siibra 1.0.1a0__py3-none-any.whl → 1.0.1a2__py3-none-any.whl

siibra/volumes/providers/neuroglancer.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");
@@ -13,8 +13,20 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from . import provider as _provider
+from io import BytesIO
+import os
+from typing import Union, Dict, Tuple
+import json
+
+import numpy as np
+import nibabel as nib
+from neuroglancer_scripts.precomputed_io import get_IO_for_existing_dataset, PrecomputedIO
+from neuroglancer_scripts.http_accessor import HttpAccessor
+from neuroglancer_scripts.mesh import read_precomputed_mesh, affine_transform_mesh
 
+from . import provider as _provider
+from ...retrieval import requests, cache
+from ...locations import boundingbox as _boundingbox
 from ...commons import (
     logger,
     MapType,
@@ -23,18 +35,6 @@ from ...commons import (
     QUIET,
     resample_img_to_img
 )
-from ...retrieval import requests, cache
-from ...locations import boundingbox as _boundingbox
-
-from neuroglancer_scripts.precomputed_io import get_IO_for_existing_dataset, PrecomputedIO
-from neuroglancer_scripts.http_accessor import HttpAccessor
-from neuroglancer_scripts.mesh import read_precomputed_mesh, affine_transform_mesh
-from io import BytesIO
-import nibabel as nib
-import os
-import numpy as np
-from typing import Union, Dict, Tuple
-import json
 
 
 def shift_ng_transfrom(
@@ -52,7 +52,7 @@ def shift_ng_transfrom(
     Parameters
     ----------
     transform_nm: np.ndarray
-        Transform array created for dispalying an image correctly from
+        Transform array created for displaying an image correctly from
         neuroglancer precomputed format in neuroglancer viewer.
     max_resolution_nm: np.ndarray
         The voxel resolution of the highest level of resolution.
@@ -174,7 +174,7 @@ class NeuroglancerProvider(_provider.VolumeProvider, srctype="neuroglancer/preco
         Parameters
         ----------
         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.
         """
         bbox = None
@@ -422,7 +422,7 @@ class NeuroglancerScale:
         return self.res_nm / 1e6
 
     def resolves(self, resolution_mm):
-        """Test wether the resolution of this scale is sufficient to provide the given resolution."""
+        """Test whether the resolution of this scale is sufficient to provide the given resolution."""
         return all(r / 1e6 <= resolution_mm for r in self.res_nm)
 
     def __lt__(self, other):
@@ -529,14 +529,7 @@ class NeuroglancerScale:
         if voi is None:
             bbox_ = _boundingbox.BoundingBox((0, 0, 0), self.size, space=None)
         else:
-            bbox_ = voi.transform(np.linalg.inv(self.affine))
-
-        for dim in range(3):
-            if bbox_.shape[dim] < 1:
-                logger.warning(
-                    f"Bounding box in voxel space will be enlarged to by {self.res_mm[dim]} along axis {dim}."
-                )
-                bbox_.maxpoint[dim] = bbox_.maxpoint[dim] + self.res_mm[dim]
+            bbox_ = voi.transform(np.linalg.inv(self.affine), space=None)
 
         # extract minimum and maximum the chunk indices to be loaded
         gx0, gy0, gz0 = self._point_to_lower_chunk_idx(tuple(bbox_.minpoint))
@@ -559,8 +552,12 @@ class NeuroglancerScale:
         # exact bounding box requested, to cut off undesired borders
         data_min = np.array([gx0, gy0, gz0]) * self.chunk_sizes
         x0, y0, z0 = (np.array(bbox_.minpoint) - data_min).astype("int")
-        xd, yd, zd = np.ceil((np.array(bbox_.maxpoint))).astype(int) - np.floor((np.array(bbox_.minpoint))).astype(int)
+        xd, yd, zd = np.ceil(bbox_.maxpoint).astype(int) - np.floor(bbox_.minpoint).astype(int)
         offset = tuple(bbox_.minpoint)
+        if voi is not None:
+            logger.debug(
+                f"Input: {voi.minpoint.coordinate}, {voi.maxpoint.coordinate}.\nVoxel space: {bbox_.minpoint.coordinate}, {bbox_.maxpoint.coordinate}"
+            )
 
