siibra 0.4a33__py3-none-any.whl → 0.4a46__py3-none-any.whl

siibra/features/fibres/__init__.py

@@ -1,14 +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.

siibra/features/functional/__init__.py

@@ -1,14 +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.

siibra/features/molecular/__init__.py

@@ -1,26 +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.
-
-from .receptor_density_profile import ReceptorDensityProfile
-from .receptor_density_fingerprint import ReceptorDensityFingerprint
-from .gene_expression import GeneExpressions
-
-
-def __dir__():
-    return [
-        "ReceptorDensityProfile",
-        "ReceptorDensityFingerprint",
-        "GeneExpressions",
-    ]

siibra/samplers/bigbrain.py

@@ -1,181 +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.
-
-
-from ..commons import logger
-from ..configuration.configuration import REGISTRY
-from ..locations import Point, PointSet
-
-from ctypes import ArgumentError
-import numpy as np
-from skimage import measure
-from nilearn import image
-from tqdm import tqdm
-
-
-class BigBrainCortexSampler:
-    """Sample layerwise grayvalue statistics from BigBrain cortex.
-
-    Given a coordinate in BigBrain space, the sampler centers a fixed-size box
-    near the given location in BigBrain cortex and extracts layerwise grayvalue
-    statistics. The center is found by identifying the closest point in Layer IV
-    which is inside a specified maximum distance (default 1mm) from the given point.
-    """
-
-    def __init__(self, boxwidth_mm=3, maxdist_mm=1):
-        """Create a new cortex sample for BigBrain.
-
-        Arguments
-        ---------
-        boxwidth_mm : float
-            Sidelength of the boxes used for grayvalue sampling (default: 3mm)
-        maxdist_mm : float
-            Maximum distance allowed to shift given sampling locations towards the
-            mid surface of the cortex. If the mid surface is not found within
-            this distance, no data will be sampled.
-        """
-
-        self.space = REGISTRY.Space["bigbrain"]
-        self._layermask = REGISTRY.Parcellation["layers"].get_map(self.space)
-        self._template = self.space.get_template()
-        self.boxwidth_mm = boxwidth_mm
-        self.maxdist_mm = maxdist_mm
-
-    def sample(self, location):
-        """
-        Given sample locations in BigBrain space, the sampler centers a fixed-size box
-        near the given location in BigBrain cortex and extracts layerwise grayvalue
-        statistics. The center is found by identifying the closest point in Layer IV
-        which is inside a specified maximum distance (default 1mm) from the given point.
-        If the location is not close enough to the cortical midsurface, the data sample
-        will be empty and a warning will be printed.
-
-        Parameters
-        ----------
-        location: Point, or PointSet
-            Candidate location(s) for sampling
-
-        Return
-        ------
-        List of dicts, one per sample point, with keys:
-            - 'center': the physical coordinate of the cube used as a region of interest
-            - 'boxsize': sidelenght in mm f the cube used as a region of interest
-            - 'space': name of the space (bigbrain)
-            - 'layers': Dict of layer-wise statistics with mean gray value, standard deviation, and volume in mm
-        """
-        if location.space != self.space:
-            logger.info(
-                f"Warping sample locations from {location.space.name} to {self.space.name}"
-            )
-            loc_bb = location.warp(self.space)
-        else:
-            loc_bb = location
-
-        result = []
-        if isinstance(loc_bb, Point):
-            result.append(self._sample_single_point(loc_bb))
-        elif isinstance(loc_bb, PointSet):
-            for p in tqdm(
-                loc_bb,
-                total=len(loc_bb),
-                unit="locations",
-                desc=f"Sampling from {len(loc_bb)} locations",
-                disable=logger.level > 20,
-            ):
-                result.append(self._sample_single_point(p))
-        else:
-            raise ArgumentError(
-                f"Invalid location specification {location.__class__.__name__} BigBrain sampling."
-            )
-
-        return result
-
-    def _sample_single_point(self, point):
-        """
-        Given a coordinate in BigBrain space, the sampler centers a fixed-size box
-        near the given location in BigBrain cortex and extracts layerwise grayvalue
-        statistics. The center is found by identifying the closest point in Layer IV
-        which is inside a specified maximum distance (default 1mm) from the given point.
-
-        Parameters
-        ----------
-        point: Point
-            Candidate location for sampling
-
-        Return
-        ------
-        dict with keys:
-            - 'center': the physical coordinate of the cube used as a region of interest
-            - 'boxsize': sidelenght in mm f the cube used as a region of interest
-            - 'space': name of the space (bigbrain)
-            - 'layers': Dict of layer-wise statistics with mean gray value, standard deviation, and number of voxels
-
-        """
-        result = {
-            "center": tuple(point),
-            "boxsize": self.boxwidth_mm,
-            "space": self.space.name,
-            "layers": {},
-        }
-
-        # find closest point in layer 4, i.e. towards the mid surface,
-        # to make sure the box is well centered in the cortex.
-        voi = point.get_enclosing_cube(2 * self.maxdist_mm + 1)
-        voimask = self._layermask.fetch(voi=voi, resolution_mm=-1)
-        L = np.asanyarray(voimask.dataobj)
-        XYZ_ = np.array(np.where(L == 4)).T
-        if XYZ_.shape[0] == 0:
-            logger.warn(
-                f"The point {tuple(point)} seems too far away from Layer IV in BigBrain. "
-                f"No data sampled."
-            )
-            return result
-        XYZ = np.dot(voimask.affine, np.c_[XYZ_, np.ones(XYZ_.shape[0])].T)[:3, :].T
-        D = np.sum(np.sqrt((XYZ - tuple(point)) ** 2), axis=1)
-        p_mid = Point(XYZ[np.argmin(D), :], self.space)
-
-        # Load cube of fixed size at this cortica position
-        # from BigBrain and cortical layer maps,
-        # using maximum available resolution.
-        voi = p_mid.get_enclosing_cube(self.boxwidth_mm)
-        voidata = self._template.fetch(voi=voi, resolution_mm=-1)
-        voimask = image.resample_to_img(
-            self._layermask.fetch(voi=voi, resolution_mm=-1),
-            voidata,
-            interpolation="nearest",
-        )
-
-        # Get layer mask with possible additional segmentation
-        # components at box borders suppressed (e.g. from neighboring
-        # sulcal walls)
-        L = np.asanyarray(voimask.dataobj)
-        M = measure.label(L > 0)
-        cx, cy, cz = np.array(M.shape) // 2
-        L[M != M[cx, cy, cz]] = 0
-
-        # extract layerwise grayvalues, excluding value 255
-        # which we assume to belong to background.
-        result["center"] = tuple(p_mid)
-        arr = np.asanyarray(voidata.dataobj)
-        for layer in range(1, 7):
-            mask = (L == layer) & (arr != 255)
-            values = arr[mask].ravel()
-            result["layers"][layer] = {
-                "mean": values.mean(),
-                "std": values.std(),
-                "num_voxels": np.count_nonzero(mask),
-            }
-
-        return result

siibra-0.4a33.dist-info/RECORD

@@ -1,71 +0,0 @@
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