Add changes for c67897d

_sources/api_cxx.rst.txt

@@ -10,40 +10,60 @@ C++ API Reference
    :hidden:
 
    api_cxx/CartesianTrajectory.rst
-   api_cxx/CartesianTrajectoryView.rst
+   api_cxx/CudaContext.rst
+   api_cxx/FISPSequence.rst
    api_cxx/SimulateSignalMethod.rst
    api_cxx/SpiralTrajectory.rst
+   api_cxx/TissueParameterField.rst
+   api_cxx/TissueParameters.rst
+   api_cxx/Trajectory.rst
+   api_cxx/compute_jacobian.rst
+   api_cxx/compute_jacobian_hermitian.rst
    api_cxx/compute_residual.rst
    api_cxx/magnetization_to_signal.rst
-   api_cxx/make_cartesian_trajectory.rst
-   api_cxx/make_spiral_trajectory.rst
+   api_cxx/pSSFPSequence.rst
    api_cxx/phase_encoding.rst
-   api_cxx/prephaser.rst
-   api_cxx/rewind.rst
+   api_cxx/simulate_magnetization.rst
+   api_cxx/simulate_magnetization_derivative.rst
 
 .. raw:: html
 
-   <h2>Cartesian trajectories</h2>
+   <h2>Data structures</h2>
 
+* :doc:`CudaContext <api_cxx/CudaContext>`
+* :doc:`TissueParameterField <api_cxx/TissueParameterField>`
+* :doc:`TissueParameters <api_cxx/TissueParameters>`
+
+.. raw:: html
+
+   <h2>Jacobian computation</h2>
+
+* :doc:`compute_jacobian <api_cxx/compute_jacobian>`
+* :doc:`compute_jacobian_hermitian <api_cxx/compute_jacobian_hermitian>`
+
+.. raw:: html
+
+   <h2>Trajectories</h2>
+
+* :doc:`Trajectory <api_cxx/Trajectory>`
 * :doc:`CartesianTrajectory <api_cxx/CartesianTrajectory>`
-* :doc:`CartesianTrajectoryView <api_cxx/CartesianTrajectoryView>`
-* :doc:`make_cartesian_trajectory <api_cxx/make_cartesian_trajectory>`
-* :doc:`rewind <api_cxx/rewind>`
-* :doc:`prephaser <api_cxx/prephaser>`
-* :doc:`phase_encoding <api_cxx/phase_encoding>`
+* :doc:`SpiralTrajectory <api_cxx/SpiralTrajectory>`
 * :doc:`SimulateSignalMethod <api_cxx/SimulateSignalMethod>`
 * :doc:`magnetization_to_signal <api_cxx/magnetization_to_signal>`
+* :doc:`phase_encoding <api_cxx/phase_encoding>`
 
 .. raw:: html
 
-   <h2>Spiral trajectories</h2>
+   <h2>Sequences</h2>
 
-* :doc:`SpiralTrajectory <api_cxx/SpiralTrajectory>`
-* :doc:`make_spiral_trajectory <api_cxx/make_spiral_trajectory>`
+* :doc:`FISPSequence <api_cxx/FISPSequence>`
+* :doc:`pSSFPSequence <api_cxx/pSSFPSequence>`
+* :doc:`simulate_magnetization <api_cxx/simulate_magnetization>`
+* :doc:`simulate_magnetization_derivative <api_cxx/simulate_magnetization_derivative>`
 
 .. raw:: html
 
-   <h2>utils</h2>
+   <h2>Utilities</h2>
 
 * :doc:`compute_residual <api_cxx/compute_residual>`
 

_sources/api_cxx/prephaser.rst.txt → _sources/api_cxx/CudaContext.rst.txt

@@ -3,8 +3,8 @@
   This file has been auto-generated. DO NOT MODIFY ITS CONTENT
   ============================================================
 
-.. _prephaser:
+.. _CudaContext:
 
-prephaser
-=========
-.. doxygenfunction:: compas::prephaser
+CudaContext
+===========
+.. doxygenclass:: compas::CudaContext

