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2 changes: 1 addition & 1 deletion dev/.buildinfo
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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: 6c9ad1ae986602f0af06055a37d240c7
config: 4edfca56412c81896c5a2169bc25f523
tags: 645f666f9bcd5a90fca523b33c5a78b7
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40 changes: 20 additions & 20 deletions dev/_sources/sg_execution_times.rst.txt
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Computation times
=================
**14:16.145** total execution time for 10 files **from all galleries**:
**00:00.000** total execution time for 10 files **from all galleries**:

.. container::

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* - Example
- Time
- Mem (MB)
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_beta.py` (``../examples/workflows/plot_simulate_beta.py``)
- 03:15.930
* - :ref:`sphx_glr_auto_examples_howto_optimize_evoked.py` (``../examples/howto/optimize_evoked.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_somato.py` (``../examples/workflows/plot_simulate_somato.py``)
- 03:14.176
* - :ref:`sphx_glr_auto_examples_howto_plot_connectivity.py` (``../examples/howto/plot_connectivity.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_gamma.py` (``../examples/workflows/plot_simulate_gamma.py``)
- 02:06.590
* - :ref:`sphx_glr_auto_examples_howto_plot_firing_pattern.py` (``../examples/howto/plot_firing_pattern.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_alpha.py` (``../examples/workflows/plot_simulate_alpha.py``)
- 01:37.907
* - :ref:`sphx_glr_auto_examples_howto_plot_record_extracellular_potentials.py` (``../examples/howto/plot_record_extracellular_potentials.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_howto_plot_connectivity.py` (``../examples/howto/plot_connectivity.py``)
- 01:28.336
* - :ref:`sphx_glr_auto_examples_howto_plot_simulate_mpi_backend.py` (``../examples/howto/plot_simulate_mpi_backend.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_evoked.py` (``../examples/workflows/plot_simulate_evoked.py``)
- 01:02.795
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_alpha.py` (``../examples/workflows/plot_simulate_alpha.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_howto_plot_record_extracellular_potentials.py` (``../examples/howto/plot_record_extracellular_potentials.py``)
- 00:36.745
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_beta.py` (``../examples/workflows/plot_simulate_beta.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_howto_plot_firing_pattern.py` (``../examples/howto/plot_firing_pattern.py``)
- 00:31.276
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_evoked.py` (``../examples/workflows/plot_simulate_evoked.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_howto_plot_simulate_mpi_backend.py` (``../examples/howto/plot_simulate_mpi_backend.py``)
- 00:22.390
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_gamma.py` (``../examples/workflows/plot_simulate_gamma.py``)
- 00:00.000
- 0.0
* - :ref:`sphx_glr_auto_examples_howto_optimize_evoked.py` (``../examples/howto/optimize_evoked.py``)
* - :ref:`sphx_glr_auto_examples_workflows_plot_simulate_somato.py` (``../examples/workflows/plot_simulate_somato.py``)
- 00:00.000
- 0.0
9 changes: 1 addition & 8 deletions dev/generated/hnn_core.CellResponse.html
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<li><a class="reference internal" href="#hnn_core.CellResponse.write"><code class="docutils literal notranslate"><span class="pre">CellResponse.write()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#examples-using-hnn-core-cellresponse">Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.CellResponse</span></code></a></li>
</ul>
</li>
</ul>
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</dd></dl>

<section id="examples-using-hnn-core-cellresponse">
<span id="sphx-glr-backreferences-hnn-core-cellresponse"></span><h2>Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.CellResponse</span></code><a class="headerlink" href="#examples-using-hnn-core-cellresponse" title="Permalink to this heading"></a></h2>
<div class="sphx-glr-thumbnails"><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to inspect the firing pattern of cells in the HNN model."><img alt="" src="../_images/sphx_glr_plot_firing_pattern_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_firing_pattern.html#sphx-glr-auto-examples-howto-plot-firing-pattern-py"><span class="std std-ref">01. Plot firing pattern</span></a></p>
<div class="sphx-glr-thumbnail-title">01. Plot firing pattern</div>
</div></div></section>
</section>
<span class="target" id="sphx-glr-backreferences-hnn-core-cellresponse"></span></section>


