From 1bc999b1e42e8b93a7219acee91e109d5181d497 Mon Sep 17 00:00:00 2001 From: NiPreps Bot Date: Sat, 26 Oct 2024 06:02:34 +0000 Subject: [PATCH] docs(main): Update docs of development line --- main/.buildinfo | 2 +- main/_modules/eddymotion/cli/parser.html | 10 +- main/_modules/eddymotion/cli/run.html | 10 +- main/_modules/eddymotion/data/dmri.html | 10 +- main/_modules/eddymotion/data/filtering.html | 10 +- main/_modules/eddymotion/data/pet.html | 10 +- main/_modules/eddymotion/data/splitting.html | 10 +- main/_modules/eddymotion/data/utils.html | 10 +- main/_modules/eddymotion/estimator.html | 10 +- main/_modules/eddymotion/exceptions.html | 10 +- main/_modules/eddymotion/math/utils.html | 10 +- main/_modules/eddymotion/model/base.html | 10 +- main/_modules/eddymotion/model/dmri.html | 10 +- main/_modules/eddymotion/model/pet.html | 10 +- .../eddymotion/registration/ants.html | 10 +- .../eddymotion/registration/utils.html | 10 +- .../eddymotion/testing/simulations.html | 174 +++++++++++++++--- main/_modules/eddymotion/utils.html | 10 +- main/_modules/eddymotion/viz/signals.html | 140 +++++++++++++- main/_modules/index.html | 10 +- main/_static/documentation_options.js | 2 +- main/api/eddymotion.cli.html | 10 +- main/api/eddymotion.cli.parser.html | 10 +- main/api/eddymotion.cli.run.html | 10 +- main/api/eddymotion.data.dmri.html | 10 +- main/api/eddymotion.data.filtering.html | 10 +- main/api/eddymotion.data.html | 10 +- main/api/eddymotion.data.pet.html | 10 +- main/api/eddymotion.data.splitting.html | 10 +- main/api/eddymotion.data.utils.html | 10 +- main/api/eddymotion.estimator.html | 10 +- main/api/eddymotion.exceptions.html | 10 +- main/api/eddymotion.math.html | 10 +- main/api/eddymotion.math.utils.html | 10 +- main/api/eddymotion.model.base.html | 10 +- main/api/eddymotion.model.dmri.html | 10 +- main/api/eddymotion.model.html | 10 +- main/api/eddymotion.model.pet.html | 10 +- main/api/eddymotion.registration.ants.html | 10 +- main/api/eddymotion.registration.html | 10 +- main/api/eddymotion.registration.utils.html | 10 +- main/api/eddymotion.testing.html | 10 +- main/api/eddymotion.testing.simulations.html | 94 +++++++++- main/api/eddymotion.utils.html | 10 +- main/api/eddymotion.viz.html | 10 +- main/api/eddymotion.viz.signals.html | 50 ++++- main/changes.html | 10 +- main/developers.html | 22 ++- main/genindex.html | 34 +++- main/index.html | 10 +- main/installation.html | 10 +- main/links.html | 10 +- main/objects.inv | Bin 1979 -> 2096 bytes main/py-modindex.html | 10 +- main/running.html | 10 +- main/search.html | 10 +- main/searchindex.js | 2 +- main/usage.html | 10 +- 58 files changed, 703 insertions(+), 297 deletions(-) diff --git a/main/.buildinfo b/main/.buildinfo index 76c05bd4..a53e2add 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: a9d5bb8b7344824bc99eb24bf53514dd +config: af59bfa37d421aa6ed9c063d5322469f tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/main/_modules/eddymotion/cli/parser.html b/main/_modules/eddymotion/cli/parser.html index b1dffdb9..f4e91cda 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.dev181 documentation + eddymotion.cli.parser - eddymotion 24.0.0.dev185 documentation @@ -166,7 +166,7 @@
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                      diff --git a/main/_modules/eddymotion/model/base.html b/main/_modules/eddymotion/model/base.html index 91b344a4..ea39e71e 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.dev181 documentation + eddymotion.model.base - eddymotion 24.0.0.dev185 documentation @@ -166,7 +166,7 @@
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                                    Source code for eddymotion.testing.simulations

                                    from __future__ import annotations -# import nibabel as nib +import nibabel as nib import numpy as np from dipy.core.geometry import sphere2cart from dipy.core.gradients import gradient_table from dipy.core.sphere import HemiSphere, Sphere, disperse_charges from dipy.sims.voxel import all_tensor_evecs, single_tensor +# Bounds defined following Canales-Rodriguez, NIMG 184 2019, https://doi.org/10.1016/j.neuroimage.2018.08.071 +BOUNDS_LAMBDA1: tuple[float, float] = (1.4e-3, 1.8e-3) +BOUNDS_LAMBDA23: tuple[float, float] = (0.1e-3, 0.5e-3) +

                                    [docs] @@ -509,38 +513,166 @@

                                    Source code for eddymotion.testing.simulations

                                    [docs] -def single_fiber_voxel(gtab, S0, evals, theta=0, phi=0, snr=20): +def single_fiber_voxel(gtab, S0, evals, rng, theta=0, phi=0, snr=20): # create eigenvectors for a single fiber evecs = create_single_fiber_evecs(theta=theta, phi=phi) # Generate some data - return single_tensor(gtab, S0=S0, evals=evals, evecs=evecs, snr=snr)

