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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: 7932d083f9a06fd5b7a85bfbbdbae04b
config: 749b8690b74b37f941c919029c99e5e5
tags: 645f666f9bcd5a90fca523b33c5a78b7
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15 changes: 8 additions & 7 deletions _sources/intro.md
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| [](notebooks/basic_examples/06_stochastic_engines) | No Data Required | - | - |
| [](notebooks/basic_examples/07_gradient_based_engines) | No Data Required | - | - |
| **Experimental X-ray Data** |
| [](notebooks/experimental_xray_data/00_data_loading) | [small_data.zip](https://zenodo.org/records/11501765/files/small_data.zip?download=1) | 126 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/00_data_loading) | [small_data.zip](https://zenodo.org/records/11501765/files/small_data.zip?download=1) | 126 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/01_working_with_large_data) | [dls_i08_nanogold_spiral.zip](https://zenodo.org/records/11501765/files/dls_i08_nanogold_spiral.zip?download=1) | 1.11 GB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/02_fixing_data_issues) | [small_data.zip](https://zenodo.org/records/11501765/files/small_data.zip?download=1) | 126 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/02_fixing_data_issues) | [small_data.zip](https://zenodo.org/records/11501765/files/small_data.zip?download=1) | 126 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/03_partial_coherence) | [dls_i08_nanogold_spiral.zip](https://zenodo.org/records/11501765/files/dls_i08_nanogold_spiral.zip?download=1) | 1.11 GB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/04_position_refinement) | [dls_i14_test_structure.zip](https://zenodo.org/records/11501765/files/dls_i14_test_structure.zip?download=1) | 3.68 GB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/04_position_refinement) | [dls_i14_test_structure.zip](https://zenodo.org/records/11501765/files/dls_i14_test_structure.zip?download=1) | 3.68 GB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/05_missing_detector_frames) | [dls_i08_nanogold_raster.zip](https://zenodo.org/records/11501765/files/dls_i08_nanogold_raster.zip?download=1) | 993 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/06_testing_different_algorithms) | [dls_i13_butterfly.zip](https://zenodo.org/records/11501765/files/dls_i13_butterfly.zip?download=1) | 286 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/06_testing_different_algorithms) | [dls_i13_butterfly.zip](https://zenodo.org/records/11501765/files/dls_i13_butterfly.zip?download=1) | 286 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/experimental_xray_data/07_multi_gpu) | [dls_i08_nanogold_spiral.zip](https://zenodo.org/records/11501765/files/dls_i08_nanogold_spiral.zip?download=1) | 1.11 GB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| **Electron Ptychography Data** |
| [](notebooks/ptychography_with_electrons/00_electron_data) | [dls_epsic_80kV_graphene.zip](https://zenodo.org/records/11501765/files/dls_epsic_80kV_graphene.zip?download=1) | 270 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
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| **Advanced Examples** |
| [](notebooks/supplementary_examples/00_nearfield_ptychography) | esrf_id16_AlNi_nearfield.zip | 532 MB | TBA |
| [](notebooks/supplementary_examples/01_object_regularisation) | esrf_id16_AlNi_nearfield.zip | 532 MB | TBA |
| [](notebooks/supplementary_examples/02_live_visualisation) | [dls_i08_nanogold_spiral.zip](https://zenodo.org/records/11501765/files/dls_i08_nanogold_spiral.zip?download=1) | 1.11 GB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/supplementary_examples/02_live_visualisation) | [dls_i08_nanogold_spiral.zip](https://zenodo.org/records/11501765/files/dls_i08_nanogold_spiral.zip?download=1) | 1.11 GB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| [](notebooks/supplementary_examples/03_simulating_data) | No Data Required | - | - |
| [](notebooks/supplementary_examples/04_modified_initial_probe) | [small_data.zip](https://zenodo.org/records/11501765/files/small_data.zip?download=1) | 126 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |

| [](notebooks/supplementary_examples/04_modified_initial_probe) | [small_data.zip](https://zenodo.org/records/11501765/files/small_data.zip?download=1) | 126 MB | [DOI](https://doi.org/10.5281/zenodo.11501765) |
| **User Examples** |
| [](notebooks/user_examples/00_template.ipynb) | - | - | - |

