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image-analysis-training-resources
Commit 35c1b4ec authored by Christian Tischer's avatar Christian Tischer
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Improve module layout

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    Gemfile.lock 0 → 100644
    View file @ 35c1b4ec
    GEM
    remote: https://rubygems.org/
    specs:
    addressable (2.6.0)
    public_suffix (>= 2.0.2, < 4.0)
    colorator (1.1.0)
    commonmarker (0.17.13)
    ruby-enum (~> 0.5)
    concurrent-ruby (1.1.5)
    ffi (1.11.1)
    forwardable-extended (2.6.0)
    i18n (1.6.0)
    concurrent-ruby (~> 1.0)
    jekyll (3.4.0)
    addressable (~> 2.4)
    colorator (~> 1.0)
    jekyll-sass-converter (~> 1.0)
    jekyll-watch (~> 1.1)
    kramdown (~> 1.3)
    liquid (~> 3.0)
    mercenary (~> 0.3.3)
    pathutil (~> 0.9)
    rouge (~> 1.7)
    safe_yaml (~> 1.0)
    jekyll-commonmark (1.2.0)
    commonmarker (~> 0.14)
    jekyll (>= 3.0, < 4.0)
    jekyll-commonmark-ghpages (0.1.0)
    commonmarker (~> 0.17.6)
    jekyll-commonmark (~> 1)
    jekyll-sass-converter (1.5.2)
    sass (~> 3.4)
    jekyll-watch (1.5.1)
    listen (~> 3.0)
    kramdown (1.17.0)
    liquid (3.0.6)
    listen (3.1.5)
    rb-fsevent (~> 0.9, >= 0.9.4)
    rb-inotify (~> 0.9, >= 0.9.7)
    ruby_dep (~> 1.2)
    mercenary (0.3.6)
    pathutil (0.16.2)
    forwardable-extended (~> 2.6)
    public_suffix (3.1.0)
    rb-fsevent (0.10.3)
    rb-inotify (0.10.0)
    ffi (~> 1.0)
    rouge (1.11.1)
    ruby-enum (0.7.2)
    i18n
    ruby_dep (1.5.0)
    safe_yaml (1.0.5)
    sass (3.7.4)
    sass-listen (~> 4.0.0)
    sass-listen (4.0.0)
    rb-fsevent (~> 0.9, >= 0.9.4)
    rb-inotify (~> 0.9, >= 0.9.7)
    PLATFORMS
    ruby
    DEPENDENCIES
    jekyll (= 3.4.0)
    jekyll-commonmark-ghpages
    tzinfo-data
    RUBY VERSION
    ruby 2.6.2p47
    BUNDLED WITH
    2.0.1
    _layouts/module.html
    View file @ 35c1b4ec
    ......@@ -91,8 +91,11 @@ window.onload = set_view_defaults;
    </header>
    {% if page.prerequisites %}
    <div class="prerequisites">
    <br>
    <br>
    <h2>Prerequisites</h2>
    Before starting this lesson, you should be familiar with:
    Before starting this lesson, you should be familiar with:<br>
    <br>
    <ul>
    {% for prereq in page.prerequisites %}
    <li>{{ prereq | markdownify }}</li>
    ......@@ -101,8 +104,11 @@ window.onload = set_view_defaults;
    </div>
    {% endif %}
    <div class="learning-objectives">
    <br>
    <br>
    <h2>Learning Objectives</h2>
    After completing this lesson, learners should be able to:
    After completing this lesson, learners should be able to:<br>
    <br>
    <ul>
    {% for objective in page.objectives %}
    <li>{{ objective | markdownify }}</li>
    ......@@ -110,15 +116,21 @@ window.onload = set_view_defaults;
    </ul>
    </div>
    <br>
    <br>
    <h2>Motivation</h2>
    {{ page.motivation | markdownify }}
    <br>
    <br>
    <h2>Concept map</h2>
    <div class="mermaid">
    {{ page.concept_map }}
    </div>
    <br>
    <br>
    <h2>Example</h2>
    <figure>
    ......@@ -132,6 +144,8 @@ window.onload = set_view_defaults;
    {{ content }}
    </div>
    <br>
    <br>
    <h2>Activity</h2>
    {% if page.activity_preface %}
    ......@@ -139,7 +153,7 @@ window.onload = set_view_defaults;
    {% endif %}
    {% if page.activities %}
    Choose a platform to display instructions for: <select id="id_activity_platform" name="activityplatformlist" onchange="change_activity_content_by_platform('id_activity_platform');return false;">
    Show activity for: <select id="id_activity_platform" name="activityplatformlist" onchange="change_activity_content_by_platform('id_activity_platform');return false;">
    {% assign first = true %}
    {% endif %}
    {% for platform in page.activities %}
    ......@@ -158,7 +172,6 @@ Choose a platform to display instructions for: <select id="id_activity_platform"
    {% for platform in page.activities %}
    <div id="{{ platform[0] | slugify }}-activity-div">
    &nbsp; <br>
    &nbsp; <br>
    <h3>{{ platform[0] }}</h3>
    {% assign includefile = platform[1] %}
    {% capture activity %}{% include {{ includefile }} %}{% endcapture %}
    ......@@ -167,6 +180,9 @@ Choose a platform to display instructions for: <select id="id_activity_platform"
