From 4c2d8b5669dd8ff3053c6c8c350c62ba921a0e15 Mon Sep 17 00:00:00 2001 From: NiPreps Bot Date: Mon, 3 Jun 2024 13:25:31 +0000 Subject: [PATCH] docs(main): Update docs of development line --- main/.buildinfo | 2 +- main/_modules/eddymotion/cli/parser.html | 11 +- main/_modules/eddymotion/cli/run.html | 11 +- main/_modules/eddymotion/data/dmri.html | 11 +- main/_modules/eddymotion/data/pet.html | 11 +- main/_modules/eddymotion/data/splitting.html | 11 +- main/_modules/eddymotion/data/utils.html | 11 +- main/_modules/eddymotion/estimator.html | 11 +- main/_modules/eddymotion/math/utils.html | 60 ++- main/_modules/eddymotion/model/base.html | 11 +- .../eddymotion/model/gradient_utils.html | 407 +++++++++++++++++ main/_modules/eddymotion/utils.html | 11 +- main/_modules/eddymotion/viz.html | 11 +- main/_modules/index.html | 12 +- .../eddymotion.model.gradient_utils.rst.txt | 7 + main/_sources/api/eddymotion.model.rst.txt | 1 + main/_static/documentation_options.js | 2 +- main/api/eddymotion.cli.html | 11 +- main/api/eddymotion.cli.parser.html | 11 +- main/api/eddymotion.cli.run.html | 11 +- main/api/eddymotion.data.dmri.html | 11 +- main/api/eddymotion.data.html | 11 +- main/api/eddymotion.data.pet.html | 11 +- main/api/eddymotion.data.splitting.html | 11 +- main/api/eddymotion.data.utils.html | 11 +- main/api/eddymotion.estimator.html | 11 +- main/api/eddymotion.math.html | 11 +- main/api/eddymotion.math.utils.html | 54 ++- main/api/eddymotion.model.base.html | 17 +- main/api/eddymotion.model.gradient_utils.html | 429 ++++++++++++++++++ main/api/eddymotion.model.html | 13 +- main/api/eddymotion.utils.html | 17 +- main/api/eddymotion.viz.html | 11 +- main/changes.html | 11 +- main/developers.html | 16 +- main/genindex.html | 26 +- main/index.html | 11 +- main/installation.html | 11 +- main/links.html | 11 +- main/objects.inv | Bin 1267 -> 1328 bytes main/py-modindex.html | 17 +- main/running.html | 11 +- main/search.html | 11 +- main/searchindex.js | 2 +- main/usage.html | 11 +- 45 files changed, 1194 insertions(+), 196 deletions(-) create mode 100644 main/_modules/eddymotion/model/gradient_utils.html create mode 100644 main/_sources/api/eddymotion.model.gradient_utils.rst.txt create mode 100644 main/api/eddymotion.model.gradient_utils.html diff --git a/main/.buildinfo b/main/.buildinfo index 63afe964..fd91207a 100644 --- a/main/.buildinfo +++ b/main/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 31a67f783bff3be6c168503f149bf258 +config: c5e015a56464b1efc38a37a5557da250 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/main/_modules/eddymotion/cli/parser.html b/main/_modules/eddymotion/cli/parser.html index 93a6c974..27905de2 100644 --- a/main/_modules/eddymotion/cli/parser.html +++ b/main/_modules/eddymotion/cli/parser.html @@ -5,7 +5,7 @@ - eddymotion.cli.parser - eddymotion 24.0.0.dev24 documentation + eddymotion.cli.parser - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
+