                                    + return single_tensor(gtab, S0=S0, evals=evals, evecs=evecs, snr=snr, rng=rng)
                                    -
                                    -[docs] -def simulate_voxels(S0, evals, hsph_dirs, bval_shell=1000, snr=20, n_voxels=1, seed=None): - # Create a gradient table for a single-shell - gtab = create_single_shell_gradient_table(hsph_dirs, bval_shell) +
                                    +[docs] +def create_random_polar_angles(size, rng): + """Create polar angles drawn from a uniform distribution.""" + + return zip( + rng.uniform(0, np.pi, size=size), + rng.uniform(0, 2.0 * np.pi, size=size), + strict=True, + )
                                    + + + +
                                    +[docs] +def create_random_diffusivity_eigenvalues(size, rng): + r"""Create DTI model diffusion tensor eigenvalues ($\lambda_{1}, + \lambda_{2}, \lambda_{3}$) drawn from a uniform distribution.""" + + # lambda_2 = lambda_3 following Canales-Rodriguez, NIMG 184 2019, + # https://doi.org/10.1016/j.neuroimage.2018.08.071 + return zip( + rng.uniform(*BOUNDS_LAMBDA1, size=size), + *[rng.uniform(*BOUNDS_LAMBDA23, size=size)] * 2, + strict=True, + )
                                    + + + +
                                    +[docs] +def group_values(values, group_size): + return np.asarray([values[i : i + group_size] for i in range(0, len(values), group_size)])
                                    - rng = np.random.default_rng(seed) - angles = zip( - rng.uniform(0, np.pi, size=n_voxels), - rng.uniform(0, 2.0 * np.pi, size=n_voxels), - strict=False, - ) + +
                                    +[docs] +def simulate_one_fiber_multivoxel(gtab, S0, snr, n_voxels, rng, evals=None): + """Create a single-fiber multi-voxel DWI signal.""" + + angles = create_random_polar_angles(n_voxels, rng) + if evals is None: + _evals = create_random_diffusivity_eigenvalues(n_voxels, rng) + else: + _evals = group_values(evals, 3) + if _evals.shape[0] == 1 and n_voxels != 1: + _evals = np.repeat(_evals, n_voxels, axis=0) signal = np.vstack( [ - single_fiber_voxel(gtab, S0, evals, theta=theta, phi=phi, snr=snr) - for theta, phi in angles + single_fiber_voxel(gtab, S0, _eignvls, rng, theta=theta, phi=phi, snr=snr) + for (theta, phi), _eignvls in zip(angles, _evals, strict=True) ] ) + return signal
                                    + + + +
                                    +[docs] +def simulate_voxels(S0, hsph_dirs, bval_shell=1000, snr=20, n_voxels=1, evals=None, seed=None): + # Create a gradient table for a single-shell + gtab = create_single_shell_gradient_table(hsph_dirs, bval_shell) + + rng = np.random.default_rng(seed) + + signal = simulate_one_fiber_multivoxel(gtab, S0, snr, n_voxels, rng, evals=evals) + return signal, gtab
                                    + + +
                                    +[docs] +def serialize_dwi(dwi_data, dwi_data_fname, affine: np.ndarray | None = None): + """Serialize DWI data. + + Parameters + ---------- + dwi_data : :obj:`~numpy.ndarray` + DWI data. + dwi_data_fname : :obj:`str` + Filename of NIfTI file to save the DWI signal. + affine : :obj:`~numpy.ndarray`, optional + Affine matrix. If ``None`` an identity affine matrix is used. + """ + + if affine is None: + affine = np.eye(4) + + dwi_img = nib.Nifti1Image(dwi_data, affine=affine) + nib.save(dwi_img, dwi_data_fname)
                                    + + + +
                                    +[docs] +def serialize_gtab(gtab, bval_data_fname, bvec_data_fname): + """Serialize dMRI gradient-encoding table data into a pair of b-vals and + b-vecs files. + + Parameters + ---------- + gtab : :obj:`~dipy.core.gradients.gradient_table` + Gradient table. + bval_data_fname : :obj:`str` + Filename of NIfTI file to save the diffusion-encoding gradient b-vals. + bvec_data_fname : :obj:`str` + Filename of NIfTI file to save the diffusion-encoding gradient b-vecs. + """ + + fmt = "%d" + np.savetxt(bval_data_fname, gtab.bvals, newline=" ", fmt=fmt) + fmt = "%.3f" + np.savetxt(bvec_data_fname, gtab.bvecs.T, fmt=fmt)
                                    + + + +
                                    +[docs] +def serialize_dmri( + dwi_data, + gtab, + dwi_data_fname, + bval_data_fname, + bvec_data_fname, + affine: np.ndarray | None = None, +): + """Serialize dMRI data. + + Parameters + ---------- + dwi_data : :obj:`~numpy.ndarray` + DWI data. + gtab : :obj:`~dipy.core.gradients.gradient_table` + Gradient table. + dwi_data_fname : :obj:`str` + Filename of NIfTI file to save the DWI signal. + bval_data_fname : :obj:`str` + Filename of NIfTI file to save the diffusion-encoding gradient b-vals. + bvec_data_fname : :obj:`str` + Filename of NIfTI file to save the diffusion-encoding gradient b-vecs. + affine : :obj:`~numpy.ndarray`, optional + Affine matrix. If ``None`` an identity affine matrix is used. + """ + + serialize_dwi(dwi_data, dwi_data_fname, affine=affine) + serialize_gtab(gtab, bval_data_fname, bvec_data_fname)
                                    +
                                    @@ -573,7 +705,7 @@

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                                  eddymotion 24.0.0.dev181 documentation
                                   +
                                  eddymotion 24.0.0.dev185 documentation
                                  @@ -189,14 +189,14 @@
                                  eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                  • - 24.0.0.dev181 + 24.0.0.dev185
                                      @@ -506,7 +506,7 @@

                                      Source code for eddymotion.utils
                                      -
                                    +
                                    diff --git a/main/_modules/eddymotion/viz/signals.html b/main/_modules/eddymotion/viz/signals.html index 8e14f021..30b258a7 100644 --- a/main/_modules/eddymotion/viz/signals.html +++ b/main/_modules/eddymotion/viz/signals.html @@ -5,7 +5,7 @@ - eddymotion.viz.signals - eddymotion 24.0.0.dev181 documentation + eddymotion.viz.signals - eddymotion 24.0.0.dev185 documentation @@ -166,7 +166,7 @@
                                    -
                                    eddymotion 24.0.0.dev181 documentation
                                     +
                                    eddymotion 24.0.0.dev185 documentation
                                    @@ -189,14 +189,14 @@
                                    eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                    • - 24.0.0.dev181 + 24.0.0.dev185
                                        @@ -317,13 +317,21 @@

                                        Source code for eddymotion.viz.signals

                                         import matplotlib.gridspec as gridspec
 import numpy as np
 from matplotlib import pyplot as plt
+from scipy.spatial import ConvexHull, KDTree
 from scipy.stats import pearsonr
 
 
 
                                        
 [docs]
 def plot_error(
-    kfolds: list[int], mean: np.ndarray, std_dev: np.ndarray, xlabel: str, ylabel: str, title: str
+    kfolds: list[int],
+    mean: np.ndarray,
+    std_dev: np.ndarray,
+    xlabel: str,
+    ylabel: str,
+    title: str,
+    color: str = "orange",
+    figsize: tuple[int, int] = (19.2, 10.8),
 ) -> plt.Figure:
     """
     Plot the error and standard deviation.
@@ -342,6 +350,10 @@ 
                                        Source code for eddymotion.viz.signals
                                                 Y-axis label.
     title : :obj:`str`
         Plot title.
+    color : :obj:`str`, optional
+        Plot color.
+    figsize : :obj:`tuple`, optional
+        Figure size.
 