## Jupyter Lab/Notebooks

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{"cells": [{"cell_type": "markdown", "id": "b17cc207-0f09-4783-bc8b-271c9ffc4fdb", "metadata": {}, "source": ["# Title of user example\n", "\n", "**short description: what can be learned from this example?**"]}, {"cell_type": "markdown", "id": "d45589a1-6db7-4ea9-856b-4471b7cb2f55", "metadata": {}, "source": ["A longer description of what this example is about."]}, {"cell_type": "markdown", "id": "b9fdba5b-a01b-4849-b3ce-79d938be2525", "metadata": {}, "source": ["## The data\n", "\n", "| **Data file** | **Type** | **Download** | **Courtesy of** | **Reference** |\n", "| :- | :- | :- | :-: | :-: |\n", "| filename | Raw/Reconstruction etc. | [Link to download]() | Who to credit for providing the data | [DOI]() |\n", "\n", "Add a more detailed description of the data here, i.e. dimensions, meta parameters etc. "]}, {"cell_type": "markdown", "id": "bd29eb2c-6c2e-4a19-87a1-a4cac57f4fd5", "metadata": {}, "source": ["## Main body of tutorial\n", "\n", "Anything that adds value to this user example, i.e. background theory, highlighting certain parameters, explaining methods or pipelines, discussing challenges etc.\n", "\n", "You can use the MyST makrdown syntax, check this [cheatsheet](https://jupyterbook.org/en/stable/reference/cheatsheet.html) as a reference."]}, {"cell_type": "markdown", "id": "da74020a-6ead-4389-af38-94433bc44235", "metadata": {}, "source": ["## Admonitions\n", "\n", "The MyST syntax comes with [admonitions](https://jupyterbook.org/en/stable/reference/cheatsheet.html#admonitions) which can be useful to highlight certain things and give hints to users. \n", "To also render those admonitions nicely in plain jupyter notebooks, please use on of the following templates below. They use HTML which also renders in Jupyter notebooks, but when published they are converted to MyST admonitions by the Github actions pipeline."]}, {"cell_type": "markdown", "id": "13f8b2d2-ddb4-41a3-89ef-fdce4e470f77", "metadata": {}, "source": ["`````{admonition} Tip \n", ":class: tip\n", "Something useful</a>\n", "`````"]}, {"cell_type": "markdown", "id": "3a4b8a4d-c042-44a7-98ac-009dbe9ae2f8", "metadata": {}, "source": ["`````{admonition} Note \n", ":class: note\n", "A note with \n", "```python\nsome code\n", "```\n", "inside and <code>more code</code> inline.\n", "`````"]}, {"cell_type": "markdown", "id": "1e7d8f70-db57-4f46-acdf-2568dd116d03", "metadata": {}, "source": ["`````{admonition} Challenge \n", ":class: attention\n", "Provide some ideas for playing with and exploring this examples. \n", "`````"]}, {"cell_type": "markdown", "id": "45fe49ce-ba50-49f4-9404-cac09ea94817", "metadata": {}, "source": ["`````{admonition} Tip \n", ":class: tip\n", "Give some hints on how to get started with.\n", "`````"]}, {"cell_type": "markdown", "id": "9bed971f-2ac9-4ba0-94d6-b14e0dc0d442", "metadata": {}, "source": ["## Images\n", "\n", "For displaying any images, just upload into the _assets folder and then use \n", "\n", "```![](./_assets/some_image.png)```\n", "\n", "![](./_assets/some_image.png)"]}, {"cell_type": "markdown", "id": "7d4f0e99-2943-4e0e-bbcf-2cf342f0d167", "metadata": {}, "source": ["---"]}, {"cell_type": "code", "execution_count": null, "id": "1d7891fd-e0a0-4459-afac-43a68d1f5c22", "metadata": {"tags": []}, "outputs": [], "source": ["# Add full code of PtyPy run script here\n", "# ..."]}], "metadata": {"kernelspec": {"display_name": "PtyPy (cupy)", "language": "python", "name": "ptypy_cupy"}, "language_info": {"codemirror_mode": {"name": "ipython", "version": 3}, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.8"}}, "nbformat": 4, "nbformat_minor": 5}
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<li class="toctree-l1"><a class="reference internal" href="notebooks/supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="notebooks/user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="notebooks/supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="notebooks/supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="notebooks/user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<td class="text-center"><p>126 MB</p></td>
<td class="text-center"><p><a class="reference external" href="https://doi.org/10.5281/zenodo.11501765">DOI</a></p></td>
</tr>
<tr class="row-even"><td class="text-left"><p><strong>User Examples</strong></p></td>
<td class="text-left"><p></p></td>
<td class="text-center"><p></p></td>
<td class="text-center"><p></p></td>
</tr>
<tr class="row-odd"><td class="text-left"><p><a class="reference internal" href="notebooks/user_examples/00_template.html"><span class="std std-doc">Title of user example</span></a></p></td>
<td class="text-left"><p>-</p></td>
<td class="text-center"><p>-</p></td>
<td class="text-center"><p>-</p></td>
</tr>
</tbody>
</table>
</div>
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</div>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
</div>
</section>

<script type="text/x-thebe-config">
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
<br/>

</p>
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<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/02_live_visualisation.html">Live visualisation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/03_simulating_data.html">Simulating Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="../supplementary_examples/04_modified_initial_probe.html">Modified Initial Probe</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">User Examples</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../user_examples/00_template.html">Title of user example</a></li>
</ul>

</div>
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<p class="copyright">

© Copyright 2023.
© Copyright 2024.
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