diff --git a/main/_modules/eddymotion/cli/run.html b/main/_modules/eddymotion/cli/run.html index a25d7536..78348bef 100644 --- a/main/_modules/eddymotion/cli/run.html +++ b/main/_modules/eddymotion/cli/run.html @@ -5,7 +5,7 @@ - eddymotion.cli.run - eddymotion 24.0.0.dev24 documentation + eddymotion.cli.run - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
+
diff --git a/main/_modules/eddymotion/data/dmri.html b/main/_modules/eddymotion/data/dmri.html index 7b39635d..eadac88b 100644 --- a/main/_modules/eddymotion/data/dmri.html +++ b/main/_modules/eddymotion/data/dmri.html @@ -5,7 +5,7 @@ - eddymotion.data.dmri - eddymotion 24.0.0.dev24 documentation + eddymotion.data.dmri - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
+
diff --git a/main/_modules/eddymotion/data/pet.html b/main/_modules/eddymotion/data/pet.html index 1698498a..3e8f7e7f 100644 --- a/main/_modules/eddymotion/data/pet.html +++ b/main/_modules/eddymotion/data/pet.html @@ -5,7 +5,7 @@ - eddymotion.data.pet - eddymotion 24.0.0.dev24 documentation + eddymotion.data.pet - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
+
diff --git a/main/_modules/eddymotion/data/splitting.html b/main/_modules/eddymotion/data/splitting.html index 84987d61..ff8cd29a 100644 --- a/main/_modules/eddymotion/data/splitting.html +++ b/main/_modules/eddymotion/data/splitting.html @@ -5,7 +5,7 @@ - eddymotion.data.splitting - eddymotion 24.0.0.dev24 documentation + eddymotion.data.splitting - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
+
diff --git a/main/_modules/eddymotion/data/utils.html b/main/_modules/eddymotion/data/utils.html index 2438ea8a..dbe7a9df 100644 --- a/main/_modules/eddymotion/data/utils.html +++ b/main/_modules/eddymotion/data/utils.html @@ -5,7 +5,7 @@ - eddymotion.data.utils - eddymotion 24.0.0.dev24 documentation + eddymotion.data.utils - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
+
diff --git a/main/_modules/eddymotion/estimator.html b/main/_modules/eddymotion/estimator.html index a289d185..67beed14 100644 --- a/main/_modules/eddymotion/estimator.html +++ b/main/_modules/eddymotion/estimator.html @@ -5,7 +5,7 @@ - eddymotion.estimator - eddymotion 24.0.0.dev24 documentation + eddymotion.estimator - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
+
diff --git a/main/_modules/eddymotion/math/utils.html b/main/_modules/eddymotion/math/utils.html index 761e02bf..71a5632b 100644 --- a/main/_modules/eddymotion/math/utils.html +++ b/main/_modules/eddymotion/math/utils.html @@ -5,7 +5,7 @@ - eddymotion.math.utils - eddymotion 24.0.0.dev24 documentation + eddymotion.math.utils - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
-
eddymotion 24.0.0.dev24 documentation
 +
eddymotion 24.0.0.dev27 documentation
@@ -202,14 +202,14 @@
eddymotion - 24.0.0.dev24 + 24.0.0.dev27
  • - 24.0.0.dev24 + 24.0.0.dev27
      @@ -245,6 +245,7 @@
    • eddymotion.model package
    • eddymotion.utils module
      • @@ -320,7 +321,7 @@