     Returns
     -------
@@ -349,10 +361,10 @@ 
                                        Source code for eddymotion.viz.signals
                                                 Matplotlib figure object.
 
     """
-    fig, ax = plt.subplots()
-    ax.plot(kfolds, mean, c="orange")
-    ax.fill_between(kfolds, mean - std_dev, mean + std_dev, alpha=0.5, color="orange")
-    ax.scatter(kfolds, mean, c="orange")
+    fig, ax = plt.subplots(figsize=figsize)
+    ax.plot(kfolds, mean, c=color)
+    ax.fill_between(kfolds, mean - std_dev, mean + std_dev, alpha=0.5, color=color)
+    ax.scatter(kfolds, mean, c=color)
     ax.set_xlabel(xlabel)
     ax.set_ylabel(ylabel)
     ax.set_xticks(kfolds)
@@ -413,6 +425,114 @@ 
                                        Source code for eddymotion.viz.signals
                                         
     return fig, r
                                        
 
+
+
+
                                        
+[docs]
+def calculate_sphere_pts(points, center):
+    """Calculate the location of each point when it is expanded out to the sphere."""
+
+    kdtree = KDTree(points)  # tree of nearest points
+    # d is an array of distances, i is an array of indices
+    d, i = kdtree.query(center, points.shape[0])
+    sphere_pts = np.zeros(points.shape, dtype=float)
+
+    radius = np.amax(d)
+    for p in range(points.shape[0]):
+        sphere_pts[p] = points[i[p]] * radius / d[p]
+    # points and the indices for where they were in the original lists
+    return sphere_pts, i
                                        
+
+
+
+
                                        
+[docs]
+def compute_dmri_convex_hull(s, dirs, mask=None):
+    """Compute the convex hull of the dMRI signal s."""
+
+    if mask is None:
+        mask = np.ones(len(dirs), dtype=bool)
+
+    # Scale the original sampling directions by the corresponding signal values
+    scaled_bvecs = dirs[mask] * np.asarray(s)[:, np.newaxis]
+
+    # Create the data for the convex hull: project the scaled vectors to a
+    # sphere
+    sphere_pts, sphere_idx = calculate_sphere_pts(scaled_bvecs, [0, 0, 0])
+
+    # Create the convex hull: find the right ordering of vertices for the
+    # triangles: ConvexHull finds the simplices of the points on the outside of
+    # the data set
+    hull = ConvexHull(sphere_pts)
+    triang_idx = hull.simplices  # returns the list of indices for each triangle
+
+    return scaled_bvecs, sphere_idx, triang_idx
                                        
+
+
+
+
                                        
+[docs]
+def plot_surface(scaled_vecs, sphere_idx, triang_idx, title, cmap):
+    """Plot a surface."""
+
+    fig = plt.figure()
+    ax = fig.add_subplot(111, projection="3d")
+
+    ax.scatter3D(
+        scaled_vecs[:, 0], scaled_vecs[:, 1], scaled_vecs[:, 2], s=2, c="black", alpha=1.0
+    )
+
+    surface = ax.plot_trisurf(
+        scaled_vecs[sphere_idx, 0],
+        scaled_vecs[sphere_idx, 1],
+        scaled_vecs[sphere_idx, 2],
+        triangles=triang_idx,
+        cmap=cmap,
+        alpha=0.6,
+    )
+
+    ax.view_init(10, 45)
+    ax.set_aspect("equal", adjustable="box")
+    ax.set_title(title)
+
+    return fig, ax, surface
                                        
+
+
+
+
                                        
+[docs]
+def plot_signal_data(y, ax):
+    """Plot the data provided as a scatter plot"""
+
+    ax.scatter(
+        y[:, 0], y[:, 1], y[:, 2], color="red", marker="*", alpha=0.8, s=5, label="Original points"
+    )
                                        
+
+
+
+
                                        
+[docs]
+def plot_prediction_surface(y, y_pred, S0, y_dirs, y_pred_dirs, title, cmap):
+    """Plot the prediction surface obtained by computing the convex hull of the
+    predicted signal data, and plot the true data as a scatter plot."""
+
+    # Scale the original sampling directions by the corresponding signal values
+    y_bvecs = y_dirs * np.asarray(y)[:, np.newaxis]
+
+    # Compute the convex hull
+    y_pred_bvecs, sphere_idx, triang_idx = compute_dmri_convex_hull(y_pred, y_pred_dirs)
+
+    # Plot the surface
+    fig, ax, surface = plot_surface(y_pred_bvecs, sphere_idx, triang_idx, title, cmap)
+
+    # Add the underlying signal to the plot
+    # plot_signal_data(y_bvecs/S0, ax)
+    plot_signal_data(y_bvecs, ax)
+
+    fig.tight_layout()
+
+    return fig, ax, surface
                                        
+
 
                                        
         
       
                                        
@@ -445,7 +565,7 @@ 
                                        Source code for eddymotion.viz.signals
                                               
     
   
                                        
-
                                        
+
                                        diff --git a/main/_modules/index.html b/main/_modules/index.html index 1410a13a..d00c0e2b 100644 --- a/main/_modules/index.html +++ b/main/_modules/index.html @@ -5,7 +5,7 @@ - Overview: module code - eddymotion 24.0.0.dev181 documentation + Overview: module code - eddymotion 24.0.0.dev185 documentation @@ -166,7 +166,7 @@
                                      -
                                      eddymotion 24.0.0.dev181 documentation
                                       +
                                      eddymotion 24.0.0.dev185 documentation
                                      @@ -189,14 +189,14 @@
                                      eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                      • - 24.0.0.dev181 + 24.0.0.dev185
                                          @@ -340,7 +340,7 @@

