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# 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: e3e9e16c6b3df08155786c1fd713386f
config: 73c5429dd4dbd6e35dd69b6ed193fed6
tags: 645f666f9bcd5a90fca523b33c5a78b7
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4 changes: 2 additions & 2 deletions dev/_modules/fury.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>fury &#8212; FURY 0.12.0.dev5+g3d4ae767 documentation</title>
<title>fury &#8212; FURY 0.12.0.dev7+g6c2337c5 documentation</title>



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<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
<script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>

<script src="../_static/documentation_options.js?v=6c036d17"></script>
<script src="../_static/documentation_options.js?v=85a2681a"></script>
<script src="../_static/doctools.js?v=9a2dae69"></script>
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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9 changes: 3 additions & 6 deletions dev/_modules/fury/actor.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>fury.actor &#8212; FURY 0.12.0.dev5+g3d4ae767 documentation</title>
<title>fury.actor &#8212; FURY 0.12.0.dev7+g6c2337c5 documentation</title>



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<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
<script src="../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>

<script src="../../_static/documentation_options.js?v=6c036d17"></script>
<script src="../../_static/documentation_options.js?v=85a2681a"></script>
<script src="../../_static/doctools.js?v=9a2dae69"></script>
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
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<span class="sd"> &quot;&quot;&quot;</span>

<div class="viewcode-block" id="Container.__init__">
<a class="viewcode-back" href="../../reference/fury.actor.html#fury.actor.Container.__init__">[docs]</a>
<span class="nd">@warn_on_args_to_kwargs</span><span class="p">()</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="p">,</span> <span class="n">layout</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Parameters</span>
Expand All @@ -3641,8 +3639,7 @@ <h1>Source code for fury.actor</h1><div class="highlight"><pre>
<span class="bp">self</span><span class="o">.</span><span class="n">_position</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_visibility</span> <span class="o">=</span> <span class="kc">True</span>
<span class="bp">self</span><span class="o">.</span><span class="n">anchor</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">padding</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">6</span><span class="p">)</span></div>

<span class="bp">self</span><span class="o">.</span><span class="n">padding</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">6</span><span class="p">)</span>

<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">items</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>fury.actors.odf_slicer &#8212; FURY 0.12.0.dev5+g3d4ae767 documentation</title>
<title>fury.actors.odf_slicer &#8212; FURY 0.12.0.dev7+g6c2337c5 documentation</title>



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<link rel="preload" as="script" href="../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
<script src="../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>

<script src="../../../_static/documentation_options.js?v=6c036d17"></script>
<script src="../../../_static/documentation_options.js?v=85a2681a"></script>
<script src="../../../_static/doctools.js?v=9a2dae69"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
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<span class="sd"> &quot;&quot;&quot;</span>

<div class="viewcode-block" id="OdfSlicerActor.__init__">
<a class="viewcode-back" href="../../../reference/fury.actors.html#fury.actors.odf_slicer.OdfSlicerActor.__init__">[docs]</a>
<span class="nd">@warn_on_args_to_kwargs</span><span class="p">()</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
Expand Down Expand Up @@ -487,8 +485,7 @@ <h1>Source code for fury.actors.odf_slicer</h1><div class="highlight"><pre>
<span class="bp">self</span><span class="o">.</span><span class="n">mapper</span> <span class="o">=</span> <span class="n">PolyDataMapper</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">SetMapper</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mapper</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">slice_along_axis</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_shape</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">set_opacity</span><span class="p">(</span><span class="n">opacity</span><span class="p">)</span></div>

<span class="bp">self</span><span class="o">.</span><span class="n">set_opacity</span><span class="p">(</span><span class="n">opacity</span><span class="p">)</span>

<div class="viewcode-block" id="OdfSlicerActor.set_opacity">
<a class="viewcode-back" href="../../../reference/fury.actors.html#fury.actors.odf_slicer.OdfSlicerActor.set_opacity">[docs]</a>
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75 changes: 43 additions & 32 deletions dev/_modules/fury/actors/peak.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>fury.actors.peak &#8212; FURY 0.12.0.dev5+g3d4ae767 documentation</title>
<title>fury.actors.peak &#8212; FURY 0.12.0.dev7+g6c2337c5 documentation</title>



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<link rel="preload" as="script" href="../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
<script src="../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>

<script src="../../../_static/documentation_options.js?v=6c036d17"></script>
<script src="../../../_static/documentation_options.js?v=85a2681a"></script>
<script src="../../../_static/doctools.js?v=9a2dae69"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
Expand Down Expand Up @@ -405,43 +405,55 @@ <h1>Source code for fury.actors.peak</h1><div class="highlight"><pre>

