deploy: 3da396f

.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: 34d69c45f3ed376e594112896f0a9809
+config: cd9dd32d4568dc7bb4d3d9564ac694d2
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/intro.md

@@ -4,34 +4,10 @@ The purpose of these tutorials is to provide a comprehensive collection of examp
 
 ```{note}
 Most of the content of this tutorial has been created in the form of Jupyter Notebooks and throughout this workshop, we are going to use JupyterLab to execute and interact with the content prepared for this workshop. The JupyterLab interface is very easy to use, but should you wish to learn more about the Jupyter project and the tools it provides, visit: [https://jupyter.org](https://jupyter.org).
-```
-
-## How to Get Started
-For the duration of this workshop, all participants will be able to run the tutorials on compute resources at NERSC. In preparation for the workshop, you should have already been asked to register for a training account and should hopefully have your login credentials ready.
-
-In a browser, go to [https://jupyter.nersc.gov](https://jupyter.nersc.gov) and login with your personal training account credentials. Once your resources are allocated, you should see a JupyterLab interface looking like this
-
-```{figure} ./jupyter_hub.PNG
-:name: jupyterlab
-
-```
-
-
-First, we need to clone the GitHub repository containing all the tutorials into the ```$HOME``` directory by a opening a terminal (click on "+" and then "Terminal") and executing this command:
-```bash
-git clone https://github.com/ptycho/tutorials.git
-```
-
-followed by running this set up command
-
-```bash
-/global/common/software/ntrain3/ptypy_workshop_setup.sh
-```
-
-Now that we have cloned the tutorials and set up the correct environment, we can simply navigate to ```tutorials``` in the file panel on the left and open the [first tutorial](./notebooks/01_05_Getting_Started_with_PtyPy/1_the_parameter_tree) from within the ```notebooks``` folder.
-
+``````
 
 ## How to use a Jupyter Notebook
+
 Before we get started with PtyPy, a few words about Jupyter Notebooks, which offer a convenient way to provide executable code (e.g. Python) alongside formatted text (using markdown). All notebooks used here are structured in the same way, with some informative content at the top and a full code example at the bottom, separated by a horizontal line:
 
 ```{figure} ./jupyter_notebook_1.PNG
@@ -45,7 +21,8 @@ In order to execute the code cell (or any other cell), simply select the cell an
 ```
 
 ## Table of Contents
+
 The content of this tutorial is structured into 6 different topics from beginner level to advanced topics:
 
 ```{tableofcontents}
-```
+```

intro.html

@@ -410,7 +410,6 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#how-to-get-started">How to Get Started</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#how-to-use-a-jupyter-notebook">How to use a Jupyter Notebook</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#table-of-contents">Table of Contents</a><ul class="nav section-nav flex-column">
 </ul>
@@ -433,23 +432,6 @@ <h1>Introduction<a class="headerlink" href="#introduction" title="Link to this h
 <p class="admonition-title">Note</p>
 <p>Most of the content of this tutorial has been created in the form of Jupyter Notebooks and throughout this workshop, we are going to use JupyterLab to execute and interact with the content prepared for this workshop. The JupyterLab interface is very easy to use, but should you wish to learn more about the Jupyter project and the tools it provides, visit: <a class="reference external" href="https://jupyter.org">https://jupyter.org</a>.</p>
 </div>
-<section id="how-to-get-started">
-<h2>How to Get Started<a class="headerlink" href="#how-to-get-started" title="Link to this heading">#</a></h2>
-<p>For the duration of this workshop, all participants will be able to run the tutorials on compute resources at NERSC. In preparation for the workshop, you should have already been asked to register for a training account and should hopefully have your login credentials ready.</p>
-<p>In a browser, go to <a class="reference external" href="https://jupyter.nersc.gov">https://jupyter.nersc.gov</a> and login with your personal training account credentials. Once your resources are allocated, you should see a JupyterLab interface looking like this</p>
-<figure class="align-default" id="jupyterlab">
-<img alt="_images/jupyter_hub.PNG" src="_images/jupyter_hub.PNG" />
-</figure>
-<p>First, we need to clone the GitHub repository containing all the tutorials into the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory by a opening a terminal (click on “+” and then “Terminal”) and executing this command:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/ptycho/tutorials.git
-</pre></div>
-</div>
-<p>followed by running this set up command</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>/global/common/software/ntrain3/ptypy_workshop_setup.sh
-</pre></div>
-</div>
-<p>Now that we have cloned the tutorials and set up the correct environment, we can simply navigate to <code class="docutils literal notranslate"><span class="pre">tutorials</span></code> in the file panel on the left and open the <a class="reference internal" href="notebooks/01_05_Getting_Started_with_PtyPy/1_the_parameter_tree.html"><span class="doc std std-doc">first tutorial</span></a> from within the <code class="docutils literal notranslate"><span class="pre">notebooks</span></code> folder.</p>
-</section>
 <section id="how-to-use-a-jupyter-notebook">
 <h2>How to use a Jupyter Notebook<a class="headerlink" href="#how-to-use-a-jupyter-notebook" title="Link to this heading">#</a></h2>
 <p>Before we get started with PtyPy, a few words about Jupyter Notebooks, which offer a convenient way to provide executable code (e.g. Python) alongside formatted text (using markdown). All notebooks used here are structured in the same way, with some informative content at the top and a full code example at the bottom, separated by a horizontal line:</p>
@@ -568,7 +550,6 @@ <h2>Table of Contents<a class="headerlink" href="#table-of-contents" title="Link
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#how-to-get-started">How to Get Started</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#how-to-use-a-jupyter-notebook">How to use a Jupyter Notebook</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#table-of-contents">Table of Contents</a><ul class="nav section-nav flex-column">
 </ul>