                                          All modules for which code is available

                                        -
                                        +
                                        diff --git a/main/_static/documentation_options.js b/main/_static/documentation_options.js index 56d18e12..621fbaed 100644 --- a/main/_static/documentation_options.js +++ b/main/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '24.0.0.dev181', + VERSION: '24.0.0.dev185', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/main/api/eddymotion.cli.html b/main/api/eddymotion.cli.html index 7d5a6b3c..fa542ec5 100644 --- a/main/api/eddymotion.cli.html +++ b/main/api/eddymotion.cli.html @@ -6,7 +6,7 @@ - eddymotion.cli package - eddymotion 24.0.0.dev181 documentation + eddymotion.cli package - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                        -
                                        eddymotion 24.0.0.dev181 documentation
                                         +
                                        eddymotion 24.0.0.dev185 documentation
                                        @@ -190,14 +190,14 @@
                                        eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                        • - 24.0.0.dev181 + 24.0.0.dev185
                                            @@ -377,7 +377,7 @@

                                            Submodules +

                                          diff --git a/main/api/eddymotion.cli.parser.html b/main/api/eddymotion.cli.parser.html index 788d20fb..9dc50bdd 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.dev181 documentation + eddymotion.cli.parser module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                          -
                                          eddymotion 24.0.0.dev181 documentation
                                           +
                                          eddymotion 24.0.0.dev185 documentation
                                          @@ -190,14 +190,14 @@
                                          eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                          • - 24.0.0.dev181 + 24.0.0.dev185
                                              @@ -389,7 +389,7 @@
                                            -
                                            +
                                            diff --git a/main/api/eddymotion.cli.run.html b/main/api/eddymotion.cli.run.html index 99c30d1d..fe4517db 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.dev181 documentation + eddymotion.cli.run module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                            -
                                            eddymotion 24.0.0.dev181 documentation
                                             +
                                            eddymotion 24.0.0.dev185 documentation
                                            @@ -190,14 +190,14 @@
                                            eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                            • - 24.0.0.dev181 + 24.0.0.dev185
                                                @@ -380,7 +380,7 @@
                                              -
                                              +
                                              diff --git a/main/api/eddymotion.data.dmri.html b/main/api/eddymotion.data.dmri.html index 027158aa..bede247e 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.dev181 documentation + eddymotion.data.dmri module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                              -
                                              eddymotion 24.0.0.dev181 documentation
                                               +
                                              eddymotion 24.0.0.dev185 documentation
                                              @@ -190,14 +190,14 @@
                                              eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                              • - 24.0.0.dev181 + 24.0.0.dev185
                                                  @@ -486,7 +486,7 @@
                                                -
                                                +
                                                diff --git a/main/api/eddymotion.data.filtering.html b/main/api/eddymotion.data.filtering.html index f7a36f16..47509497 100644 --- a/main/api/eddymotion.data.filtering.html +++ b/main/api/eddymotion.data.filtering.html @@ -6,7 +6,7 @@ - eddymotion.data.filtering module - eddymotion 24.0.0.dev181 documentation + eddymotion.data.filtering module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                -
                                                eddymotion 24.0.0.dev181 documentation
                                                 +
                                                eddymotion 24.0.0.dev185 documentation
                                                @@ -190,14 +190,14 @@
                                                eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                • - 24.0.0.dev181 + 24.0.0.dev185
                                                    @@ -408,7 +408,7 @@
                                                  -
                                                  +
                                                  diff --git a/main/api/eddymotion.data.html b/main/api/eddymotion.data.html index da4054fe..18a4c3b2 100644 --- a/main/api/eddymotion.data.html +++ b/main/api/eddymotion.data.html @@ -6,7 +6,7 @@ - eddymotion.data package - eddymotion 24.0.0.dev181 documentation + eddymotion.data package - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                  -
                                                  eddymotion 24.0.0.dev181 documentation
                                                   +
                                                  eddymotion 24.0.0.dev185 documentation
                                                  @@ -190,14 +190,14 @@
                                                  eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                  • - 24.0.0.dev181 + 24.0.0.dev185
                                                      @@ -380,7 +380,7 @@

                                                      Submodules +

                                                    diff --git a/main/api/eddymotion.data.pet.html b/main/api/eddymotion.data.pet.html index 1a1f76fd..23fd36c6 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.dev181 documentation + eddymotion.data.pet module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                    -
                                                    eddymotion 24.0.0.dev181 documentation
                                                     +
                                                    eddymotion 24.0.0.dev185 documentation
                                                    @@ -190,14 +190,14 @@
                                                    eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                    • - 24.0.0.dev181 + 24.0.0.dev185
                                                        @@ -456,7 +456,7 @@
                                                      -
                                                      +
                                                      diff --git a/main/api/eddymotion.data.splitting.html b/main/api/eddymotion.data.splitting.html index d1e3c4ed..e91093e0 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.dev181 documentation + eddymotion.data.splitting module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                      -
                                                      eddymotion 24.0.0.dev181 documentation
                                                       +
                                                      eddymotion 24.0.0.dev185 documentation
                                                      @@ -190,14 +190,14 @@
                                                      eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                      • - 24.0.0.dev181 + 24.0.0.dev185
                                                          @@ -392,7 +392,7 @@
                                                        -
                                                        +
                                                        diff --git a/main/api/eddymotion.data.utils.html b/main/api/eddymotion.data.utils.html index e73acfb6..d65f2b63 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.dev181 documentation + eddymotion.data.utils module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                        -
                                                        eddymotion 24.0.0.dev181 documentation
                                                         +
                                                        eddymotion 24.0.0.dev185 documentation
                                                        @@ -190,14 +190,14 @@
                                                        eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                        • - 24.0.0.dev181 + 24.0.0.dev185
                                                            @@ -389,7 +389,7 @@
                                                          -
                                                          +
                                                          diff --git a/main/api/eddymotion.estimator.html b/main/api/eddymotion.estimator.html index eaed0064..b3ae4e66 100644 --- a/main/api/eddymotion.estimator.html +++ b/main/api/eddymotion.estimator.html @@ -6,7 +6,7 @@ - eddymotion.estimator module - eddymotion 24.0.0.dev181 documentation + eddymotion.estimator module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                          -
                                                          eddymotion 24.0.0.dev181 documentation
                                                           +
                                                          eddymotion 24.0.0.dev185 documentation
                                                          @@ -190,14 +190,14 @@
                                                          eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                          • - 24.0.0.dev181 + 24.0.0.dev185
                                                              @@ -411,7 +411,7 @@
                                                            -
                                                            +
                                                            diff --git a/main/api/eddymotion.exceptions.html b/main/api/eddymotion.exceptions.html index 5120b270..928c306c 100644 --- a/main/api/eddymotion.exceptions.html +++ b/main/api/eddymotion.exceptions.html @@ -6,7 +6,7 @@ - eddymotion.exceptions module - eddymotion 24.0.0.dev181 documentation + eddymotion.exceptions module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                            -
                                                            eddymotion 24.0.0.dev181 documentation
                                                             +
                                                            eddymotion 24.0.0.dev185 documentation
                                                            @@ -190,14 +190,14 @@
                                                            eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                            • - 24.0.0.dev181 + 24.0.0.dev185
                                                                @@ -377,7 +377,7 @@
                                                              -
                                                              +
                                                              diff --git a/main/api/eddymotion.math.html b/main/api/eddymotion.math.html index b70bf7d9..bfa8c8d8 100644 --- a/main/api/eddymotion.math.html +++ b/main/api/eddymotion.math.html @@ -6,7 +6,7 @@ - eddymotion.math package - eddymotion 24.0.0.dev181 documentation + eddymotion.math package - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                              -
                                                              eddymotion 24.0.0.dev181 documentation
                                                               +
                                                              eddymotion 24.0.0.dev185 documentation
                                                              @@ -190,14 +190,14 @@
                                                              eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                              • - 24.0.0.dev181 + 24.0.0.dev185
                                                                  @@ -376,7 +376,7 @@