</div>
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33 changes: 1 addition & 32 deletions dev/generated/hnn_core.Network.html
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<li><a class="reference internal" href="#hnn_core.Network.write"><code class="docutils literal notranslate"><span class="pre">Network.write()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#examples-using-hnn-core-network">Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.Network</span></code></a></li>
</ul>
</li>
</ul>
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</dd></dl>

<section id="examples-using-hnn-core-network">
<span id="sphx-glr-backreferences-hnn-core-network"></span><h2>Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.Network</span></code><a class="headerlink" href="#examples-using-hnn-core-network" title="Permalink to this heading"></a></h2>
<div class="sphx-glr-thumbnails"><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate a threshold level tactile evoked response, as detaile..."><img alt="" src="../_images/sphx_glr_plot_simulate_evoked_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_evoked.html#sphx-glr-auto-examples-workflows-plot-simulate-evoked-py"><span class="std std-ref">01. Simulate Event Related Potentials (ERPs)</span></a></p>
<div class="sphx-glr-thumbnail-title">01. Simulate Event Related Potentials (ERPs)</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate alpha and beta frequency activity in the alpha/beta c..."><img alt="" src="../_images/sphx_glr_plot_simulate_alpha_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_alpha.html#sphx-glr-auto-examples-workflows-plot-simulate-alpha-py"><span class="std std-ref">02. Simulate Alpha and Beta Rhythms</span></a></p>
<div class="sphx-glr-thumbnail-title">02. Simulate Alpha and Beta Rhythms</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate gamma rhythms via the well established pyramidal-inte..."><img alt="" src="../_images/sphx_glr_plot_simulate_gamma_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_gamma.html#sphx-glr-auto-examples-workflows-plot-simulate-gamma-py"><span class="std std-ref">03. Simulate Gamma Rhythms</span></a></p>
<div class="sphx-glr-thumbnail-title">03. Simulate Gamma Rhythms</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to calculate an inverse solution of the median nerve evoked respo..."><img alt="" src="../_images/sphx_glr_plot_simulate_somato_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_somato.html#sphx-glr-auto-examples-workflows-plot-simulate-somato-py"><span class="std std-ref">04. From MEG sensor-space data to HNN simulation</span></a></p>
<div class="sphx-glr-thumbnail-title">04. From MEG sensor-space data to HNN simulation</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how event related potentials (ERP) are modulated by prestimulus beta ..."><img alt="" src="../_images/sphx_glr_plot_simulate_beta_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_beta.html#sphx-glr-auto-examples-workflows-plot-simulate-beta-py"><span class="std std-ref">05. Simulate beta modulated ERP</span></a></p>
<div class="sphx-glr-thumbnail-title">05. Simulate beta modulated ERP</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to inspect the firing pattern of cells in the HNN model."><img alt="" src="../_images/sphx_glr_plot_firing_pattern_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_firing_pattern.html#sphx-glr-auto-examples-howto-plot-firing-pattern-py"><span class="std std-ref">01. Plot firing pattern</span></a></p>
<div class="sphx-glr-thumbnail-title">01. Plot firing pattern</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="The main output of HNN simulations is the &#x27;dipole&#x27; waveform, i.e., the net intracellular curren..."><img alt="" src="../_images/sphx_glr_plot_record_extracellular_potentials_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_record_extracellular_potentials.html#sphx-glr-auto-examples-howto-plot-record-extracellular-potentials-py"><span class="std std-ref">02. Record extracellular potentials</span></a></p>
<div class="sphx-glr-thumbnail-title">02. Record extracellular potentials</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to modify the network connectivity."><img alt="" src="../_images/sphx_glr_plot_connectivity_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_connectivity.html#sphx-glr-auto-examples-howto-plot-connectivity-py"><span class="std std-ref">03. Modifying local connectivity</span></a></p>
<div class="sphx-glr-thumbnail-title">03. Modifying local connectivity</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use the MPI backend for simulating dipoles using HNN-core."><img alt="" src="../_images/sphx_glr_plot_simulate_mpi_backend_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_simulate_mpi_backend.html#sphx-glr-auto-examples-howto-plot-simulate-mpi-backend-py"><span class="std std-ref">04. Use MPI backend for parallelization</span></a></p>
<div class="sphx-glr-thumbnail-title">04. Use MPI backend for parallelization</div>
</div></div></section>
</section>
<span class="target" id="sphx-glr-backreferences-hnn-core-network"></span></section>