         # build the nifti image
         trans = np.identity(4)[[2, 1, 0, 3], :]  # zyx -> xyz
@@ -594,7 +591,7 @@ class NeuroglancerMesh(_provider.VolumeProvider, srctype="neuroglancer/precompme
         elif isinstance(resource, dict):
             self._meshes = {n: self._fragmentinfo(u) for n, u in resource.items()}
         else:
-            raise ValueError(f"Resource specificaton not understood for {self.__class__.__name__}: {resource}")
+            raise ValueError(f"Resource specification not understood for {self.__class__.__name__}: {resource}")
 
     @property
     def _url(self) -> Union[str, Dict[str, str]]:
@@ -635,7 +632,7 @@ class NeuroglancerMesh(_provider.VolumeProvider, srctype="neuroglancer/precompme
                 result[name] = (f"{spec['url']}/{mesh_key}/{fragment_names[0]}", transform)
             else:
                 # only one mesh was configures, so we might still
-                # see muliple fragments under the mesh url
+                # see multiple fragments under the mesh url
                 for fragment_name in fragment_names:
                     result[fragment_name] = (f"{spec['url']}/{mesh_key}/{fragment_name}", transform)
 

siibra/volumes/providers/nifti.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");
@@ -13,17 +13,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from . import provider as _provider
+import os
+from typing import Union, Dict, Tuple
+
+import numpy as np
+import nibabel as nib
 
+from . import provider as _provider
 from ...commons import logger, resample_img_to_img
 from ...retrieval import requests
 from ...locations import pointcloud, boundingbox as _boundingbox
 
-from typing import Union, Dict, Tuple
-import nibabel as nib
-import os
-import numpy as np
-
 
 class NiftiProvider(_provider.VolumeProvider, srctype="nii"):
 

siibra/volumes/providers/provider.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");
@@ -17,12 +17,13 @@ from __future__ import annotations
 
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING, Union, Dict, List
-from nibabel import Nifti1Image
 import json
+
+from nibabel import Nifti1Image
+
 if TYPE_CHECKING:
     from ...locations.boundingbox import BoundingBox
 
-# TODO add mesh primitive. Check nibabel implementation? Use trimesh? Do we want to add yet another dependency?
 VolumeData = Union[Nifti1Image, Dict]
 
 

siibra/volumes/sparsemap.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");
@@ -13,19 +13,20 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Represents lists of probabilistic brain region maps."""
-from . import parcellationmap, volume as _volume
 
+from os import path, makedirs
+from typing import Dict, List
+
+import numpy as np
+from nilearn import image
+
+from . import parcellationmap, volume as _volume
 from .providers import provider
 from ..commons import MapIndex, logger, connected_components, siibra_tqdm
 from ..locations import boundingbox
 from ..retrieval.cache import CACHE
 from ..retrieval.requests import HttpRequest, FileLoader
 
-from os import path, makedirs
-from typing import Dict, List
-from nilearn import image
-import numpy as np
-
 
 class SparseIndex:
 

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");
@@ -14,27 +14,26 @@
 # 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 dataclasses import dataclass
 from time import sleep
 import json
-from skimage import feature as skimage_feature, filters
 from functools import lru_cache
 
+import numpy as np
+from nibabel import Nifti1Image
+from skimage import feature as skimage_feature, filters
+
+from . import providers as _providers
+from ..commons import resample_img_to_img, siibra_tqdm, affine_scaling, connected_components, logger
+from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError, EmptyPointCloudError
+from ..retrieval import requests
+from ..core import space as _space, structure
+from ..core.concept import get_registry
+from ..locations import point, pointcloud, boundingbox
+
 if TYPE_CHECKING:
-    from ..retrieval.datasets import EbrainsDataset
-    TypeDataset = EbrainsDataset
+    from ..retrieval.datasets import EbrainsDataset as TypeDataset
 