                                                                  Submodules +

                                                                diff --git a/main/api/eddymotion.math.utils.html b/main/api/eddymotion.math.utils.html index 4dadfb74..01e295ad 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.dev181 documentation + eddymotion.math.utils module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                -
                                                                eddymotion 24.0.0.dev181 documentation
                                                                 +
                                                                eddymotion 24.0.0.dev185 documentation
                                                                @@ -190,14 +190,14 @@
                                                                eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                • - 24.0.0.dev181 + 24.0.0.dev185
                                                                    @@ -423,7 +423,7 @@
                                                                  -
                                                                  +
                                                                  diff --git a/main/api/eddymotion.model.base.html b/main/api/eddymotion.model.base.html index 1cec22e3..dd2a8ca2 100644 --- a/main/api/eddymotion.model.base.html +++ b/main/api/eddymotion.model.base.html @@ -6,7 +6,7 @@ - eddymotion.model.base module - eddymotion 24.0.0.dev181 documentation + eddymotion.model.base module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                  -
                                                                  eddymotion 24.0.0.dev181 documentation
                                                                   +
                                                                  eddymotion 24.0.0.dev185 documentation
                                                                  @@ -190,14 +190,14 @@
                                                                  eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                  • - 24.0.0.dev181 + 24.0.0.dev185
                                                                      @@ -491,7 +491,7 @@
                                                                    -
                                                                    +
                                                                    diff --git a/main/api/eddymotion.model.dmri.html b/main/api/eddymotion.model.dmri.html index 52a330ea..8d88ec20 100644 --- a/main/api/eddymotion.model.dmri.html +++ b/main/api/eddymotion.model.dmri.html @@ -6,7 +6,7 @@ - eddymotion.model.dmri module - eddymotion 24.0.0.dev181 documentation + eddymotion.model.dmri module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                    -
                                                                    eddymotion 24.0.0.dev181 documentation
                                                                     +
                                                                    eddymotion 24.0.0.dev185 documentation
                                                                    @@ -190,14 +190,14 @@
                                                                    eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                    • - 24.0.0.dev181 + 24.0.0.dev185
                                                                        @@ -530,7 +530,7 @@
                                                                      -
                                                                      +
                                                                      diff --git a/main/api/eddymotion.model.html b/main/api/eddymotion.model.html index ecdbc15d..de5e6f25 100644 --- a/main/api/eddymotion.model.html +++ b/main/api/eddymotion.model.html @@ -6,7 +6,7 @@ - eddymotion.model package - eddymotion 24.0.0.dev181 documentation + eddymotion.model package - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                      -
                                                                      eddymotion 24.0.0.dev181 documentation
                                                                       +
                                                                      eddymotion 24.0.0.dev185 documentation
                                                                      @@ -190,14 +190,14 @@
                                                                      eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                      • - 24.0.0.dev181 + 24.0.0.dev185
                                                                          @@ -546,7 +546,7 @@

                                                                          Submodules +

                                                                        diff --git a/main/api/eddymotion.model.pet.html b/main/api/eddymotion.model.pet.html index cc2a1144..e9e409f5 100644 --- a/main/api/eddymotion.model.pet.html +++ b/main/api/eddymotion.model.pet.html @@ -6,7 +6,7 @@ - eddymotion.model.pet module - eddymotion 24.0.0.dev181 documentation + eddymotion.model.pet module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                        -
                                                                        eddymotion 24.0.0.dev181 documentation
                                                                         +
                                                                        eddymotion 24.0.0.dev185 documentation
                                                                        @@ -190,14 +190,14 @@
                                                                        eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                        • - 24.0.0.dev181 + 24.0.0.dev185
                                                                            @@ -405,7 +405,7 @@
                                                                          -
                                                                          +
                                                                          diff --git a/main/api/eddymotion.registration.ants.html b/main/api/eddymotion.registration.ants.html index 21b996aa..9e3a8861 100644 --- a/main/api/eddymotion.registration.ants.html +++ b/main/api/eddymotion.registration.ants.html @@ -6,7 +6,7 @@ - eddymotion.registration.ants module - eddymotion 24.0.0.dev181 documentation + eddymotion.registration.ants module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                          -
                                                                          eddymotion 24.0.0.dev181 documentation
                                                                           +
                                                                          eddymotion 24.0.0.dev185 documentation
                                                                          @@ -190,14 +190,14 @@
                                                                          eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                          • - 24.0.0.dev181 + 24.0.0.dev185
                                                                              @@ -436,7 +436,7 @@
                                                                            -
                                                                            +
                                                                            diff --git a/main/api/eddymotion.registration.html b/main/api/eddymotion.registration.html index e1fc1bad..00ecb83d 100644 --- a/main/api/eddymotion.registration.html +++ b/main/api/eddymotion.registration.html @@ -6,7 +6,7 @@ - eddymotion.registration package - eddymotion 24.0.0.dev181 documentation + eddymotion.registration package - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                            -
                                                                            eddymotion 24.0.0.dev181 documentation
                                                                             +
                                                                            eddymotion 24.0.0.dev185 documentation
                                                                            @@ -190,14 +190,14 @@
                                                                            eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                            • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                @@ -377,7 +377,7 @@