      Source code for eddymotion.math.utils

           matrix and its conjugate transpose by performing the Cholesky decomposition.
     Parameters
     ----------
-    matrix : np.ndarray
+    matrix : :obj:`~numpy.ndarray`
         The matrix to check.
     Returns
     -------
@@ -335,6 +336,53 @@ 
      Source code for eddymotion.math.utils
               # Matrix is not positive definite
         return False
      
 
+
+
+
      
+[docs]
+def compute_angle(v1, v2, closest_polarity=False):
+    """Compute the angle between two vectors.
+
+    Parameters
+    ----------
+    v1 : :obj:`~numpy.ndarray`
+        First vector.
+    v2 : :obj:`~numpy.ndarray`
+        Second vector.
+    closest_polarity : :obj:`bool`
+        ``True`` to consider the smallest of the two angles between the crossing
+         lines resulting from reversing both vectors.
+
+    Returns
+    -------
+    :obj:`float`
+        The angle between the two vectors in radians.
+
+    Examples
+    --------
+    >>> compute_angle(
+    ...     np.array((1.0, 0.0, 0.0)),
+    ...     np.array((-1.0, 0.0, 0.0)),
+    ... )  # doctest: +ELLIPSIS
+    3.1415...
+    >>> compute_angle(
+    ...     np.array((1.0, 0.0, 0.0)),
+    ...     np.array((-1.0, 0.0, 0.0)),
+    ...     closest_polarity=True,
+    ... )
+    0.0
+
+    """
+
+    cosine_angle = (v1 / np.linalg.norm(v1)) @ (v2 / np.linalg.norm(v2))
+    # Clip values to handle numerical errors
+    cosine_angle = np.clip(
+        np.abs(cosine_angle) if closest_polarity else cosine_angle,
+        -1.0,
+        1.0,
+    )
+    return np.arccos(cosine_angle)
      
+
    @@ -367,7 +415,7 @@

    Source code for eddymotion.math.utils
    -
    +
    diff --git a/main/_modules/eddymotion/model/base.html b/main/_modules/eddymotion/model/base.html index edca1002..5d75c228 100644 --- a/main/_modules/eddymotion/model/base.html +++ b/main/_modules/eddymotion/model/base.html @@ -5,7 +5,7 @@ - eddymotion.model.base - eddymotion 24.0.0.dev24 documentation + eddymotion.model.base - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -202,14 +202,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    +
    diff --git a/main/_modules/eddymotion/model/gradient_utils.html b/main/_modules/eddymotion/model/gradient_utils.html new file mode 100644 index 00000000..2ab15873 --- /dev/null +++ b/main/_modules/eddymotion/model/gradient_utils.html @@ -0,0 +1,407 @@ + + + + + + + + eddymotion.model.gradient_utils - eddymotion 24.0.0.dev27 documentation + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + Auto light/dark, in light mode + + + + + + + + + + + + + + + Auto light/dark, in dark mode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    eddymotion 24.0.0.dev27 documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    +
    + +
    + +
    +
    +

    Source code for eddymotion.model.gradient_utils

    +# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <nipreps@gmail.com>
+#
+# 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.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+import numpy as np
+
+
+
    
+[docs]
+def compute_pairwise_angles(bvecs, closest_polarity):
+    r"""Compute pairwise angles across diffusion gradient encoding directions.
+
+    Following [Andersson15]_, it computes the smallest of the angles between
+    each pair if ``closest_polarity`` is ``True``, i.e.
+
+    .. math::
+
+        \theta(\mathbf{g}, \mathbf{g'}) = \arccos(\abs{\langle \mathbf{g}, \mathbf{g'} \rangle})
+
+    Parameters
+    ----------
+    bvecs : :obj:`~numpy.ndarray`
+        Diffusion gradient encoding directions in FSL format.
+    closest_polarity : :obj:`bool`
+        ``True`` to consider the smallest of the two angles between the crossing
+         lines resulting from reversing each vector pair.
+
+    Returns
+    -------
+    :obj:`~numpy.ndarray`
+        Pairwise angles across diffusion gradient encoding directions.
+
+    Examples
+    --------
+    >>> compute_pairwise_angles(
+    ...     ((1.0, -1.0), (0.0, 0.0), (0.0, 0.0)),
+    ...     False,
+    ... )[0, 1]  # doctest: +ELLIPSIS
+    3.1415...
+    >>> compute_pairwise_angles(
+    ...     ((1.0, -1.0), (0.0, 0.0), (0.0, 0.0)),
+    ...     True,
+    ... )[0, 1]
+    0.0
+
+    References
+    ----------
+    .. [Andersson15] J. L. R. Andersson. et al., An integrated approach to
+       correction for off-resonance effects and subject movement in diffusion MR
+       imaging, NeuroImage 125 (2016) 1063–1078
+    """
+
+    if np.shape(bvecs)[0] != 3:
+        raise ValueError(f"bvecs must be of shape (3, N). Found: {bvecs.shape}")
+
+    # Ensure b-vectors are unit-norm
+    bvecs = np.array(bvecs) / np.linalg.norm(bvecs, axis=0)
+    cosines = np.clip(bvecs.T @ bvecs, -1.0, 1.0)
+    return np.arccos(np.abs(cosines) if closest_polarity else cosines)
    