 
 @dataclass
@@ -129,7 +128,7 @@ class Volume(structure.BrainStructure):
     def __init__(
         self,
         space_spec: dict,
-        providers: List['_provider.VolumeProvider'],
+        providers: List[_providers.provider.VolumeProvider],
         name: str = "",
         variant: str = None,
         datasets: List['TypeDataset'] = [],
@@ -138,7 +137,7 @@ class Volume(structure.BrainStructure):
         self._name = name
         self._space_spec = space_spec
         self.variant = variant
-        self._providers: Dict[str, _provider.VolumeProvider] = {}
+        self._providers: Dict[str, _providers.provider.VolumeProvider] = {}
         self.datasets = datasets
         self._boundingbox = bbox
         for provider in providers:
@@ -191,7 +190,7 @@ class Volume(structure.BrainStructure):
             ----
             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`.
 
@@ -206,7 +205,7 @@ class Volume(structure.BrainStructure):
         if not self.provides_image:
             raise NotImplementedError("Bounding box calculation of meshes is not implemented yet.")
 
-        if clip:  # clippin requires fetching the image
+        if clip:  # clipping requires fetching the image
             img = self.fetch(**fetch_kwargs)
             assert isinstance(img, Nifti1Image)
             return boundingbox.from_array(
@@ -214,7 +213,7 @@ class Volume(structure.BrainStructure):
                 background=background,
             ).transform(img.affine, space=self.space)
 
-        # if clipping is not required, providers migth have methods of creating
+        # 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):
@@ -365,7 +364,7 @@ class Volume(structure.BrainStructure):
         this map.
 
 
-        Paramaters
+        Parameters
         ----------
         points: PointCloud
         keep_labels: bool
@@ -407,7 +406,7 @@ class Volume(structure.BrainStructure):
             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)
@@ -461,7 +460,7 @@ class Volume(structure.BrainStructure):
             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]
@@ -519,7 +518,7 @@ class Volume(structure.BrainStructure):
                     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:
@@ -539,7 +538,7 @@ class Volume(structure.BrainStructure):
         """
         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 (
@@ -569,7 +568,7 @@ class Volume(structure.BrainStructure):
     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:
@@ -714,7 +713,7 @@ class Subvolume(Volume):
             self,
             space_spec=parent_volume._space_spec,
             providers=[
-                _provider.SubvolumeProvider(p, z=z)
+                _providers.provider.SubvolumeProvider(p, z=z)
                 for p in parent_volume._providers.values()
             ],
             name=parent_volume.name + f" - z: {z}"
@@ -722,25 +721,21 @@ class Subvolume(Volume):
 
 
 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
+    """Builds a nifti volume from a filename."""
     spaceobj = get_registry("Space").get(space)
     return Volume(
         space_spec={"@id": spaceobj.id},
-        providers=[NiftiProvider(filename)],
+        providers=[_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))],
+        providers=[_providers.NiftiProvider((np.asanyarray(nifti.dataobj), nifti.affine))],
         name=name
     )
 
@@ -754,13 +749,11 @@ def from_array(
     """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))],
+        providers=[_providers.NiftiProvider((data, affine))],
         name=name,
     )
 
@@ -814,7 +807,7 @@ def from_pointcloud(
     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.")
+        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:
@@ -841,7 +834,7 @@ 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
     -------

{siibra-1.0.1a0.dist-info → siibra-1.0.1a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: siibra
-Version: 1.0.1a0
+Version: 1.0.1a2
 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)
@@ -27,6 +27,15 @@ Requires-Dist: nilearn
 Requires-Dist: typing-extensions; python_version < "3.8"
 Requires-Dist: filelock
 Requires-Dist: ebrains-drive>=0.6.0
+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: ebrains-drive>=0.6.0
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2020-2024, Forschungszentrum Jülich GmbH
+Copyright 2018-2024, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*
@@ -50,6 +59,14 @@ It aims to facilitate programmatic and reproducible incorporation of brain parce
 It supports both discretely labelled and statistical (probabilistic) parcellation maps, which can be used to assign brain regions to spatial locations and image signals, to retrieve region-specific neuroscience datasets from multiple online repositories, and to sample information from high-resolution image data. 
 The datasets anchored to brain regions address features of molecular, cellular and architecture as well as connectivity, and are complemented with live queries to external repositories as well as dynamic extraction from "big" image volumes such as the 20 micrometer BigBrain model.
 