                                                                                Submodules +

                                                                              diff --git a/main/api/eddymotion.registration.utils.html b/main/api/eddymotion.registration.utils.html index 26e1926e..99b8966b 100644 --- a/main/api/eddymotion.registration.utils.html +++ b/main/api/eddymotion.registration.utils.html @@ -6,7 +6,7 @@ - eddymotion.registration.utils module - eddymotion 24.0.0.dev181 documentation + eddymotion.registration.utils module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                              -
                                                                              eddymotion 24.0.0.dev181 documentation
                                                                               +
                                                                              eddymotion 24.0.0.dev185 documentation
                                                                              @@ -190,14 +190,14 @@
                                                                              eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                              • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                  @@ -419,7 +419,7 @@
                                                                                -
                                                                                +
                                                                                diff --git a/main/api/eddymotion.testing.html b/main/api/eddymotion.testing.html index 94f138f0..8fd69b22 100644 --- a/main/api/eddymotion.testing.html +++ b/main/api/eddymotion.testing.html @@ -6,7 +6,7 @@ - eddymotion.testing package - eddymotion 24.0.0.dev181 documentation + eddymotion.testing package - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                -
                                                                                eddymotion 24.0.0.dev181 documentation
                                                                                 +
                                                                                eddymotion 24.0.0.dev185 documentation
                                                                                @@ -190,14 +190,14 @@
                                                                                eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                    @@ -376,7 +376,7 @@

                                                                                    Submodules +

                                                                                  diff --git a/main/api/eddymotion.testing.simulations.html b/main/api/eddymotion.testing.simulations.html index 699136a8..b38f97ea 100644 --- a/main/api/eddymotion.testing.simulations.html +++ b/main/api/eddymotion.testing.simulations.html @@ -6,7 +6,7 @@ - eddymotion.testing.simulations module - eddymotion 24.0.0.dev181 documentation + eddymotion.testing.simulations module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                  -
                                                                                  eddymotion 24.0.0.dev181 documentation
                                                                                   +
                                                                                  eddymotion 24.0.0.dev185 documentation
                                                                                  @@ -190,14 +190,14 @@
                                                                                  eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                  • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                      @@ -340,6 +340,19 @@ +
                                                                                      +
                                                                                      +eddymotion.testing.simulations.create_random_diffusivity_eigenvalues(size, rng)[source]¶
                                                                                      +

                                                                                      Create DTI model diffusion tensor eigenvalues ($lambda_{1}, +lambda_{2}, lambda_{3}$) drawn from a uniform distribution.

                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      +eddymotion.testing.simulations.create_random_polar_angles(size, rng)[source]¶
                                                                                      +

                                                                                      Create polar angles drawn from a uniform distribution.

                                                                                      +
                                                                                      +
                                                                                      eddymotion.testing.simulations.create_random_polar_coordinates(hsph_dirs: int, seed: int = 1234) → tuple[numpy.ndarray, numpy.ndarray][source]¶
                                                                                      @@ -424,14 +437,74 @@
                                                                                      +
                                                                                      +
                                                                                      +eddymotion.testing.simulations.group_values(values, group_size)[source]¶
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      +eddymotion.testing.simulations.serialize_dmri(dwi_data, gtab, dwi_data_fname, bval_data_fname, bvec_data_fname, affine: np.ndarray | None = None)[source]¶
                                                                                      +

                                                                                      Serialize dMRI data.

                                                                                      +
                                                                                      +
                                                                                      Parameters:
                                                                                      +
                                                                                        +

                                                                                      • dwi_data (ndarray) – DWI data.

                                                                                        • +

                                                                                      • gtab (gradient_table) – Gradient table.

                                                                                        • +

                                                                                      • dwi_data_fname (str) – Filename of NIfTI file to save the DWI signal.

                                                                                        • +

                                                                                      • bval_data_fname (str) – Filename of NIfTI file to save the diffusion-encoding gradient b-vals.

                                                                                        • +

                                                                                      • bvec_data_fname (str) – Filename of NIfTI file to save the diffusion-encoding gradient b-vecs.

                                                                                        • +

                                                                                      • affine (ndarray, optional) – Affine matrix. If None an identity affine matrix is used.

                                                                                        • +
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      +eddymotion.testing.simulations.serialize_dwi(dwi_data, dwi_data_fname, affine: np.ndarray | None = None)[source]¶
                                                                                      +

                                                                                      Serialize DWI data.

                                                                                      +
                                                                                      +
                                                                                      Parameters:
                                                                                      +
                                                                                        +

                                                                                      • dwi_data (ndarray) – DWI data.

                                                                                        • +

                                                                                      • dwi_data_fname (str) – Filename of NIfTI file to save the DWI signal.

                                                                                        • +

                                                                                      • affine (ndarray, optional) – Affine matrix. If None an identity affine matrix is used.

                                                                                        • +
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      +eddymotion.testing.simulations.serialize_gtab(gtab, bval_data_fname, bvec_data_fname)[source]¶
                                                                                      +

                                                                                      Serialize dMRI gradient-encoding table data into a pair of b-vals and +b-vecs files.

                                                                                      +
                                                                                      +
                                                                                      Parameters:
                                                                                      +
                                                                                        +

                                                                                      • gtab (gradient_table) – Gradient table.

                                                                                        • +

                                                                                      • bval_data_fname (str) – Filename of NIfTI file to save the diffusion-encoding gradient b-vals.

                                                                                        • +

                                                                                      • bvec_data_fname (str) – Filename of NIfTI file to save the diffusion-encoding gradient b-vecs.

                                                                                        • +
                                                                                      +
                                                                                      +
                                                                                      +
                                                                                      + +
                                                                                      +
                                                                                      +eddymotion.testing.simulations.simulate_one_fiber_multivoxel(gtab, S0, snr, n_voxels, rng, evals=None)[source]¶
                                                                                      +

                                                                                      Create a single-fiber multi-voxel DWI signal.