<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>

<span class="sd"> directions : ndarray</span>
<span class="sd"> Peak directions. The shape of the array should be (X, Y, Z, D, 3).</span>

<span class="sd"> Peak directions. The shape of the array should be (X, Y, Z, D, 3).</span>

<span class="sd"> indices : tuple</span>
<span class="sd"> Indices given in tuple(x_indices, y_indices, z_indices)</span>
<span class="sd"> format for mapping 2D ODF array to 3D voxel grid.</span>

<span class="sd"> Indices given in tuple(x_indices, y_indices, z_indices)</span>
<span class="sd"> format for mapping 2D ODF array to 3D voxel grid.</span>

<span class="sd"> values : ndarray, optional</span>
<span class="sd"> Peak values. The shape of the array should be (X, Y, Z, D).</span>

<span class="sd"> Peak values. The shape of the array should be (X, Y, Z, D).</span>

<span class="sd"> affine : array, optional</span>
<span class="sd"> 4x4 transformation array from native coordinates to world coordinates.</span>
<span class="sd"> colors : None or string (&#39;rgb_standard&#39;) or tuple (3D or 4D) or</span>
<span class="sd"> array/ndarray (N, 3 or 4) or array/ndarray (K, 3 or 4) or</span>
<span class="sd"> array/ndarray(N, ) or array/ndarray (K, )</span>
<span class="sd"> If None a standard orientation colormap is used for every line.</span>
<span class="sd"> If one tuple of color is used. Then all streamlines will have the same</span>
<span class="sd"> color.</span>
<span class="sd"> If an array (N, 3 or 4) is given, where N is equal to the number of</span>
<span class="sd"> points. Then every point is colored with a different RGB(A) color.</span>
<span class="sd"> If an array (K, 3 or 4) is given, where K is equal to the number of</span>
<span class="sd"> lines. Then every line is colored with a different RGB(A) color.</span>
<span class="sd"> If an array (N, ) is given, where N is the number of points then these</span>
<span class="sd"> are considered as the values to be used by the colormap.</span>
<span class="sd"> If an array (K,) is given, where K is the number of lines then these</span>
<span class="sd"> are considered as the values to be used by the colormap.</span>

<span class="sd"> 4x4 transformation array from native coordinates to world coordinates.</span>

<span class="sd"> colors : None or string (&#39;rgb_standard&#39;) or tuple (3D or 4D) or array/ndarray (N, 3 or 4) or array/ndarray (K, 3 or 4) or array/ndarray(N, ) or array/ndarray (K, )</span>

<span class="sd"> If None a standard orientation colormap is used for every line.</span>
<span class="sd"> If one tuple of color is used. Then all streamlines will have the same</span>
<span class="sd"> color.</span>
<span class="sd"> If an array (N, 3 or 4) is given, where N is equal to the number of</span>
<span class="sd"> points. Then every point is colored with a different RGB(A) color.</span>
<span class="sd"> If an array (K, 3 or 4) is given, where K is equal to the number of</span>
<span class="sd"> lines. Then every line is colored with a different RGB(A) color.</span>
<span class="sd"> If an array (N, ) is given, where N is the number of points then these</span>
<span class="sd"> are considered as the values to be used by the colormap.</span>
<span class="sd"> If an array (K,) is given, where K is the number of lines then these</span>
<span class="sd"> are considered as the values to be used by the colormap.</span>

<span class="sd"> lookup_colormap : vtkLookupTable, optional</span>
<span class="sd"> Add a default lookup table to the colormap. Default is None which calls</span>
<span class="sd"> :func:`fury.actor.colormap_lookup_table`.</span>

<span class="sd"> Add a default lookup table to the colormap. Default is None which calls</span>
<span class="sd"> :func:`fury.actor.colormap_lookup_table`.</span>

<span class="sd"> linewidth : float, optional</span>
<span class="sd"> Line thickness. Default is 1.</span>

<span class="sd"> Line thickness. Default is 1.</span>

<span class="sd"> symmetric: bool, optional</span>
<span class="sd"> If True, peaks are drawn for both peaks_dirs and -peaks_dirs. Else,</span>
<span class="sd"> peaks are only drawn for directions given by peaks_dirs. Default is</span>
<span class="sd"> True.</span>

<span class="sd"> &quot;&quot;&quot;</span>
<span class="sd"> If True, peaks are drawn for both peaks_dirs and -peaks_dirs. Else,</span>
<span class="sd"> peaks are only drawn for directions given by peaks_dirs. Default is</span>
<span class="sd"> True.</span>

<span class="sd"> &quot;&quot;&quot;</span> <span class="c1"># noqa: E501</span>

<div class="viewcode-block" id="PeakActor.__init__">
<a class="viewcode-back" href="../../../reference/fury.actors.html#fury.actors.peak.PeakActor.__init__">[docs]</a>
<span class="nd">@warn_on_args_to_kwargs</span><span class="p">()</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
Expand Down Expand Up @@ -593,8 +605,7 @@ <h1>Source code for fury.actors.peak</h1><div class="highlight"><pre>