_sources/api_cxx/CartesianTrajectoryView.rst.txt → _sources/api_cxx/FISPSequence.rst.txt

@@ -3,8 +3,8 @@
   This file has been auto-generated. DO NOT MODIFY ITS CONTENT
   ============================================================
 
-.. _CartesianTrajectoryView:
+.. _FISPSequence:
 
-CartesianTrajectoryView
-=======================
-.. doxygenclass:: compas::CartesianTrajectoryView
+FISPSequence
+============
+.. doxygenclass:: compas::FISPSequence

_sources/api_cxx/TissueParameterField.rst.txt

@@ -0,0 +1,10 @@
+..
+  ============================================================
+  This file has been auto-generated. DO NOT MODIFY ITS CONTENT
+  ============================================================
+
+.. _TissueParameterField:
+
+TissueParameterField
+====================
+.. doxygenclass:: compas::TissueParameterField

_sources/api_cxx/TissueParameters.rst.txt

@@ -0,0 +1,10 @@
+..
+  ============================================================
+  This file has been auto-generated. DO NOT MODIFY ITS CONTENT
+  ============================================================
+
+.. _TissueParameters:
+
+TissueParameters
+================
+.. doxygenclass:: compas::TissueParameters

_sources/api_cxx/rewind.rst.txt → _sources/api_cxx/Trajectory.rst.txt

@@ -3,8 +3,8 @@
   This file has been auto-generated. DO NOT MODIFY ITS CONTENT
   ============================================================
 
-.. _rewind:
+.. _Trajectory:
 
-rewind
-======
-.. doxygenfunction:: compas::rewind
+Trajectory
+==========
+.. doxygenclass:: compas::Trajectory

_sources/api_cxx/compute_jacobian.rst.txt

@@ -0,0 +1,10 @@
+..
+  ============================================================
+  This file has been auto-generated. DO NOT MODIFY ITS CONTENT
+  ============================================================
+
+.. _compute_jacobian:
+
+compute_jacobian
+================
+.. doxygenfunction:: compas::compute_jacobian

_sources/api_cxx/make_cartesian_trajectory.rst.txt → _sources/api_cxx/compute_jacobian_hermitian.rst.txt

@@ -3,8 +3,8 @@
   This file has been auto-generated. DO NOT MODIFY ITS CONTENT
   ============================================================
 
-.. _make_cartesian_trajectory:
+.. _compute_jacobian_hermitian:
 
-make_cartesian_trajectory
-=========================
-.. doxygenfunction:: compas::make_cartesian_trajectory
+compute_jacobian_hermitian
+==========================
+.. doxygenfunction:: compas::compute_jacobian_hermitian

_sources/api_cxx/pSSFPSequence.rst.txt

@@ -0,0 +1,10 @@
+..
+  ============================================================
+  This file has been auto-generated. DO NOT MODIFY ITS CONTENT
+  ============================================================
+
+.. _pSSFPSequence:
+
+pSSFPSequence
+=============
+.. doxygenfunction:: compas::pSSFPSequence

_sources/api_cxx/make_spiral_trajectory.rst.txt → _sources/api_cxx/simulate_magnetization.rst.txt

@@ -3,8 +3,8 @@
   This file has been auto-generated. DO NOT MODIFY ITS CONTENT
   ============================================================
 
-.. _make_spiral_trajectory:
+.. _simulate_magnetization:
 
-make_spiral_trajectory
+simulate_magnetization
 ======================
-.. doxygenfunction:: compas::make_spiral_trajectory
+.. doxygenfunction:: compas::simulate_magnetization

