siibra 0.5a2__py3-none-any.whl → 1.0.0a1__py3-none-any.whl

{siibra-0.5a2.dist-info → siibra-1.0.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: siibra
-Version: 0.5a2
+Version: 1.0.0a1
 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)
@@ -10,6 +10,8 @@ Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Operating System :: OS Independent
 Classifier: Intended Audience :: Developers
 Requires-Python: >=3.7
@@ -22,16 +24,17 @@ 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"
+Requires-Dist: ebrains-drive>=0.6.0
 
 |License| |PyPI version| |doi| |Python versions| |Documentation Status|
 
+==============================================================
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2020-2023, Forschungszentrum Jülich GmbH
+Copyright 2020-2024, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*
@@ -64,7 +67,7 @@ It aims to provide a safe way of using maps defined across multiple spatial scal
 .. getting-started-start
 
 Installation
-------------
+============
 
 ``siibra`` is available on pypi. 
 To install the latest released version, simply run ``pip install siibra``. 
@@ -80,27 +83,9 @@ There is also an image based on jupyter:scipy-notebook, which already includes `
         --name siibra \
         docker-registry.ebrains.eu/siibra/siibra-python:latest
 
-Access to EBRAINS
------------------
-
-While the core features in ``siibra`` can be accessed without any authentication, siibra can perform dynamic queries to regional datasets stored in the `EBRAINS Knowledge Graph <https://kg.ebrains.eu>`__. 
-To use this functionality, you need to obtain an EBRAINS authentication token with a valid EBRAINS user account.
-`Registering to EBRAINS <https://ebrains.eu/register/>`__ is easy and free of charge, so we strongly recommend to sign up.
-To use your EBRAINS access token in siibra:
-
-1. If you do not yet have an EBRAINS account, register `here <https://ebrains.eu/register>`__.
-2. When using siibra, fetch an authentication token by using `siibra.fetch_ebrains_token()`. You will be asked to visit an ebrains login website. Login, and accept the requested detail.
-
-Since tokens are temporary, step 2. needs to be repeated regularly.
-If you prefer, you can also create your token by visiting `the EBRAINS authorization endpoint <https://nexus-iam.humanbrainproject.org/v0/oauth2/authorize>`__.
-Copy the token, and either store it in the environment variable ``$HBP_AUTH_TOKEN`` or pass it explicitly to ``siibra`` using `siibra.set_ebrains_token()`.
-The token is a string sequence with more than 1000 characters, usually starting with with “ey”.
-
-Note that as of now, you need to to step 2 approximately every day to perform EBRAINS data queries.
-However, ``siibra`` maintains a local cache on disk, so once retrieved, data features become usable and accessible without refreshing the token.
 
 Documentation & Help
---------------------
+====================
 
 ``siibra-python``\ ’s documentation is hosted on https://siibra-python.readthedocs.io.
 The documentation includes a catalogue of documented code examples that walk you through the different concepts and functionalities.
@@ -117,9 +102,8 @@ While care is taken to make everything work reliably, the API of the library is
 
 .. contribute-start
 
-
 How to contribute
------------------
+=================
 
 If you want to contribute to ``siibra``, feel free to fork it and open a pull request with your changes.
 You are also welcome to contribute to discussions in the issue tracker and of course to report issues you are facing.
@@ -131,7 +115,7 @@ You can also star the project to show us that you are using it.
 .. acknowledgments-start
 
 Acknowledgements
-----------------
+================
 
 This software code is funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).
 
@@ -140,7 +124,7 @@ This software code is funded from the European Union’s Horizon 2020 Framework
 .. howtocite-start
 
 How to cite
------------
+===========
 Please cite the version used according to the citation file
 or all versions by
 `Timo Dickscheid, Xiayun Gui, Ahmet Nihat Simsek, Vadim Marcenko,
@@ -161,3 +145,16 @@ 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-1.0.0a1.dist-info/RECORD

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{siibra-0.5a2.dist-info → siibra-1.0.0a1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