    {% endfor %}
    {% if page.exercises_preface or page.exercises %}
    <br>
    <br>
    <h2>Formative assessment</h2>
    {% endif %}
    ......@@ -175,7 +191,7 @@ Choose a platform to display instructions for: <select id="id_activity_platform"
    {% endif %}
    {% if page.exercises %}
    Choose a platform to display instructions for: <select id="id_exercises_platform" name="exercisesplatformlist" onchange="change_exercises_content_by_platform('id_exercises_platform');return false;">
    Perform additional excercises for: <select id="id_exercises_platform" name="exercisesplatformlist" onchange="change_exercises_content_by_platform('id_exercises_platform');return false;">
    {% assign first = true %}
    {% endif %}
    {% for platform in page.exercises %}
    ......@@ -192,6 +208,7 @@ Choose a platform to display instructions for: <select id="id_exercises_platform
    {% endif %}
    {% for platform in page.exercises %}
    <div id="{{ platform[0] | slugify }}-exercises-div">
    &nbsp; <br>
    <h3>{{ platform[0] }}</h3>
    {% assign includefile = platform[1] %}
    {% capture exercise %}{% include {{ includefile }} %}{% endcapture %}
    ......@@ -199,6 +216,8 @@ Choose a platform to display instructions for: <select id="id_exercises_platform
    </div>
    {% endfor %}
    <br>
    <br>
    <h2>Follow-up material</h2>
    <ul>
    ......@@ -207,6 +226,8 @@ Choose a platform to display instructions for: <select id="id_exercises_platform
    {% endfor %}
    </ul>
    <br>
    <br>
    <h2>Learn more</h2>
    <ul>
    ......
    _site/CONTRIBUTING.html 0 → 100644
    View file @ 35c1b4ec
    <!DOCTYPE html>
    <html>
    <head>
    <meta charset="utf-8">
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">
    <title>Image Analysis Training</title>
    <meta name="description" content="A collection of material for teaching image analysis. Includes concept maps, exercises, example data
    ">
    <link rel="stylesheet" href="/image-analysis-training-resources/css/main.css">
    <link rel="canonical" href="http://localhost:4000/image-analysis-training-resources/CONTRIBUTING.html">
    <link rel="alternate" type="application/rss+xml" title="Image Analysis Training" href="http://localhost:4000/image-analysis-training-resources/feed.xml">
    <script src="https://unpkg.com/mermaid@8.0.0/dist/mermaid.min.js"></script>
    <script>mermaid.initialize({startOnLoad:true});</script>
    </head>
    <body>
    <header class="site-header">
    <div class="wrapper">
    <a class="site-title" href="/image-analysis-training-resources/">Image Analysis Training</a>
    <nav class="site-nav">
    <a href="#" class="menu-icon">
    <svg viewBox="0 0 18 15">
    <path fill="#424242" d="M18,1.484c0,0.82-0.665,1.484-1.484,1.484H1.484C0.665,2.969,0,2.304,0,1.484l0,0C0,0.665,0.665,0,1.484,0 h15.031C17.335,0,18,0.665,18,1.484L18,1.484z"/>
    <path fill="#424242" d="M18,7.516C18,8.335,17.335,9,16.516,9H1.484C0.665,9,0,8.335,0,7.516l0,0c0-0.82,0.665-1.484,1.484-1.484 h15.031C17.335,6.031,18,6.696,18,7.516L18,7.516z"/>
    <path fill="#424242" d="M18,13.516C18,14.335,17.335,15,16.516,15H1.484C0.665,15,0,14.335,0,13.516l0,0 c0-0.82,0.665-1.484,1.484-1.484h15.031C17.335,12.031,18,12.696,18,13.516L18,13.516z"/>
    </svg>
    </a>
    <div class="trigger">
    <a class="page-link" href="/image-analysis-training-resources/modules/basic_image_analysis_workflow.html">Basic image analysis workflow</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/binarization.html">Image binarization</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/calibration.html">Image calibration</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/connected_components.html">Connected components</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/display.html">Image display</a>
    <a class="page-link" href="/image-analysis-training-resources/example-images/">Example Images</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/filter_convolution.html">Image math</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/filter_difference_of_gaussian.html">Difference of Gaussian</a>