_sources/api_cxx/simulate_magnetization_derivative.rst.txt

@@ -0,0 +1,10 @@
+..
+  ============================================================
+  This file has been auto-generated. DO NOT MODIFY ITS CONTENT
+  ============================================================
+
+.. _simulate_magnetization_derivative:
+
+simulate_magnetization_derivative
+=================================
+.. doxygenfunction:: compas::simulate_magnetization_derivative

api_cxx.html

@@ -51,16 +51,21 @@
 <li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">C++ API Reference</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="api_cxx/CartesianTrajectory.html">CartesianTrajectory</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api_cxx/CartesianTrajectoryView.html">CartesianTrajectoryView</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/CudaContext.html">CudaContext</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/FISPSequence.html">FISPSequence</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api_cxx/SimulateSignalMethod.html">SimulateSignalMethod</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api_cxx/SpiralTrajectory.html">SpiralTrajectory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/TissueParameterField.html">TissueParameterField</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/TissueParameters.html">TissueParameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/Trajectory.html">Trajectory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/compute_jacobian.html">compute_jacobian</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/compute_jacobian_hermitian.html">compute_jacobian_hermitian</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api_cxx/compute_residual.html">compute_residual</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api_cxx/magnetization_to_signal.html">magnetization_to_signal</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api_cxx/make_cartesian_trajectory.html">make_cartesian_trajectory</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api_cxx/make_spiral_trajectory.html">make_spiral_trajectory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/pSSFPSequence.html">pSSFPSequence</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api_cxx/phase_encoding.html">phase_encoding</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api_cxx/prephaser.html">prephaser</a></li>
-<li class="toctree-l2"><a class="reference internal" href="api_cxx/rewind.html">rewind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/simulate_magnetization.html">simulate_magnetization</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api_cxx/simulate_magnetization_derivative.html">simulate_magnetization_derivative</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference external" href="https://nlesc-compas.github.io/compas-toolkit/api_julia">Julia API</a></li>
@@ -95,21 +100,30 @@
 <h1>C++ API Reference<a class="headerlink" href="#c-api-reference" title="Permalink to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 </div>
-<h2>Cartesian trajectories</h2><ul class="simple">
+<h2>Data structures</h2><ul class="simple">
+<li><p><a class="reference internal" href="api_cxx/CudaContext.html"><span class="doc">CudaContext</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/TissueParameterField.html"><span class="doc">TissueParameterField</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/TissueParameters.html"><span class="doc">TissueParameters</span></a></p></li>
+</ul>
+<h2>Jacobian computation</h2><ul class="simple">
+<li><p><a class="reference internal" href="api_cxx/compute_jacobian.html"><span class="doc">compute_jacobian</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/compute_jacobian_hermitian.html"><span class="doc">compute_jacobian_hermitian</span></a></p></li>
+</ul>
+<h2>Trajectories</h2><ul class="simple">
+<li><p><a class="reference internal" href="api_cxx/Trajectory.html"><span class="doc">Trajectory</span></a></p></li>
 <li><p><a class="reference internal" href="api_cxx/CartesianTrajectory.html"><span class="doc">CartesianTrajectory</span></a></p></li>
-<li><p><a class="reference internal" href="api_cxx/CartesianTrajectoryView.html"><span class="doc">CartesianTrajectoryView</span></a></p></li>
-<li><p><a class="reference internal" href="api_cxx/make_cartesian_trajectory.html"><span class="doc">make_cartesian_trajectory</span></a></p></li>
-<li><p><a class="reference internal" href="api_cxx/rewind.html"><span class="doc">rewind</span></a></p></li>
-<li><p><a class="reference internal" href="api_cxx/prephaser.html"><span class="doc">prephaser</span></a></p></li>
-<li><p><a class="reference internal" href="api_cxx/phase_encoding.html"><span class="doc">phase_encoding</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/SpiralTrajectory.html"><span class="doc">SpiralTrajectory</span></a></p></li>
 <li><p><a class="reference internal" href="api_cxx/SimulateSignalMethod.html"><span class="doc">SimulateSignalMethod</span></a></p></li>
 <li><p><a class="reference internal" href="api_cxx/magnetization_to_signal.html"><span class="doc">magnetization_to_signal</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/phase_encoding.html"><span class="doc">phase_encoding</span></a></p></li>
 </ul>
-<h2>Spiral trajectories</h2><ul class="simple">
-<li><p><a class="reference internal" href="api_cxx/SpiralTrajectory.html"><span class="doc">SpiralTrajectory</span></a></p></li>
-<li><p><a class="reference internal" href="api_cxx/make_spiral_trajectory.html"><span class="doc">make_spiral_trajectory</span></a></p></li>
+<h2>Sequences</h2><ul class="simple">
+<li><p><a class="reference internal" href="api_cxx/FISPSequence.html"><span class="doc">FISPSequence</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/pSSFPSequence.html"><span class="doc">pSSFPSequence</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/simulate_magnetization.html"><span class="doc">simulate_magnetization</span></a></p></li>
+<li><p><a class="reference internal" href="api_cxx/simulate_magnetization_derivative.html"><span class="doc">simulate_magnetization_derivative</span></a></p></li>
 </ul>
-<h2>utils</h2><ul class="simple">
+<h2>Utilities</h2><ul class="simple">
 <li><p><a class="reference internal" href="api_cxx/compute_residual.html"><span class="doc">compute_residual</span></a></p></li>
 </ul>
 </section>

