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

siibra/experimental/cortical_profile_sampler.py

@@ -1,57 +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 . import contour
-from ..locations import point
-from ..core import parcellation
-
-import numpy as np
-
-
-class CorticalProfileSampler:
-    """Samples cortical profiles from the cortical layer maps."""
-
-    def __init__(self):
-        self.layermap = parcellation.Parcellation.get_instance(
-            "cortical layers"
-        ).get_map(space="bigbrain", maptype="labelled")
-
-    def query(self, query_point: point.Point):
-        q = query_point.warp(self.layermap.space)
-        smallest_dist = np.inf
-        best_match = None
-        for layername in self.layermap.regions:
-            vertices = self.layermap.fetch(region=layername, format="mesh")["verts"]
-            dists = np.sqrt(((vertices - q.coordinate) ** 2).sum(1))
-            best = np.argmin(dists)
-            if dists[best] < smallest_dist:
-                best_match = (layername, best)
-                smallest_dist = dists[best]
-
-        best_vertex = best_match[1]
-        hemisphere = "left" if "left" in best_match[0] else "right"
-        print(f"Best match is vertex #{best_match[1]} in {best_match[0]}.")
-
-        profile = [
-            (_, self.layermap.fetch(region=_, format="mesh")["verts"][best_vertex])
-            for _ in self.layermap.regions
-            if hemisphere in _
-        ]
-
-        return contour.Contour(
-            [p[1] for p in profile],
-            space=self.layermap.space,
-            labels=[p[0] for p in profile],
-        )

siibra/experimental/patch.py

@@ -1,98 +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 ..volumes import volume
-from ..locations import pointcloud, boundingbox
-from ..commons import translation_matrix, y_rotation_matrix
-
-import numpy as np
-import math
-from nilearn import image
-
-
-class Patch:
-
-    def __init__(self, corners: pointcloud.PointCloud):
-        """Construct a patch in physical coordinates.
-        As of now, only patches aligned in the y plane of the physical space
-        are supported."""
-        # TODO: need to ensure that the points are planar, if more than 3
-        assert len(corners) == 4
-        assert len(np.unique(corners.coordinates[:, 1])) == 1
-        self.corners = corners
-
-    @property
-    def space(self):
-        return self.corners.space
-
-    def flip(self):
-        """Flips the patch. """
-        self.corners._coordinates = self.corners.coordinates[[2, 3, 0, 1]]
-
-    def extract_volume(self, image_volume: volume.Volume, resolution_mm: float):
-        """
-        fetches image data in a planar patch.
-        TODO The current implementation only covers patches which are strictly
-        define in the y plane. A future implementation should accept arbitrary
-        oriented patches.accept arbitrary oriented patches.
-        """
-        assert image_volume.space == self.space
-
-        # Extend the 2D patch into a 3D structure
-        # this is only valid if the patch plane lies within the image canvas.
-        canvas = image_volume.get_boundingbox()
-        assert canvas.minpoint[1] <= self.corners.coordinates[0, 1]
-        assert canvas.maxpoint[1] >= self.corners.coordinates[0, 1]
-        XYZ = self.corners.coordinates
-        voi = boundingbox.BoundingBox(
-            XYZ.min(0)[:3], XYZ.max(0)[:3], space=image_volume.space
-        )
-        # enforce the patch to have the same y dimensions
-        voi.minpoint[1] = canvas.minpoint[1]
-        voi.maxpoint[1] = canvas.maxpoint[1]
-        patch = image_volume.fetch(voi=voi, resolution_mm=resolution_mm)
-        assert patch is not None
-
-        # patch rotation defined in physical space
-        vx, vy, vz = XYZ[1] - XYZ[0]
-        alpha = -math.atan2(-vz, -vx)
-        cx, cy, cz = XYZ.mean(0)
-        rot_phys = np.linalg.multi_dot(
-            [
-                translation_matrix(cx, cy, cz),
-                y_rotation_matrix(alpha),
-                translation_matrix(-cx, -cy, -cz),
-            ]
-        )
-
-        # rotate the patch in physical space
-        affine_rot = np.dot(rot_phys, patch.affine)
-
-        # crop in the rotated space
-        pixels = (
-            np.dot(np.linalg.inv(affine_rot), self.corners.homogeneous.T)
-            .astype("int")
-            .T
-        )
-        # keep a pixel distance to avoid black border pixels
-        xmin, ymin, zmin = pixels.min(0)[:3] + 1
-        xmax, ymax, zmax = pixels.max(0)[:3] - 1
-        h, w = xmax - xmin, zmax - zmin
-        affine = np.dot(affine_rot, translation_matrix(xmin, 0, zmin))
-        return volume.from_nifti(
-            image.resample_img(patch, target_affine=affine, target_shape=[h, 1, w]),
-            space=image_volume.space,
-            name=f"Rotated patch with corner points {self.corners} sampled from {image_volume.name}",
-        )

siibra-1.0.1a0.dist-info/RECORD

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