notebooks/01_05_Getting_Started_with_PtyPy/1_the_parameter_tree.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/01_05_Getting_Started_with_PtyPy/1_the_parameter_tree.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/01_05_Getting_Started_with_PtyPy/1_the_parameter_tree.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/01_05_Getting_Started_with_PtyPy/2_yaml_json_config.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/01_05_Getting_Started_with_PtyPy/2_yaml_json_config.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/01_05_Getting_Started_with_PtyPy/2_yaml_json_config.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/01_05_Getting_Started_with_PtyPy/3_input_output.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/01_05_Getting_Started_with_PtyPy/3_input_output.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/01_05_Getting_Started_with_PtyPy/3_input_output.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/01_05_Getting_Started_with_PtyPy/4_scan_models.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/01_05_Getting_Started_with_PtyPy/4_scan_models.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/01_05_Getting_Started_with_PtyPy/4_scan_models.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/01_05_Getting_Started_with_PtyPy/5_reconstruction_engines.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/01_05_Getting_Started_with_PtyPy/5_reconstruction_engines.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/01_05_Getting_Started_with_PtyPy/5_reconstruction_engines.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/06_09_From_Data_to_Reconstruction/6_the_hdf5_loader.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/06_09_From_Data_to_Reconstruction/6_the_hdf5_loader.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/06_09_From_Data_to_Reconstruction/6_the_hdf5_loader.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/06_09_From_Data_to_Reconstruction/7_working_with_electron_data.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/06_09_From_Data_to_Reconstruction/7_working_with_electron_data.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/06_09_From_Data_to_Reconstruction/7_working_with_electron_data.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/06_09_From_Data_to_Reconstruction/8_chaining_multiple_engines.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/06_09_From_Data_to_Reconstruction/8_chaining_multiple_engines.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/06_09_From_Data_to_Reconstruction/8_chaining_multiple_engines.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/06_09_From_Data_to_Reconstruction/9_fixing_data_issues.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/06_09_From_Data_to_Reconstruction/9_fixing_data_issues.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/06_09_From_Data_to_Reconstruction/9_fixing_data_issues.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/10_13_Processing_Large_Datasets/10_working_with_large_data.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/10_13_Processing_Large_Datasets/10_working_with_large_data.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/10_13_Processing_Large_Datasets/10_working_with_large_data.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/10_13_Processing_Large_Datasets/11_multi_gpu.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/10_13_Processing_Large_Datasets/11_multi_gpu.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/10_13_Processing_Large_Datasets/11_multi_gpu.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/10_13_Processing_Large_Datasets/12_start_from_previous_reconstruction.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/10_13_Processing_Large_Datasets/12_start_from_previous_reconstruction.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/10_13_Processing_Large_Datasets/12_start_from_previous_reconstruction.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/10_13_Processing_Large_Datasets/13_nearfield_ptychography.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/10_13_Processing_Large_Datasets/13_nearfield_ptychography.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/10_13_Processing_Large_Datasets/13_nearfield_ptychography.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/14_17_Working_with_Messy_Data/14_partial_coherence.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/14_17_Working_with_Messy_Data/14_partial_coherence.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/14_17_Working_with_Messy_Data/14_partial_coherence.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
    title="Launch onBinder"
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notebooks/14_17_Working_with_Messy_Data/15_position_refinement.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/14_17_Working_with_Messy_Data/15_position_refinement.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/14_17_Working_with_Messy_Data/15_position_refinement.ipynb" target="_blank"
    class="btn btn-sm dropdown-item"
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notebooks/14_17_Working_with_Messy_Data/16_testing_different_algorithms.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/14_17_Working_with_Messy_Data/16_testing_different_algorithms.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/14_17_Working_with_Messy_Data/16_testing_different_algorithms.ipynb" target="_blank"
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notebooks/14_17_Working_with_Messy_Data/17_missing_detector_frames.html

@@ -268,7 +268,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/14_17_Working_with_Messy_Data/17_missing_detector_frames.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/14_17_Working_with_Messy_Data/17_missing_detector_frames.ipynb" target="_blank"
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    data-bs-placement="left" data-bs-toggle="tooltip"

notebooks/18_21_Advanced_Topics/18_object_regularisation.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/18_21_Advanced_Topics/18_object_regularisation.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/18_21_Advanced_Topics/18_object_regularisation.ipynb" target="_blank"
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notebooks/18_21_Advanced_Topics/19_live_visualisation.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/18_21_Advanced_Topics/19_live_visualisation.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/18_21_Advanced_Topics/19_live_visualisation.ipynb" target="_blank"
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notebooks/18_21_Advanced_Topics/20_simulating_data.html

@@ -266,7 +266,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/18_21_Advanced_Topics/20_simulating_data.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/18_21_Advanced_Topics/20_simulating_data.ipynb" target="_blank"
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notebooks/18_21_Advanced_Topics/21_simulated_initial_probe.html

@@ -265,7 +265,7 @@
 
 
 
-      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/notebooks/18_21_Advanced_Topics/21_simulated_initial_probe.ipynb" target="_blank"
+      <li><a href="https://mybinder.org/v2/gh/ptycho/tutorials/main?urlpath=lab/tree/notebooks/18_21_Advanced_Topics/21_simulated_initial_probe.ipynb" target="_blank"
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    title="Launch onBinder"
    data-bs-placement="left" data-bs-toggle="tooltip"