    <a class="page-link" href="/image-analysis-training-resources/">Image Analysis Training Material</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/measure_intensities.html">Intensity measurements</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/measure_shapes.html">Object shape measurements</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/object_splitting.html">Object splitting</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/pixel_data_types.html">Pixel data types</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/pixel_math.html">Image math</a>
    <a class="page-link" href="/image-analysis-training-resources/modules/pixels.html">Pixels</a>
    </div>
    </nav>
    </div>
    </header>
    <div class="page-content">
    <div class="wrapper">
    <h1 id="guidelines-for-contributing">Guidelines for Contributing</h1>
    <p>Contributions to this project are very welcome.
    Changes should be submitted by merge request from a new branch to <code>master</code>.
    Merge requests should be reviewed by at least one Maintainer before merging.</p>
    <p>See <code>README.md</code> for information on the structure of the repository.</p>
    <h2 id="step-by-step-guide">Step by step guide</h2>
    <p>To contribute to this project, please follow those steps:</p>
    <ol>
    <li>Clone this repository: <code>git clone https://git.embl.de/grp-bio-it/image-analysis-training-resources.git</code></li>
    <li>On your computer, make a new branch. For example, if you would like to contribute python code to the binarization.md module you may: <code>git checkout -b pythonBinarization</code></li>
    <li>Now add your changes on your computer (staying in this branch) - see &quot;Adding a new module&quot; section, below.</li>
    <li>When you are done, please <code>git add .; git commit -m &quot;some message&quot;</code></li>
    <li>Now you can upload your branch to the online repository by typing: <code>git push --set-upstream origin pythonBinarization</code>.</li>
    <li>Go to the online repository on gitlab: https://git.embl.de/grp-bio-it/image-analysis-training-resources</li>
    <li>On gitlab, there will now be button at the top of the page. Click this button to stage a &quot;merge request&quot; of your contribution (in your branch) to the master branch. There will also a possibility to assign a project maintainer to review your contribution and to merge it. Please select someone appropriate here.</li>
    <li>Thank you for your contribution!</li>
    </ol>
    <h2 id="adding-a-new-module">Adding a new module</h2>
    <p>Each module page is built from a template (<code>_layouts/module.html</code>),
    ensuring a consistent structure and style for the whole collection.
    To create a new module, you will need to add a few files
    in a few different places in this repository.</p>
    <h3 id="module-file">Module file</h3>
    <p>Most important is the module file itself.
    This module file should be saved with a short, descriptive name (no spaces!)
    ending with the <code>.md</code> (Markdown) extension.
    Typically, the only content of this Markdown file should be a header
    written in YAML. See the specification below.
    All fields not marked as optional are required for the page to build.
    You can check that your YAML is valid with <a href="http://www.yamllint.com/">this tool</a>.</p>
    <pre><code class="language-yaml">---
    title: Title of the Module
    layout: module # don't change this
    prerequisites:
    - &quot;a list of things that learners should know&quot;
    - &quot;in order to understand this module&quot;
    objectives:
    - &quot;a list of learning objectives&quot;
    - &quot;see note 1 below for more info&quot;
    motivation: &gt;
    A description of *why* you would want to learn this.
    Can be written in
    (GitHub-flavoured) [Markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)
    and split
    across
    multiple
    lines.
    concept_map: &gt; # see note 2
    graph TD
    A[Christmas] --&gt;|Get money| B(Go shopping)
    B --&gt; C{Let me think}
    C --&gt;|One| D[Laptop]
    C --&gt;|Two| E[iPhone]
    C --&gt;|Three| F[fa:fa-car Car];
    figure: /figures/mymodule.png # store the example image for your module in the `figures` folder and provide the absolute path from the root of the site here.
    figure_legend: Some description of the figure. (optional)
    activity_preface: &gt;
    Some general description of the activity for
    that learners will do while studying the module.