+
+
    +
    +
    +
    + +
    + + +
    +
    +
    +
    + Copyright © Copyright 2021, The eddymotion developers +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    + +
    +
    + +
    +
    + +
    +
    + + + + + + \ No newline at end of file diff --git a/main/_modules/eddymotion/utils.html b/main/_modules/eddymotion/utils.html index 80913ab8..d8f4bf20 100644 --- a/main/_modules/eddymotion/utils.html +++ b/main/_modules/eddymotion/utils.html @@ -5,7 +5,7 @@ - eddymotion.utils - eddymotion 24.0.0.dev24 documentation + eddymotion.utils - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -202,14 +202,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    +
    diff --git a/main/_modules/eddymotion/viz.html b/main/_modules/eddymotion/viz.html index 5067fd07..fc5a25b1 100644 --- a/main/_modules/eddymotion/viz.html +++ b/main/_modules/eddymotion/viz.html @@ -5,7 +5,7 @@ - eddymotion.viz - eddymotion 24.0.0.dev24 documentation + eddymotion.viz - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -202,14 +202,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    +
    diff --git a/main/_modules/index.html b/main/_modules/index.html index 5d5f882c..499e5daf 100644 --- a/main/_modules/index.html +++ b/main/_modules/index.html @@ -5,7 +5,7 @@ - Overview: module code - eddymotion 24.0.0.dev24 documentation + Overview: module code - eddymotion 24.0.0.dev27 documentation @@ -179,7 +179,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -202,14 +202,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    @@ -330,7 +332,7 @@