</div>
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29 changes: 1 addition & 28 deletions dev/generated/hnn_core.jones_2009_model.html
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Expand Up @@ -199,34 +199,7 @@ <h1>hnn_core.jones_2009_model<a class="headerlink" href="#hnn-core-jones-2009-mo

<section id="examples-using-hnn-core-jones-2009-model">
<span id="sphx-glr-backreferences-hnn-core-jones-2009-model"></span><h2>Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.jones_2009_model</span></code><a class="headerlink" href="#examples-using-hnn-core-jones-2009-model" title="Permalink to this heading"></a></h2>
<div class="sphx-glr-thumbnails"><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate a threshold level tactile evoked response, as detaile..."><img alt="" src="../_images/sphx_glr_plot_simulate_evoked_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_evoked.html#sphx-glr-auto-examples-workflows-plot-simulate-evoked-py"><span class="std std-ref">01. Simulate Event Related Potentials (ERPs)</span></a></p>
<div class="sphx-glr-thumbnail-title">01. Simulate Event Related Potentials (ERPs)</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate alpha and beta frequency activity in the alpha/beta c..."><img alt="" src="../_images/sphx_glr_plot_simulate_alpha_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_alpha.html#sphx-glr-auto-examples-workflows-plot-simulate-alpha-py"><span class="std std-ref">02. Simulate Alpha and Beta Rhythms</span></a></p>
<div class="sphx-glr-thumbnail-title">02. Simulate Alpha and Beta Rhythms</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to simulate gamma rhythms via the well established pyramidal-inte..."><img alt="" src="../_images/sphx_glr_plot_simulate_gamma_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_gamma.html#sphx-glr-auto-examples-workflows-plot-simulate-gamma-py"><span class="std std-ref">03. Simulate Gamma Rhythms</span></a></p>
<div class="sphx-glr-thumbnail-title">03. Simulate Gamma Rhythms</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to calculate an inverse solution of the median nerve evoked respo..."><img alt="" src="../_images/sphx_glr_plot_simulate_somato_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_somato.html#sphx-glr-auto-examples-workflows-plot-simulate-somato-py"><span class="std std-ref">04. From MEG sensor-space data to HNN simulation</span></a></p>
<div class="sphx-glr-thumbnail-title">04. From MEG sensor-space data to HNN simulation</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how event related potentials (ERP) are modulated by prestimulus beta ..."><img alt="" src="../_images/sphx_glr_plot_simulate_beta_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_beta.html#sphx-glr-auto-examples-workflows-plot-simulate-beta-py"><span class="std std-ref">05. Simulate beta modulated ERP</span></a></p>
<div class="sphx-glr-thumbnail-title">05. Simulate beta modulated ERP</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to inspect the firing pattern of cells in the HNN model."><img alt="" src="../_images/sphx_glr_plot_firing_pattern_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_firing_pattern.html#sphx-glr-auto-examples-howto-plot-firing-pattern-py"><span class="std std-ref">01. Plot firing pattern</span></a></p>
<div class="sphx-glr-thumbnail-title">01. Plot firing pattern</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="The main output of HNN simulations is the &#x27;dipole&#x27; waveform, i.e., the net intracellular curren..."><img alt="" src="../_images/sphx_glr_plot_record_extracellular_potentials_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_record_extracellular_potentials.html#sphx-glr-auto-examples-howto-plot-record-extracellular-potentials-py"><span class="std std-ref">02. Record extracellular potentials</span></a></p>
<div class="sphx-glr-thumbnail-title">02. Record extracellular potentials</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to modify the network connectivity."><img alt="" src="../_images/sphx_glr_plot_connectivity_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_connectivity.html#sphx-glr-auto-examples-howto-plot-connectivity-py"><span class="std std-ref">03. Modifying local connectivity</span></a></p>
<div class="sphx-glr-thumbnail-title">03. Modifying local connectivity</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use the MPI backend for simulating dipoles using HNN-core."><img alt="" src="../_images/sphx_glr_plot_simulate_mpi_backend_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_simulate_mpi_backend.html#sphx-glr-auto-examples-howto-plot-simulate-mpi-backend-py"><span class="std std-ref">04. Use MPI backend for parallelization</span></a></p>
<div class="sphx-glr-thumbnail-title">04. Use MPI backend for parallelization</div>
</div><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to optimize the parameters of the model simulation to match an ex..."><img alt="" src="../_images/sphx_glr_optimize_evoked_thumb.png" />
<div class="sphx-glr-thumbnails"><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to optimize the parameters of the model simulation to match an ex..."><img alt="" src="../_images/sphx_glr_optimize_evoked_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/optimize_evoked.html#sphx-glr-auto-examples-howto-optimize-evoked-py"><span class="std std-ref">05. Optimize simulated evoked response parameters</span></a></p>
<div class="sphx-glr-thumbnail-title">05. Optimize simulated evoked response parameters</div>
</div></div></section>
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9 changes: 1 addition & 8 deletions dev/generated/hnn_core.law_2021_model.html
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aria-labelledby="dLabelLocalToc"><ul>
<li><a class="reference internal" href="#">hnn_core.law_2021_model</a><ul>
<li><a class="reference internal" href="#hnn_core.law_2021_model"><code class="docutils literal notranslate"><span class="pre">law_2021_model()</span></code></a></li>
<li><a class="reference internal" href="#examples-using-hnn-core-law-2021-model">Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.law_2021_model</span></code></a></li>
</ul>
</li>
</ul>
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</div>
</dd></dl>