api_cxx/CartesianTrajectory.html

@@ -22,7 +22,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="CartesianTrajectoryView" href="CartesianTrajectoryView.html" />
+    <link rel="next" title="CudaContext" href="CudaContext.html" />
     <link rel="prev" title="C++ API Reference" href="../api_cxx.html" /> 
 </head>
 
@@ -51,16 +51,21 @@
 <li class="toctree-l1"><a class="reference internal" href="../install.html">Installation</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="../api_cxx.html">C++ API Reference</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">CartesianTrajectory</a></li>
-<li class="toctree-l2"><a class="reference internal" href="CartesianTrajectoryView.html">CartesianTrajectoryView</a></li>
+<li class="toctree-l2"><a class="reference internal" href="CudaContext.html">CudaContext</a></li>
+<li class="toctree-l2"><a class="reference internal" href="FISPSequence.html">FISPSequence</a></li>
 <li class="toctree-l2"><a class="reference internal" href="SimulateSignalMethod.html">SimulateSignalMethod</a></li>
 <li class="toctree-l2"><a class="reference internal" href="SpiralTrajectory.html">SpiralTrajectory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TissueParameterField.html">TissueParameterField</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TissueParameters.html">TissueParameters</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Trajectory.html">Trajectory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compute_jacobian.html">compute_jacobian</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compute_jacobian_hermitian.html">compute_jacobian_hermitian</a></li>
 <li class="toctree-l2"><a class="reference internal" href="compute_residual.html">compute_residual</a></li>
 <li class="toctree-l2"><a class="reference internal" href="magnetization_to_signal.html">magnetization_to_signal</a></li>
-<li class="toctree-l2"><a class="reference internal" href="make_cartesian_trajectory.html">make_cartesian_trajectory</a></li>
-<li class="toctree-l2"><a class="reference internal" href="make_spiral_trajectory.html">make_spiral_trajectory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pSSFPSequence.html">pSSFPSequence</a></li>
 <li class="toctree-l2"><a class="reference internal" href="phase_encoding.html">phase_encoding</a></li>
-<li class="toctree-l2"><a class="reference internal" href="prephaser.html">prephaser</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rewind.html">rewind</a></li>
+<li class="toctree-l2"><a class="reference internal" href="simulate_magnetization.html">simulate_magnetization</a></li>
+<li class="toctree-l2"><a class="reference internal" href="simulate_magnetization_derivative.html">simulate_magnetization_derivative</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference external" href="https://nlesc-compas.github.io/compas-toolkit/api_julia">Julia API</a></li>
@@ -105,7 +110,7 @@
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="../api_cxx.html" class="btn btn-neutral float-left" title="C++ API Reference" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="CartesianTrajectoryView.html" class="btn btn-neutral float-right" title="CartesianTrajectoryView" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="CudaContext.html" class="btn btn-neutral float-right" title="CudaContext" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
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