    All modules for which code is available

    -
    +
    diff --git a/main/_sources/api/eddymotion.model.gradient_utils.rst.txt b/main/_sources/api/eddymotion.model.gradient_utils.rst.txt new file mode 100644 index 00000000..81404045 --- /dev/null +++ b/main/_sources/api/eddymotion.model.gradient_utils.rst.txt @@ -0,0 +1,7 @@ +eddymotion.model.gradient\_utils module +======================================= + +.. automodule:: eddymotion.model.gradient_utils + :members: + :undoc-members: + :show-inheritance: diff --git a/main/_sources/api/eddymotion.model.rst.txt b/main/_sources/api/eddymotion.model.rst.txt index dbf767c9..d77b0782 100644 --- a/main/_sources/api/eddymotion.model.rst.txt +++ b/main/_sources/api/eddymotion.model.rst.txt @@ -13,3 +13,4 @@ Submodules :maxdepth: 1 eddymotion.model.base + eddymotion.model.gradient_utils diff --git a/main/_static/documentation_options.js b/main/_static/documentation_options.js index a8df0e62..bf3dbb6f 100644 --- a/main/_static/documentation_options.js +++ b/main/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '24.0.0.dev24', + VERSION: '24.0.0.dev27', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/main/api/eddymotion.cli.html b/main/api/eddymotion.cli.html index 66515e65..03cf54d3 100644 --- a/main/api/eddymotion.cli.html +++ b/main/api/eddymotion.cli.html @@ -6,7 +6,7 @@ - eddymotion.cli package - eddymotion 24.0.0.dev24 documentation + eddymotion.cli package - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    diff --git a/main/api/eddymotion.cli.parser.html b/main/api/eddymotion.cli.parser.html index 32e2b43b..2a2732c9 100644 --- a/main/api/eddymotion.cli.parser.html +++ b/main/api/eddymotion.cli.parser.html @@ -6,7 +6,7 @@ - eddymotion.cli.parser module - eddymotion 24.0.0.dev24 documentation + eddymotion.cli.parser module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    -
    +
    diff --git a/main/api/eddymotion.cli.run.html b/main/api/eddymotion.cli.run.html index afb1ab4e..b6cb7930 100644 --- a/main/api/eddymotion.cli.run.html +++ b/main/api/eddymotion.cli.run.html @@ -6,7 +6,7 @@ - eddymotion.cli.run module - eddymotion 24.0.0.dev24 documentation + eddymotion.cli.run module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    -
    +
    diff --git a/main/api/eddymotion.data.dmri.html b/main/api/eddymotion.data.dmri.html index f417e301..c488048b 100644 --- a/main/api/eddymotion.data.dmri.html +++ b/main/api/eddymotion.data.dmri.html @@ -6,7 +6,7 @@ - eddymotion.data.dmri module - eddymotion 24.0.0.dev24 documentation + eddymotion.data.dmri module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    -
    +
    diff --git a/main/api/eddymotion.data.html b/main/api/eddymotion.data.html index 296cd3b4..2acfd1ca 100644 --- a/main/api/eddymotion.data.html +++ b/main/api/eddymotion.data.html @@ -6,7 +6,7 @@ - eddymotion.data package - eddymotion 24.0.0.dev24 documentation + eddymotion.data package - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    diff --git a/main/api/eddymotion.data.pet.html b/main/api/eddymotion.data.pet.html index c3df30c7..f76793a9 100644 --- a/main/api/eddymotion.data.pet.html +++ b/main/api/eddymotion.data.pet.html @@ -6,7 +6,7 @@ - eddymotion.data.pet module - eddymotion 24.0.0.dev24 documentation + eddymotion.data.pet module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    -
    +
    diff --git a/main/api/eddymotion.data.splitting.html b/main/api/eddymotion.data.splitting.html index 12b72f64..6855802a 100644 --- a/main/api/eddymotion.data.splitting.html +++ b/main/api/eddymotion.data.splitting.html @@ -6,7 +6,7 @@ - eddymotion.data.splitting module - eddymotion 24.0.0.dev24 documentation + eddymotion.data.splitting module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    -
    +
    diff --git a/main/api/eddymotion.data.utils.html b/main/api/eddymotion.data.utils.html index 544341f2..20275fb0 100644 --- a/main/api/eddymotion.data.utils.html +++ b/main/api/eddymotion.data.utils.html @@ -6,7 +6,7 @@ - eddymotion.data.utils module - eddymotion 24.0.0.dev24 documentation + eddymotion.data.utils module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    -
    +
    diff --git a/main/api/eddymotion.estimator.html b/main/api/eddymotion.estimator.html index c71ca1be..3887d830 100644 --- a/main/api/eddymotion.estimator.html +++ b/main/api/eddymotion.estimator.html @@ -6,7 +6,7 @@ - eddymotion.estimator module - eddymotion 24.0.0.dev24 documentation + eddymotion.estimator module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    -
    +
    diff --git a/main/api/eddymotion.math.html b/main/api/eddymotion.math.html index 0d01ae0b..52245950 100644 --- a/main/api/eddymotion.math.html +++ b/main/api/eddymotion.math.html @@ -6,7 +6,7 @@ - eddymotion.math package - eddymotion 24.0.0.dev24 documentation + eddymotion.math package - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    diff --git a/main/api/eddymotion.math.utils.html b/main/api/eddymotion.math.utils.html index a5eb7d47..25ab5971 100644 --- a/main/api/eddymotion.math.utils.html +++ b/main/api/eddymotion.math.utils.html @@ -6,7 +6,7 @@ - eddymotion.math.utils module - eddymotion 24.0.0.dev24 documentation + eddymotion.math.utils module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
    -
    eddymotion 24.0.0.dev24 documentation
     +
    eddymotion 24.0.0.dev27 documentation
    @@ -203,14 +203,14 @@
    eddymotion - 24.0.0.dev24 + 24.0.0.dev27
    • - 24.0.0.dev24 + 24.0.0.dev27
        @@ -246,6 +246,7 @@
      • eddymotion.model package
      • eddymotion.utils module
        • @@ -295,13 +296,53 @@

        eddymotion.math.utils module

        +
        +
        +eddymotion.math.utils.compute_angle(v1, v2, closest_polarity=False)[source]
        +

        Compute the angle between two vectors.