<section id="examples-using-hnn-core-law-2021-model">
<span id="sphx-glr-backreferences-hnn-core-law-2021-model"></span><h2>Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.law_2021_model</span></code><a class="headerlink" href="#examples-using-hnn-core-law-2021-model" title="Permalink to this heading"></a></h2>
<div class="sphx-glr-thumbnails"><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how event related potentials (ERP) are modulated by prestimulus beta ..."><img alt="" src="../_images/sphx_glr_plot_simulate_beta_thumb.png" />
<p><a class="reference internal" href="../auto_examples/workflows/plot_simulate_beta.html#sphx-glr-auto-examples-workflows-plot-simulate-beta-py"><span class="std std-ref">05. Simulate beta modulated ERP</span></a></p>
<div class="sphx-glr-thumbnail-title">05. Simulate beta modulated ERP</div>
</div></div></section>
</section>
<span class="target" id="sphx-glr-backreferences-hnn-core-law-2021-model"></span></section>


</div>
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9 changes: 1 addition & 8 deletions dev/generated/hnn_core.pick_connection.html
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aria-labelledby="dLabelLocalToc"><ul>
<li><a class="reference internal" href="#">hnn_core.pick_connection</a><ul>
<li><a class="reference internal" href="#hnn_core.pick_connection"><code class="docutils literal notranslate"><span class="pre">pick_connection()</span></code></a></li>
<li><a class="reference internal" href="#examples-using-hnn-core-pick-connection">Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.pick_connection</span></code></a></li>
</ul>
</li>
</ul>
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dendrites and have ampa receptors.</p>
</dd></dl>

<section id="examples-using-hnn-core-pick-connection">
<span id="sphx-glr-backreferences-hnn-core-pick-connection"></span><h2>Examples using <code class="docutils literal notranslate"><span class="pre">hnn_core.pick_connection</span></code><a class="headerlink" href="#examples-using-hnn-core-pick-connection" title="Permalink to this heading"></a></h2>
<div class="sphx-glr-thumbnails"><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to modify the network connectivity."><img alt="" src="../_images/sphx_glr_plot_connectivity_thumb.png" />
<p><a class="reference internal" href="../auto_examples/howto/plot_connectivity.html#sphx-glr-auto-examples-howto-plot-connectivity-py"><span class="std std-ref">03. Modifying local connectivity</span></a></p>
<div class="sphx-glr-thumbnail-title">03. Modifying local connectivity</div>
</div></div></section>
</section>
<span class="target" id="sphx-glr-backreferences-hnn-core-pick-connection"></span></section>


</div>
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