+``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
+By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
+It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
+
+.. intro-end
+
+.. about-start
+
 ``siibra`` was developed in the frame of the `Human Brain Project <https://humanbrainproject.eu>`__ for accessing the `EBRAINS
 human brain atlas <https://ebrains.eu/service/human-brain-atlas>`__. 
 It stores most of its contents as sustainable and open datasets in the `EBRAINS Knowledge Graph <https://kg.ebrains.eu>`__, and is designed to support the `OpenMINDS metadata standards <https://github.com/HumanBrainProject/openMINDS_SANDS>`__. 
@@ -58,11 +75,7 @@ In fact, the viewer is a good resource for exploring ``siibra``\ ’s core funct
 Feature queries in ``siibra`` are parameterized by data modality and anatomical location, while the latter could be a brain region, brain parcellation, or location in reference space. 
 Beyond the explorative focus of ``siibra-explorer``, the Python library supports a range of data analysis functions suitable for typical neuroscience workflows.
 
-``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
-By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
-It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
-
-.. intro-end
+.. about-end
 
 .. getting-started-start
 

siibra-1.0.1a2.dist-info/RECORD

@@ -0,0 +1,80 @@
+siibra/VERSION,sha256=tnNU724QbIsJd2y5y9A2yYp48XeoqEJ_sfDYRgMGdrg,14
+siibra/__init__.py,sha256=1uWhsE93KG4N9wiWoMdEokUXxfoRcyznXDktjAGhpEI,4496
+siibra/commons.py,sha256=i4qS4CPteESu2NlchZuLjJrc23PYc0_WMiPr7WMi9ro,27646
+siibra/exceptions.py,sha256=6MlXOadwXcCsceOE4lmy4fLJyAaBCCVvJF6BZlMYjU8,1371
+siibra/configuration/__init__.py,sha256=ArqQ_B8C_O61KA4Fk3ho8ksckbjLu-COOlPGiXyf8LE,752
+siibra/configuration/configuration.py,sha256=FhJ2MF925BeI3KHk8r68-1PnMzIqTfsZEM8ZpvbtqzQ,7263
+siibra/configuration/factory.py,sha256=WPOP0hugX47cTWMGsXo99B4RER14pGllJDUvcC3kMko,22628
+siibra/core/__init__.py,sha256=zW887SH2txImUfvU80k83NbxxnlHlbdzBjdryY-3-48,766
+siibra/core/assignment.py,sha256=7TL3cV2uU8XHatpOkrt5uMju04HfDtcgRR7HM3B1chU,3820
+siibra/core/atlas.py,sha256=Iwqgcf8sG8_iL4mlw_4Nzi7HWVR-wxYLESqnIS0CFTw,8549
+siibra/core/concept.py,sha256=rLqgJ72Mt1Mc8mlh-bGYOyq65rV7Vc8vCZGs-amJp1w,10891
+siibra/core/parcellation.py,sha256=JzrnoB8G0XupffP8mnwE3oHYmHjo2Mzn4-pXnZ2R6Ow,14480
+siibra/core/region.py,sha256=036Fjck1H6wGSubJomjEHUN1I-XMPSPqx3_78MEYbG8,44108
+siibra/core/space.py,sha256=X7FyKgdhao3ezSWQZ0MAjDxlQh305S-4a4D630RaM-c,4588
+siibra/core/structure.py,sha256=M2li4PPiJf27dOc3b2ycCfHf7Ad1AWxBYc9OpSFazJM,4498
+siibra/explorer/__init__.py,sha256=XBAeYm4W3HlbWsKtt8gOwqE_FinIEY7RdA6Rg4Y275A,781
+siibra/explorer/url.py,sha256=ja5i-VkEMYwqhlQ-K5tEfnlYTcgMpPFYJCK7IV0d3Us,7069
+siibra/explorer/util.py,sha256=ul82TQZAULdupr4tJBACdkjlHm2mt8LJ9UpwNWGHYhE,2083
+siibra/features/__init__.py,sha256=FER6DMnkPhXSV1XMZWibZdyBwVhIgWYSUGYMEYEKb9c,3970
+siibra/features/anchor.py,sha256=Umu_Ljkr656h7jvgp43Wi6thMFEycxz_Lf8Bj_QOTZA,9129
+siibra/features/feature.py,sha256=mpQ0M7sMYJEqOkx91rvaDlV_W5iRi_-z4S3eJLAZR8M,35283
+siibra/features/connectivity/__init__.py,sha256=FkPf0vyrLo3ERxrDbsRHUd7FUgJyajD87NiiXIiXhmY,1161
+siibra/features/connectivity/functional_connectivity.py,sha256=9lQoOXv8lZUnyMduAbWABwDIkQC0QTI8V23yx0NjOBg,2122
+siibra/features/connectivity/regional_connectivity.py,sha256=V401G_EOTIDVz3IJJR4d2xOxLiWmIb9qQAMFD46qPlM,18283
+siibra/features/connectivity/streamline_counts.py,sha256=JaAYf6-1S8NYhkE4lhshCSY__EQ5BFcL2i_XXdFfgrM,1064
+siibra/features/connectivity/streamline_lengths.py,sha256=QeuoW_ZDVa9dxCguaemj4Cq9CCPB8ur8_alhATto2-w,1067
+siibra/features/connectivity/tracing_connectivity.py,sha256=rkYgD8mOZzDp0STo5djhDqOaEdz-9j5EuLffXE0F01A,1083
+siibra/features/dataset/__init__.py,sha256=qRV_P0335b4LnSMiONRpSC4elGckp0FXmtJz_QQuVLA,748
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+siibra-1.0.1a2.dist-info/RECORD,,