siibra/locations/pointset.py

@@ -1,198 +0,0 @@
-# Copyright 2018-2021
-# 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 set of coordinates on a reference space."""
-
-from . import location, point, boundingbox
-
-from ..retrieval.requests import HttpRequest
-from ..commons import logger
-
-import numbers
-import json
-import numpy as np
-from nibabel import Nifti1Image
-from typing import Union
-
-
-class PointSet(location.Location):
-    """A set of 3D points in the same reference space,
-    defined by a list of coordinates."""
-
-    def __init__(self, coordinates, space=None, sigma_mm=0):
-        """
-        Construct a 3D point set in the given reference space.
-
-        Parameters
-        ----------
-        coordinates : list of Point, 3-tuples or string specs
-            Coordinates in mm of the given space
-        space : reference space (id, name, or Space object)
-            The reference space
-        sigma_mm : float, or list of float
-            Optional standard deviation of point locations.
-        """
-        location.Location.__init__(self, space)
-        if isinstance(sigma_mm, numbers.Number):
-            self.points = [point.Point(c, self.space, sigma_mm) for c in coordinates]
-        else:
-            self.points = [
-                point.Point(c, self.space, s) for c, s in zip(coordinates, sigma_mm)
-            ]
-
-    def intersection(self, other: Union[location.Location, Nifti1Image]):
-        """Return the subset of points that are inside the given mask.
-
-        NOTE: The affine matrix of the image must be set to warp voxels
-        coordinates into the reference space of this Bounding Box.
-        """
-        if isinstance(other, point.Point):
-            return self if other in self else None
-        elif isinstance(other, PointSet):
-            return [p for p in self if p in other]
-        elif isinstance(other, boundingbox.BoundingBox):
-            return [p for p in self if p.contained_in(other)]
-        inside = [p for p in self if p.intersects(other)]
-        if len(inside) == 0:
-            return None
-        elif len(inside) == 1:
-            return inside[0]
-        else:
-            return PointSet(
-                [p.coordinate for p in inside],
-                space=self.space,
-                sigma_mm=[p.sigma for p in inside],
-            )
-
-    def intersects(self, other: Union[location.Location, Nifti1Image]):
-        return len(self.intersection(other)) > 0
-
-    @property
-    def sigma(self):
-        return [p.sigma for p in self]
-
-    @property
-    def has_constant_sigma(self):
-        return len(set(self.sigma)) == 1
-
-    def warp(self, space, chunksize=1000):
-        """Creates a new point set by warping its points to another space"""
-        from ..core.space import Space
-        spaceobj = Space.get_instance(space)
-        if spaceobj == self.space:
-            return self
-        if any(_ not in location.Location.SPACEWARP_IDS for _ in [self.space.id, spaceobj.id]):
-            raise ValueError(
-                f"Cannot convert coordinates between {self.space.id} and {spaceobj.id}"
-            )
-
-        src_points = self.as_list()
-        tgt_points = []
-        N = len(src_points)
-        if N > 10e5:
-            logger.info(f"Warping {N} points from {self.space.name} to {spaceobj.name} space")
-        for i0 in range(0, N, chunksize):
-
-            i1 = min(i0 + chunksize, N)
-            data = json.dumps({
-                "source_space": location.Location.SPACEWARP_IDS[self.space.id],
-                "target_space": location.Location.SPACEWARP_IDS[spaceobj.id],
-                "source_points": src_points[i0:i1]
-            })
-            response = HttpRequest(
-                url=f"{location.Location.SPACEWARP_SERVER}/transform-points",
-                post=True,
-                headers={
-                    "accept": "application/json",
-                    "Content-Type": "application/json",
-                },
-                data=data,
-                func=lambda b: json.loads(b.decode()),
-            ).data
-            tgt_points.extend(list(response["target_points"]))
-
-        return self.__class__(coordinates=tuple(tgt_points), space=spaceobj)
-
-    def transform(self, affine: np.ndarray, space=None):
-        """Returns a new PointSet obtained by transforming the
-        coordinates of this one with the given affine matrix.
-
-        Parameters
-        ----------
-        affine : numpy 4x4 ndarray
-            affine matrix
-        space : reference space (id, name, or Space)
-            Target reference space which is reached after
-            applying the transform. Note that the consistency
-            of this cannot be checked and is up to the user.
-        """
-        return self.__class__(
-            [c.transform(affine, space) for c in self.points], space
-        )
-
-    def __getitem__(self, index: int):
-        if (index >= self.__len__()) or (index < 0):
-            raise IndexError(
-                f"Pointset has only {self.__len__()} points, "
-                f"but index of {index} was requested."
-            )
-        else:
-            return self.points[index]
-
-    def __iter__(self):
-        """Return an iterator over the coordinate locations."""
-        return iter(self.points)
-
-    def __len__(self):
-        """The number of points in this PointSet."""
-        return len(self.points)
-
-    def __str__(self):
-        return f"Set of {len(self)} points in the {self.boundingbox}"
-
-    @property
-    def boundingbox(self):
-        """
-        Return the bounding box of these points.
-        """
-        from .boundingbox import BoundingBox
-        XYZ = self.homogeneous[:, :3]
-        sigma_min = max(self.sigma[i] for i in XYZ.argmin(0))
-        sigma_max = max(self.sigma[i] for i in XYZ.argmax(0))
-        return BoundingBox(
-            point1=XYZ.min(0) - max(sigma_min, 1e-6),
-            point2=XYZ.max(0) + max(sigma_max, 1e-6),
-            space=self.space,
-            sigma_mm=[sigma_min, sigma_max]
-        )
-
-    @property
-    def centroid(self):
-        return point.Point(self.homogeneous[:, :3].mean(0), space=self.space)
-
-    @property
-    def volume(self):
-        if len(self) < 2:
-            return 0
-        else:
-            return self.boundingbox.volume
-
-    def as_list(self):
-        """Return the point set as a list of 3D tuples."""
-        return [tuple(p) for p in self]
-
-    @property
-    def homogeneous(self):
-        """Access the list of 3D point as an Nx4 array of homogeneous coorindates."""
-        return np.array([c.homogeneous for c in self.points]).reshape((-1, 4))

siibra-0.5a2.dist-info/RECORD

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