvolume(Volume):
             providers=[
                 _provider.SubvolumeProvider(p, z=z)
                 for p in parent_volume._providers.values()
-            ]
+            ],
+            name=parent_volume.name + f" - z: {z}"
         )
 
 
@@ -682,8 +765,8 @@ def from_array(
     )
 
 
-def from_pointset(
-    points: pointset.PointSet,
+def from_pointcloud(
+    points: pointcloud.PointCloud,
     label: int = None,
     target: Volume = None,
     normalize=True,
@@ -695,7 +778,7 @@ def from_pointset(
 
     Parameters
     ----------
-    points: pointset.PointSet
+    points: pointcloud.PointCloud
     label: int, default: None
         If None, finds the KDE for all points. Otherwise, selects the points
         labelled with this integer value.
@@ -727,11 +810,11 @@ def from_pointset(
     )
     voxelcount_img[tuple(unique_coords.T)] = counts
 
-    # TODO: consider how to handle pointsets with varied sigma_mm
+    # 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 pointset uses average bandwith {bandwidth} instead of the points' individual sigmas.")
+        logger.warning(f"KDE of pointcloud uses average bandwidth {bandwidth} instead of the points' individual sigmas.")
 
     filtered_arr = filters.gaussian(voxelcount_img, bandwidth)
     if normalize:
@@ -747,7 +830,7 @@ def from_pointset(
 
 def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volume:
     """
-    Merge a list of volumes in the same space into a single volume.
+    Merge a list of nifti volumes in the same space into a single volume.
 
     Note
     ----
@@ -758,7 +841,7 @@ def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volu
     ----------
     volumes : List[Volume]
     labels : List[int], optional
-        Supply new labels to replace exisiting values per volume.
+        Supply new labels to replace existing values per volume.
 
     Returns
     -------
@@ -775,8 +858,14 @@ def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volu
     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='uint8')
+    merged_array = np.zeros(template_img.shape, dtype=dtype)
 
     for i, vol in siibra_tqdm(
         enumerate(volumes),

{siibra-1.0a19.dist-info → siibra-1.0.1a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: siibra
-Version: 1.0a19
+Version: 1.0.1a1
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)
@@ -24,9 +24,18 @@ Requires-Dist: scikit-image
 Requires-Dist: requests
 Requires-Dist: neuroglancer-scripts
 Requires-Dist: nilearn
+Requires-Dist: typing-extensions; python_version < "3.8"
 Requires-Dist: filelock
 Requires-Dist: ebrains-drive>=0.6.0
-Requires-Dist: typing-extensions; python_version < "3.8"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 |License| |PyPI version| |doi| |Python versions| |Documentation Status|
 
@@ -34,7 +43,7 @@ Requires-Dist: typing-extensions; python_version < "3.8"
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2020-2023, Forschungszentrum Jülich GmbH
+Copyright 2018-2024, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*
@@ -145,3 +154,16 @@ https://doi.org/10.5281/zenodo.7885728`.
    :target: https://siibra-python.readthedocs.io/en/latest/?badge=latest
 .. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7885728.svg
    :target: https://doi.org/10.5281/zenodo.7885728
+
+
+Versioning
+==========
+Given a version number MAJOR.MINOR.PATCH, increments imply:
+   - MAJOR: incompatible API changes
+   - MINOR: a functionality in a backward compatible manner is added
+   - PATCH: backward compatible bug fixes and new configuration added such as new maps or features
+
+Pre-release
+-----------
+For x.y.z, a full release,
+- `x.y.z-alpha.t` is the development prerelease. By changing `t`, different siibra-configurations are targeted.

siibra-1.0.1a1.dist-info/RECORD

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