                                                                                      +
                                                                                      +
                                                                                      -eddymotion.testing.simulations.simulate_voxels(S0, evals, hsph_dirs, bval_shell=1000, snr=20, n_voxels=1, seed=None)[source]¶
                                                                                      +eddymotion.testing.simulations.simulate_voxels(S0, hsph_dirs, bval_shell=1000, snr=20, n_voxels=1, evals=None, seed=None)[source]¶
                                                                                      -eddymotion.testing.simulations.single_fiber_voxel(gtab, S0, evals, theta=0, phi=0, snr=20)[source]¶
                                                                                      +eddymotion.testing.simulations.single_fiber_voxel(gtab, S0, evals, rng, theta=0, phi=0, snr=20)[source]¶
                                                                                      @@ -494,10 +567,17 @@
                                                                                    • eddymotion.testing.simulations module @@ -511,7 +591,7 @@
                                                                                    -
                                                                                    +
                                                                                    diff --git a/main/api/eddymotion.utils.html b/main/api/eddymotion.utils.html index af3593b4..fe8d5948 100644 --- a/main/api/eddymotion.utils.html +++ b/main/api/eddymotion.utils.html @@ -6,7 +6,7 @@ - eddymotion.utils module - eddymotion 24.0.0.dev181 documentation + eddymotion.utils module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                    -
                                                                                    eddymotion 24.0.0.dev181 documentation
                                                                                     +
                                                                                    eddymotion 24.0.0.dev185 documentation
                                                                                    @@ -190,14 +190,14 @@
                                                                                    eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                    • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                        @@ -478,7 +478,7 @@
                                                                                      -
                                                                                      +
                                                                                      diff --git a/main/api/eddymotion.viz.html b/main/api/eddymotion.viz.html index 05476645..e64cb742 100644 --- a/main/api/eddymotion.viz.html +++ b/main/api/eddymotion.viz.html @@ -6,7 +6,7 @@ - eddymotion.viz package - eddymotion 24.0.0.dev181 documentation + eddymotion.viz package - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                      -
                                                                                      eddymotion 24.0.0.dev181 documentation
                                                                                       +
                                                                                      eddymotion 24.0.0.dev185 documentation
                                                                                      @@ -190,14 +190,14 @@
                                                                                      eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                      • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                          @@ -376,7 +376,7 @@

                                                                                          Submodules +

                                                                                        diff --git a/main/api/eddymotion.viz.signals.html b/main/api/eddymotion.viz.signals.html index aaae8ce6..b7e36e55 100644 --- a/main/api/eddymotion.viz.signals.html +++ b/main/api/eddymotion.viz.signals.html @@ -6,7 +6,7 @@ - eddymotion.viz.signals module - eddymotion 24.0.0.dev181 documentation + eddymotion.viz.signals module - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                        -
                                                                                        eddymotion 24.0.0.dev181 documentation
                                                                                         +
                                                                                        eddymotion 24.0.0.dev185 documentation
                                                                                        @@ -190,14 +190,14 @@
                                                                                        eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                        • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                            @@ -299,6 +299,18 @@

                                                                                            eddymotion.viz.signals module¶

                                                                                            Visualizing signals and intermediate aspects of models.

                                                                                            +
                                                                                            +
                                                                                            +eddymotion.viz.signals.calculate_sphere_pts(points, center)[source]¶
                                                                                            +

                                                                                            Calculate the location of each point when it is expanded out to the sphere.

                                                                                            +
                                                                                            + +
                                                                                            +
                                                                                            +eddymotion.viz.signals.compute_dmri_convex_hull(s, dirs, mask=None)[source]¶
                                                                                            +

                                                                                            Compute the convex hull of the dMRI signal s.

                                                                                            +
                                                                                            +
                                                                                            eddymotion.viz.signals.plot_correlation(x, y, title)[source]¶
                                                                                            @@ -306,7 +318,7 @@
                                                                                            -eddymotion.viz.signals.plot_error(kfolds: list[int], mean: numpy.ndarray, std_dev: numpy.ndarray, xlabel: str, ylabel: str, title: str) → matplotlib.pyplot.Figure[source]¶
                                                                                            +eddymotion.viz.signals.plot_error(kfolds: list[int], mean: numpy.ndarray, std_dev: numpy.ndarray, xlabel: str, ylabel: str, title: str, color: str = 'orange', figsize: tuple[int, int] = (19.2, 10.8)) → matplotlib.pyplot.Figure[source]¶

                                                                                            Plot the error and standard deviation.

                                                                                            Parameters:
                                                                                            @@ -317,6 +329,8 @@

                                                                                          • xlabel (str) – X-axis label.

                                                                                          • ylabel (str) – Y-axis label.

                                                                                          • title (str) – Plot title.

                                                                                            • +

                                                                                          • color (str, optional) – Plot color.

                                                                                            • +

                                                                                          • figsize (tuple, optional) – Figure size.

                                                                                          Returns:
                                                                                          @@ -333,6 +347,25 @@ eddymotion.viz.signals.plot_estimation_carpet(gt_nii, gp_nii, gtab, suptitle, **kwargs)[source]¶
                                                                                          +
                                                                                          +
                                                                                          +eddymotion.viz.signals.plot_prediction_surface(y, y_pred, S0, y_dirs, y_pred_dirs, title, cmap)[source]¶
                                                                                          +

                                                                                          Plot the prediction surface obtained by computing the convex hull of the +predicted signal data, and plot the true data as a scatter plot.

                                                                                          +
                                                                                          + +
                                                                                          +
                                                                                          +eddymotion.viz.signals.plot_signal_data(y, ax)[source]¶
                                                                                          +

                                                                                          Plot the data provided as a scatter plot

                                                                                          +
                                                                                          + +
                                                                                          +
                                                                                          +eddymotion.viz.signals.plot_surface(scaled_vecs, sphere_idx, triang_idx, title, cmap)[source]¶
                                                                                          +

                                                                                          Plot a surface.