        +
        +
        Parameters:
        +
          +

        • v1 (ndarray) – First vector.

          • +

        • v2 (ndarray) – Second vector.

          • +

        • closest_polarity (bool) –

          +
          +
          True to consider the smallest of the two angles between the crossing

          lines resulting from reversing both vectors.

          +
          +
          +
          • +
        +
        +
        Returns:
        +

        The angle between the two vectors in radians.

        +
        +
        Return type:
        +

        float

        +
        +
        +

        Examples

        +
        >>> compute_angle(
+...     np.array((1.0, 0.0, 0.0)),
+...     np.array((-1.0, 0.0, 0.0)),
+... )  
+3.1415...
+>>> compute_angle(
+...     np.array((1.0, 0.0, 0.0)),
+...     np.array((-1.0, 0.0, 0.0)),
+...     closest_polarity=True,
+... )
+0.0
+
        +
        +
        +
        eddymotion.math.utils.is_positive_definite(matrix)[source]

        Check whether the given matrix is positive definite. Any positive definite matrix can be decomposed as the product of a lower triangular matrix and its conjugate transpose by performing the Cholesky decomposition. -:Parameters: matrix (np.ndarray) – The matrix to check.

        +:Parameters: matrix (ndarray) – The matrix to check.

        Return type:

        True is the matrix is positive definite; False otherwise

        @@ -367,6 +408,7 @@
        -
      +
      diff --git a/main/api/eddymotion.model.base.html b/main/api/eddymotion.model.base.html index ba22fa6a..218e92bc 100644 --- a/main/api/eddymotion.model.base.html +++ b/main/api/eddymotion.model.base.html @@ -3,10 +3,10 @@ - + - eddymotion.model.base module - eddymotion 24.0.0.dev24 documentation + eddymotion.model.base module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      +
      diff --git a/main/api/eddymotion.model.gradient_utils.html b/main/api/eddymotion.model.gradient_utils.html new file mode 100644 index 00000000..3e1e248e --- /dev/null +++ b/main/api/eddymotion.model.gradient_utils.html @@ -0,0 +1,429 @@ + + + + + + + + + eddymotion.model.gradient_utils module - eddymotion 24.0.0.dev27 documentation + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + Auto light/dark, in light mode + + + + + + + + + + + + + + + Auto light/dark, in dark mode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      +
      + +
      +
      +
      eddymotion 24.0.0.dev27 documentation
       +
      +
      +
      + +
      + +
      +
      + +
      +
      +
      + + + + + Back to top + +
      +
      + + + + +
      +
      + +
      + +
      +
      +
      +

      eddymotion.model.gradient_utils module

      +
      +
      +eddymotion.model.gradient_utils.compute_pairwise_angles(bvecs, closest_polarity)[source]
      +

      Compute pairwise angles across diffusion gradient encoding directions.

      +

      Following [Andersson15], it computes the smallest of the angles between +each pair if closest_polarity is True, i.e.

      +
      +
      +\[\theta(\mathbf{g}, \mathbf{g'}) = \arccos(\abs{\langle \mathbf{g}, \mathbf{g'} \rangle})\]
      +
      +
      +
      Parameters:
      +
        +

      • bvecs (ndarray) – Diffusion gradient encoding directions in FSL format.

        • +

      • closest_polarity (bool) –

        +
        +
        True to consider the smallest of the two angles between the crossing

        lines resulting from reversing each vector pair.

        +
        +
        +
        • +
      +
      +
      Returns:
      +

      Pairwise angles across diffusion gradient encoding directions.