    It will be followed by platform-specific instructions/example code.
    (optional)
    activities: # platform-specific activity instruction/example code files (see note 3) (optional)
    &quot;ImageJ GUI&quot;: &quot;mymodule/activities/mymodule_imagejgui.md&quot;
    &quot;ImageJ Macro&quot;: &quot;mymodule/activities/mymodule_imagejmacro.md&quot;
    &quot;Jython&quot;: &quot;mymodule/activities/mymodule_jython.md&quot;
    exercises_preface: &gt;
    You could put general, language-agnostic questions here...
    (optional)
    exercises: # platform-specific exercises (in Markdown files) (see note 3) (optional)
    &quot;ImageJ GUI&quot;: &quot;mymodule/exercises/mymodule_imagejgui.md&quot;
    &quot;ImageJ Macro&quot;: &quot;mymodule/exercises/mymodule_imagejmacro.md&quot;
    &quot;Jython&quot;: &quot;mymodule/exercises/mymodule_jython.md&quot;
    &quot;MATLAB&quot;: &quot;mymodule/exercises/mymodule_matlab.md&quot;
    learn_next: # see note 4
    - &quot;[name_of_one](calibration)&quot;
    - &quot;[or_more_modules](object_splitting)&quot;
    - &quot;[to link to next](display)&quot;
    external_links:
    - &quot;[link to](https://external.page.com)&quot;
    ---
    </code></pre>
    <p>Notes:</p>
    <ol>
    <li>Learning objectives should be worded as endings to a sentence beginning &quot;After completing this lesson, learners should be able to...&quot;. We recommend starting each learning objective with a verb from <a href="https://cft.vanderbilt.edu/guides-sub-pages/blooms-taxonomy/">Bloom's Taxonomy</a></li>
    <li>Concept maps are drawn with <a href="https://mermaidjs.github.io/flowchart.html">Mermaid.js</a>. The indentation of the chart description is important, so be careful!</li>
    <li>The <code>activities</code> and <code>exercises</code> fields should be populated with key-value pairs, where the key is the name of the platform (e.g. &quot;ImageJ GUI&quot;, &quot;Python&quot;, etc) and the value is the path (relative to <code>_includes/</code>) to the file containing the activity instructions/exercises for that platform.</li>
    <li>The points in &quot;Learn Next&quot; are Markdown links, which should be formed as <code>[Module Title](modulefilename)</code>, where the extension has been removed from the filename.</li>
    </ol>
    <h3 id="associated-files">Associated files</h3>
    <p>Below is a list of all the other files that you should provide
    to accompany a new module,
    as well as the appropriate location for each
    (relative to the top level of the repository).
    Examples are given for a <code>/modules/mymodule.md</code></p>
    <ul>
    <li>The <code>figure</code> image
    <ul>
    <li>an file containing an example image to illustrate the concept being taught in the module</li>
    <li>location: <code>/figures/mymodule.md</code></li>
    </ul>
    </li>
    <li>The <code>activities</code> files
    <ul>
    <li>Markdown files containing instructions and/or example code for an activity that learners should follow to learn how to apply the concept on a particular platform (ImageJ Macro, MATLAB, etc)</li>
    <li>location: <code>_includes/mymodule/activities/mymodule_platformnospaces.md</code></li>
    </ul>
    </li>
    <li>The <code>exercises</code> files
    <ul>
    <li>Markdown files containing exercises to test the learner's understanding of applying the concept on a particular platform</li>
    <li>location: <code>_includes/mymodule/exercises/mymodule_platformnospaces.md</code></li>
    </ul>
    </li>
    </ul>
    <h2 id="adding-exercisesactivity-instructions-for-a-new-platform">Adding exercises/activity instructions for a new platform</h2>
    <p>Contributions of instructions and exercises for more platforms are very welcome - please see the &quot;Associated files&quot; subsection above for details of where these contributed files should be added.</p>
    <h2 id="questions-about-the-module-layout">Questions about the module layout</h2>
    <p>If you have questions about the module layout, please contact <a href="mailto:toby.hodges@embl.de">Toby Hodges</a>.</p>
    </div>
    </div>
    <footer class="site-footer">
    <div class="wrapper">
    <h2 class="footer-heading">Image Analysis Training</h2>
    <div class="footer-col-wrapper">
    <div class="footer-col footer-col-1">
    <ul class="contact-list">
    <li>Image Analysis Training</li>
    <li><a href="mailto:image-analysis-support@embl.de">image-analysis-support@embl.de</a></li>
    <li><a href="https://git.embl.de/grp-bio-it/image-analysis-training-resources/">Source code</a></li>
    <li><a href="/image-analysis-training-resources/CONTRIBUTING">Contributions to this material are very welcome.</a></li>
    </ul>
    </div>
    <div class="footer-col footer-col-2">
    </div>
    <div class="footer-col footer-col-3">
    <p>A collection of material for teaching image analysis. Includes concept maps, exercises, example data
    </p>
    <p>Use of this site falls under <a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL's Privacy Policy</a>.</p>
    </div>
    </div>
    </div>
    </footer>
    </body>
    </html>
    _site/Gemfile 0 → 100644
    View file @ 35c1b4ec
    source "https://rubygems.org"