                                                                                          +
                                                                                          + @@ -391,9 +424,14 @@
                                                                                          @@ -405,7 +443,7 @@
                                                                                          -
                                                                                          +
                                                                                          diff --git a/main/changes.html b/main/changes.html index b718faf1..0ad7ccee 100644 --- a/main/changes.html +++ b/main/changes.html @@ -6,7 +6,7 @@ - What’s new? - eddymotion 24.0.0.dev181 documentation + What’s new? - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                          -
                                                                                          eddymotion 24.0.0.dev181 documentation
                                                                                           +
                                                                                          eddymotion 24.0.0.dev185 documentation
                                                                                          @@ -190,14 +190,14 @@
                                                                                          eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                          • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                              @@ -442,7 +442,7 @@

                                                                                              0.1.4 (April 12, 2021) +

                                                                                            diff --git a/main/developers.html b/main/developers.html index 4da6077d..1dc7c4a9 100644 --- a/main/developers.html +++ b/main/developers.html @@ -6,7 +6,7 @@ - For developers - eddymotion 24.0.0.dev181 documentation + For developers - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                            -
                                                                                            eddymotion 24.0.0.dev181 documentation
                                                                                             +
                                                                                            eddymotion 24.0.0.dev185 documentation
                                                                                            @@ -190,14 +190,14 @@
                                                                                            eddymotion - 24.0.0.dev181 + 24.0.0.dev185 diff --git a/main/genindex.html b/main/genindex.html index 9c665257..0f7b2a00 100644 --- a/main/genindex.html +++ b/main/genindex.html @@ -4,7 +4,7 @@ - Index - eddymotion 24.0.0.dev181 documentation + Index - eddymotion 24.0.0.dev185 documentation @@ -165,7 +165,7 @@
                                                                                            -
                                                                                            eddymotion 24.0.0.dev181 documentation
                                                                                             +
                                                                                            eddymotion 24.0.0.dev185 documentation
                                                                                            @@ -188,14 +188,14 @@
                                                                                            eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                              +
                                                                                            • plot_surface() (in module eddymotion.viz.signals) +
                                                                                            • predict() (eddymotion.model.AverageDWModel method)
                                                                                                @@ -885,6 +901,12 @@

                                                                                                R

                                                                                                S

                                                                                                  +
                                                                                                • simulate_one_fiber_multivoxel() (in module eddymotion.testing.simulations) +
                                                                                                • simulate_voxels() (in module eddymotion.testing.simulations)
                                                                                                • single_fiber_voxel() (in module eddymotion.testing.simulations) @@ -963,7 +987,7 @@

                                                                                                  T

                                                                                                  - + diff --git a/main/index.html b/main/index.html index 4dde8f62..bd501671 100644 --- a/main/index.html +++ b/main/index.html @@ -6,7 +6,7 @@ - eddymotion 24.0.0.dev181 documentation + eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                                  -
                                                                                                  eddymotion 24.0.0.dev181 documentation
                                                                                                   +
                                                                                                  eddymotion 24.0.0.dev185 documentation
                                                                                                  @@ -190,14 +190,14 @@
                                                                                                  eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                  • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                      @@ -461,7 +461,7 @@

                                                                                                      Contents

                                                                                                    -
                                                                                                    +
                                                                                                    diff --git a/main/installation.html b/main/installation.html index 1242e015..2b4465a3 100644 --- a/main/installation.html +++ b/main/installation.html @@ -6,7 +6,7 @@ - Installation - eddymotion 24.0.0.dev181 documentation + Installation - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                                    -
                                                                                                    eddymotion 24.0.0.dev181 documentation
                                                                                                     +
                                                                                                    eddymotion 24.0.0.dev185 documentation
                                                                                                    @@ -190,14 +190,14 @@
                                                                                                    eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                    • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                        @@ -382,7 +382,7 @@

                                                                                                        External Dependencies

                                                                                                      -
                                                                                                      +
                                                                                                      diff --git a/main/links.html b/main/links.html index 0efc0984..6f421122 100644 --- a/main/links.html +++ b/main/links.html @@ -6,7 +6,7 @@ - <no title> - eddymotion 24.0.0.dev181 documentation + <no title> - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
                                                                                                      -
                                                                                                      eddymotion 24.0.0.dev181 documentation
                                                                                                       +
                                                                                                      eddymotion 24.0.0.dev185 documentation
                                                                                                      @@ -190,14 +190,14 @@
                                                                                                      eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                      • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                          @@ -328,7 +328,7 @@
                                                                                                        -
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"eddymotion.utils module", "eddymotion.viz package", "eddymotion.viz.signals module", "What\u2019s new?", "For developers", "Eddymotion", "Installation", "<no title>", "Running Eddymotion", "How to Use"], "titleterms": {"": 25, "0": 25, "1": 25, "12": 25, "13": 25, "15": 25, "2021": 25, "2024": 25, "4": 25, "For": 26, "ant": 18, "api": 26, "applic": 26, "april": 25, "argument": 30, "base": 14, "cli": [0, 1, 2], "command": 30, "content": 27, "contribut": 26, "data": [3, 4, 5, 6, 7, 8], "depend": 28, "develop": 26, "dmri": [4, 15], "document": 26, "eddymot": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31], "estim": 9, "except": 10, "extern": 28, "filter": 5, "how": 31, "incorpor": 31, "instal": 28, "interfac": [26, 30], "librari": 26, "line": 30, "mai": 25, "math": [11, 12], "model": [13, 14, 15, 16], "modul": [1, 2, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 21, 22, 24, 31], "name": 30, "new": 25, "packag": [0, 3, 11, 13, 17, 20, 23], "parser": 1, "pet": [6, 16], "posit": 30, "program": 26, "python": 31, "registr": [17, 18, 19], "run": [2, 30], "script": 31, "signal": 24, "simul": 21, "split": 7, "submodul": [0, 3, 11, 13, 17, 20, 23], "test": [20, 21], "us": 31, "util": [8, 12, 19, 22], "viz": [23, 24], "what": 25}}) \ No newline at end of file diff --git a/main/usage.html b/main/usage.html index 0c52378f..74230123 100644 --- a/main/usage.html +++ b/main/usage.html @@ -6,7 +6,7 @@ - How to Use - eddymotion 24.0.0.dev181 documentation + How to Use - eddymotion 24.0.0.dev185 documentation @@ -167,7 +167,7 @@
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                                                                                                              eddymotion 24.0.0.dev181 documentation
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                                                                                                              eddymotion 24.0.0.dev185 documentation
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                                                                                                              eddymotion - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                              • - 24.0.0.dev181 + 24.0.0.dev185
                                                                                                                  @@ -464,7 +464,7 @@

                                                                                                                  Incorporating Eddymotion into a Python module or script

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