      +
      +
      Return type:
      +

      ndarray

      +
      +
      +

      Examples

      +
      >>> compute_pairwise_angles(
+...     ((1.0, -1.0), (0.0, 0.0), (0.0, 0.0)),
+...     False,
+... )[0, 1]  
+3.1415...
+>>> compute_pairwise_angles(
+...     ((1.0, -1.0), (0.0, 0.0), (0.0, 0.0)),
+...     True,
+... )[0, 1]
+0.0
+
      +
      +

      References

      +
      +
      +[Andersson15] +

      J. L. R. Andersson. et al., An integrated approach to +correction for off-resonance effects and subject movement in diffusion MR +imaging, NeuroImage 125 (2016) 1063–1078

      +
      +
      +
      + +
      + +
      +
      + +
      + +
      +
      + + + + + + + \ No newline at end of file diff --git a/main/api/eddymotion.model.html b/main/api/eddymotion.model.html index 6610e4f9..3596e9a8 100644 --- a/main/api/eddymotion.model.html +++ b/main/api/eddymotion.model.html @@ -6,7 +6,7 @@ - eddymotion.model package - eddymotion 24.0.0.dev24 documentation + eddymotion.model package - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      @@ -491,10 +493,11 @@

      Submodules +

      + \ No newline at end of file diff --git a/main/api/eddymotion.utils.html b/main/api/eddymotion.utils.html index cbf96c17..979fde6d 100644 --- a/main/api/eddymotion.utils.html +++ b/main/api/eddymotion.utils.html @@ -3,10 +3,10 @@ - + - eddymotion.utils module - eddymotion 24.0.0.dev24 documentation + eddymotion.utils module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
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      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      - +
      Previous
      -
      eddymotion.model.base module
      +
      eddymotion.model.gradient_utils module
       @@ -475,7 +476,7 @@
      -
      +
      diff --git a/main/api/eddymotion.viz.html b/main/api/eddymotion.viz.html index a9874538..392823d2 100644 --- a/main/api/eddymotion.viz.html +++ b/main/api/eddymotion.viz.html @@ -6,7 +6,7 @@ - eddymotion.viz module - eddymotion 24.0.0.dev24 documentation + eddymotion.viz module - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      -
      +
      diff --git a/main/changes.html b/main/changes.html index e369c51e..bad5d6e0 100644 --- a/main/changes.html +++ b/main/changes.html @@ -6,7 +6,7 @@ - What’s new? - eddymotion 24.0.0.dev24 documentation + What’s new? - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      diff --git a/main/developers.html b/main/developers.html index d867627a..a6f40e17 100644 --- a/main/developers.html +++ b/main/developers.html @@ -6,7 +6,7 @@ - For developers - eddymotion 24.0.0.dev24 documentation + For developers - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      diff --git a/main/genindex.html b/main/genindex.html index 5749643f..c39d4f89 100644 --- a/main/genindex.html +++ b/main/genindex.html @@ -4,7 +4,7 @@ - Index - eddymotion 24.0.0.dev24 documentation + Index - eddymotion 24.0.0.dev27 documentation @@ -178,7 +178,7 @@
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      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -201,14 +201,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      -
      +
      diff --git a/main/index.html b/main/index.html index 025b1596..bf3ca759 100644 --- a/main/index.html +++ b/main/index.html @@ -6,7 +6,7 @@ - eddymotion 24.0.0.dev24 documentation + eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      -
      +
      diff --git a/main/installation.html b/main/installation.html index bdaf6983..00b8e99d 100644 --- a/main/installation.html +++ b/main/installation.html @@ -6,7 +6,7 @@ - Installation - eddymotion 24.0.0.dev24 documentation + Installation - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
      -
      +
      diff --git a/main/links.html b/main/links.html index 604eddbc..d76df633 100644 --- a/main/links.html +++ b/main/links.html @@ -6,7 +6,7 @@ - <no title> - eddymotion 24.0.0.dev24 documentation + <no title> - eddymotion 24.0.0.dev27 documentation @@ -180,7 +180,7 @@
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       +
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      @@ -203,14 +203,14 @@
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      +
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      eddymotion 24.0.0.dev24 documentation
       +
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      @@ -201,14 +201,14 @@
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      +
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      -
      eddymotion 24.0.0.dev24 documentation
       +
      eddymotion 24.0.0.dev27 documentation
      @@ -203,14 +203,14 @@
      eddymotion - 24.0.0.dev24 + 24.0.0.dev27
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      +