    ruby RUBY_VERSION
    # This will help ensure the proper Jekyll version is running.
    gem "jekyll", "3.4.0"
    # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
    gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
    # install GH-flavoured MD plugin
    group :jekyll_plugins do
    gem 'jekyll-commonmark-ghpages'
    end
    _site/Gemfile.lock 0 → 100644
    View file @ 35c1b4ec
    GEM
    remote: https://rubygems.org/
    specs:
    addressable (2.6.0)
    public_suffix (>= 2.0.2, < 4.0)
    colorator (1.1.0)
    commonmarker (0.17.13)
    ruby-enum (~> 0.5)
    concurrent-ruby (1.1.5)
    ffi (1.11.1)
    forwardable-extended (2.6.0)
    i18n (1.6.0)
    concurrent-ruby (~> 1.0)
    jekyll (3.4.0)
    addressable (~> 2.4)
    colorator (~> 1.0)
    jekyll-sass-converter (~> 1.0)
    jekyll-watch (~> 1.1)
    kramdown (~> 1.3)
    liquid (~> 3.0)
    mercenary (~> 0.3.3)
    pathutil (~> 0.9)
    rouge (~> 1.7)
    safe_yaml (~> 1.0)
    jekyll-commonmark (1.2.0)
    commonmarker (~> 0.14)
    jekyll (>= 3.0, < 4.0)
    jekyll-commonmark-ghpages (0.1.0)
    commonmarker (~> 0.17.6)
    jekyll-commonmark (~> 1)
    jekyll-sass-converter (1.5.2)
    sass (~> 3.4)
    jekyll-watch (1.5.1)
    listen (~> 3.0)
    kramdown (1.17.0)
    liquid (3.0.6)
    listen (3.1.5)
    rb-fsevent (~> 0.9, >= 0.9.4)
    rb-inotify (~> 0.9, >= 0.9.7)
    ruby_dep (~> 1.2)
    mercenary (0.3.6)
    pathutil (0.16.2)
    forwardable-extended (~> 2.6)
    public_suffix (3.1.0)
    rb-fsevent (0.10.3)
    rb-inotify (0.10.0)
    ffi (~> 1.0)
    rouge (1.11.1)
    ruby-enum (0.7.2)
    i18n
    ruby_dep (1.5.0)
    safe_yaml (1.0.5)
    sass (3.7.4)
    sass-listen (~> 4.0.0)
    sass-listen (4.0.0)
    rb-fsevent (~> 0.9, >= 0.9.4)
    rb-inotify (~> 0.9, >= 0.9.7)
    PLATFORMS
    ruby
    DEPENDENCIES
    jekyll (= 3.4.0)
    jekyll-commonmark-ghpages
    tzinfo-data
    RUBY VERSION
    ruby 2.6.2p47
    BUNDLED WITH
    2.0.1
    _site/LICENSE.md 0 → 100644
    View file @ 35c1b4ec
    This material is made available under the [Creative Commons Attribution license][cc-by-human].
    The following is a human-readable summary of (and not a substitute for)
    the [full legal text of the CC BY 4.0 license][cc-by-legal].
    You are free:
    * to **Share**---copy and redistribute the material in any medium or format
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    for any purpose, even commercially.
    The licensor cannot revoke these freedoms as long as you follow the
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