{siibra-1.0.1a0.dist-info → siibra-1.0.1a2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

siibra/experimental/__init__.py

@@ -1,19 +0,0 @@
-# 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.
-
-from .plane3d import Plane3D
-from .contour import Contour
-from .cortical_profile_sampler import CorticalProfileSampler
-from .patch import Patch

siibra/experimental/contour.py

@@ -1,61 +0,0 @@
-# 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.
-
-from ..locations import point, pointcloud, boundingbox
-
-import numpy as np
-
-
-class Contour(pointcloud.PointCloud):
-    """
-    A PointCloud that represents a contour line.
-    The only difference is that the point order is relevant,
-    and consecutive points are thought as being connected by an edge.
-
-    In fact, PointCloud assumes order as well, but no connections between points.
-    """
-
-    def __init__(self, coordinates, space=None, sigma_mm=0, labels: list = None):
-        pointcloud.PointCloud.__init__(self, coordinates, space, sigma_mm, labels)
-
-    def crop(self, voi: boundingbox.BoundingBox):
-        """
-        Crop the contour with a volume of interest.
-        Since the contour might be split from the cropping,
-        returns a set of contour segments.
-        """
-        segments = []
-
-        # set the contour point labels to a linear numbering
-        # so we can use them after the intersection to detect splits.
-        old_labels = self.labels
-        self.labels = list(range(len(self)))
-        cropped = self.intersection(voi)
-
-        if cropped is not None and not isinstance(cropped, point.Point):
-            assert isinstance(cropped, pointcloud.PointCloud)
-            # Identifiy contour splits are by discontinuouities ("jumps")
-            # of their labels, which denote positions in the original contour
-            jumps = np.diff([self.labels.index(lb) for lb in cropped.labels])
-            splits = [0] + list(np.where(jumps > 1)[0] + 1) + [len(cropped)]
-            for i, j in zip(splits[:-1], splits[1:]):
-                segments.append(
-                    self.__class__(cropped.coordinates[i:j, :], space=cropped.space)
-                )
-
-        # reset labels of the input contour points.
-        self.labels = old_labels
-
-        return segments