<span class="bp">self</span><span class="o">.</span><span class="n">__mapper</span><span class="o">.</span><span class="n">AddObserver</span><span class="p">(</span>
<span class="n">Command</span><span class="o">.</span><span class="n">UpdateShaderEvent</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">__display_peaks_vtk_callback</span><span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="p">)</span></div>

<span class="p">)</span>

<span class="nd">@warn_on_args_to_kwargs</span><span class="p">()</span>
<span class="nd">@calldata_type</span><span class="p">(</span><span class="n">VTK_OBJECT</span><span class="p">)</span>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>fury.actors.tensor &#8212; FURY 0.12.0.dev5+g3d4ae767 documentation</title>
<title>fury.actors.tensor &#8212; FURY 0.12.0.dev7+g6c2337c5 documentation</title>



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<link rel="preload" as="script" href="../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
<script src="../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>

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Expand Down Expand Up @@ -783,18 +783,22 @@ <h1>Source code for fury.actors.tensor</h1><div class="highlight"><pre>
<span class="sd"> ----------</span>
<span class="sd"> evals : ndarray (3, ) or (N, 3)</span>
<span class="sd"> Eigenvalues.</span>

<span class="sd"> evecs : ndarray (3, 3) or (N, 3, 3)</span>
<span class="sd"> Eigenvectors.</span>

<span class="sd"> signal : 3D or 4D ndarray</span>
<span class="sd"> Predicted signal.</span>

<span class="sd"> sigma : ndarray</span>
<span class="sd"> Standard deviation of the noise.</span>

<span class="sd"> b_matrix : array (N, 7)</span>
<span class="sd"> Design matrix for DTI.</span>

<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> angles: array</span>
<span class="sd"> angles : array</span>

<span class="sd"> Notes</span>
<span class="sd"> -----</span>
Expand All @@ -804,12 +808,12 @@ <h1>Source code for fury.actors.tensor</h1><div class="highlight"><pre>
<span class="sd"> directly from estimated D and its estimated covariance matrix</span>
<span class="sd"> :math:`\\Delta D` (see [2]_, equation 4). The angle :math:`\\Theta`</span>
<span class="sd"> between the perturbed principal eigenvector of D,</span>
<span class="sd"> :math:`\\epsilon_1+\\Delta\\epsilon_1`, and the estimated eigenvector</span>
<span class="sd"> :math:`\\epsilon_1 + \\Delta\\epsilon_1`, and the estimated eigenvector</span>
<span class="sd"> :math:`\\epsilon_1`, measures the angular deviation of the main fiber</span>
<span class="sd"> direction and can be approximated by:</span>

<span class="sd"> .. math::</span>
<span class="sd"> \\Theta=tan^{-1}(\\|\\Delta\\epsilon_1\\|)</span>
<span class="sd"> \\Theta = tan^{-1}(\\|\\Delta \\ epsilon_1\\|)</span>

<span class="sd"> Giving way to a graphical construct for displaying both the main</span>
<span class="sd"> eigenvector of D and its associated uncertainty, with the so-called</span>
Expand All @@ -818,13 +822,13 @@ <h1>Source code for fury.actors.tensor</h1><div class="highlight"><pre>
<span class="sd"> References</span>
<span class="sd"> ----------</span>
<span class="sd"> .. [1] Basser, P. J. (1997). Quantifying errors in fiber direction and</span>
<span class="sd"> diffusion tensor field maps resulting from MR noise. In 5th Scientific</span>
<span class="sd"> Meeting of the ISMRM (Vol. 1740).</span>
<span class="sd"> diffusion tensor field maps resulting from MR noise. In 5th Scientific</span>
<span class="sd"> Meeting of the ISMRM (Vol. 1740).</span>

<span class="sd"> .. [2] Chang, L. C., Koay, C. G., Pierpaoli, C., &amp; Basser, P. J. (2007).</span>
<span class="sd"> Variance of estimated DTI-derived parameters via first-order perturbation</span>
<span class="sd"> methods. Magnetic Resonance in Medicine: An Official Journal of the</span>
<span class="sd"> International Society for Magnetic Resonance in Medicine, 57(1), 141-149.</span>
<span class="sd"> Variance of estimated DTI-derived parameters via first-order perturbation</span>
<span class="sd"> methods. Magnetic Resonance in Medicine: An Official Journal of the</span>
<span class="sd"> International Society for Magnetic Resonance in Medicine, 57(1), 141-149.</span>

<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">angles</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="n">evecs</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
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