add svg tutorial

MannLabs · Jun 5, 2023 · 090d5ba · 090d5ba
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diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/nbsphinx/pages/notebooks/generate_cutting_mask_svg.ipynb b/docs/doctrees/nbsphinx/pages/notebooks/generate_cutting_mask_svg.ipynb
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_generate_cutting_mask_svg_5_0.png b/docs/doctrees/nbsphinx/pages_notebooks_generate_cutting_mask_svg_5_0.png
diff --git a/docs/doctrees/pages/example_notebooks.doctree b/docs/doctrees/pages/example_notebooks.doctree
diff --git a/docs/doctrees/pages/notebooks/generate_cutting_mask_svg.doctree b/docs/doctrees/pages/notebooks/generate_cutting_mask_svg.doctree
diff --git a/docs/html/_images/pages_notebooks_generate_cutting_mask_svg_5_0.png b/docs/html/_images/pages_notebooks_generate_cutting_mask_svg_5_0.png
diff --git a/docs/html/_sources/pages/example_notebooks.rst.txt b/docs/html/_sources/pages/example_notebooks.rst.txt
@@ -11,4 +11,5 @@ Here you will find a collection of jupyter notebooks using py-lmd to highlight t
 
    notebooks/generate_xml_from_segmentation_mask
    notebooks/generate_xml_from_qupath_export
+   notebooks/generate_cutting_mask_svg
 
diff --git a/docs/html/_sources/pages/notebooks/generate_cutting_mask_svg.ipynb.txt b/docs/html/_sources/pages/notebooks/generate_cutting_mask_svg.ipynb.txt
diff --git a/docs/html/_static/pyLMD_text.svg b/docs/html/_static/pyLMD_text.svg
diff --git a/docs/html/genindex.html b/docs/html/genindex.html
@@ -79,6 +79,11 @@
 <li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_xml_from_qupath_export.html#write-to-XML">3.2.6. write to XML</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html">3.3. Convert SVG graphic into LMD excision instructions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html#Visualize-Results">3.3.1. Visualize Results</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html#Export-to-XML">3.3.2. Export to XML</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pages/modules.html">4. py-lmd Modules</a><ul>

diff --git a/docs/html/index.html b/docs/html/index.html
@@ -81,6 +81,11 @@
 <li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_xml_from_qupath_export.html#write-to-XML">3.2.6. write to XML</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html">3.3. Convert SVG graphic into LMD excision instructions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html#Visualize-Results">3.3.1. Visualize Results</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html#Export-to-XML">3.3.2. Export to XML</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pages/modules.html">4. py-lmd Modules</a><ul>
@@ -189,6 +194,11 @@ <h2>Citing our Work<a class="headerlink" href="#citing-our-work" title="Permalin
 <li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_xml_from_qupath_export.html#write-to-XML">3.2.6. write to XML</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html">3.3. Convert SVG graphic into LMD excision instructions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html#Visualize-Results">3.3.1. Visualize Results</a></li>
+<li class="toctree-l3"><a class="reference internal" href="pages/notebooks/generate_cutting_mask_svg.html#Export-to-XML">3.3.2. Export to XML</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pages/modules.html">4. py-lmd Modules</a><ul>

diff --git a/docs/html/objects.inv b/docs/html/objects.inv
diff --git a/docs/html/pages/example_notebooks.html b/docs/html/pages/example_notebooks.html
@@ -82,6 +82,11 @@
 <li class="toctree-l3"><a class="reference internal" href="notebooks/generate_xml_from_qupath_export.html#write-to-XML">3.2.6. write to XML</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html">3.3. Convert SVG graphic into LMD excision instructions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html#Visualize-Results">3.3.1. Visualize Results</a></li>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html#Export-to-XML">3.3.2. Export to XML</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">4. py-lmd Modules</a><ul>
@@ -143,6 +148,11 @@ <h1><span class="section-number">3. </span>Example Notebooks<a class="headerlink
 <li class="toctree-l2"><a class="reference internal" href="notebooks/generate_xml_from_qupath_export.html#write-to-XML">3.2.6. write to XML</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html">3.3. Convert SVG graphic into LMD excision instructions</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html#Visualize-Results">3.3.1. Visualize Results</a></li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html#Export-to-XML">3.3.2. Export to XML</a></li>
+</ul>
+</li>
 </ul>
 </div>
 </section>

diff --git a/docs/html/pages/modules.html b/docs/html/pages/modules.html
@@ -26,7 +26,7 @@
     <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="prev" title="3.2. Generate cutting XML from exported results from QUPath" href="notebooks/generate_xml_from_qupath_export.html" />
+    <link rel="prev" title="3.3. Convert SVG graphic into LMD excision instructions" href="notebooks/generate_cutting_mask_svg.html" />
     <link href="../_static/style.css" rel="stylesheet" type="text/css">
 
 </head>
@@ -83,6 +83,11 @@
 <li class="toctree-l3"><a class="reference internal" href="notebooks/generate_xml_from_qupath_export.html#write-to-XML">3.2.6. write to XML</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html">3.3. Convert SVG graphic into LMD excision instructions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html#Visualize-Results">3.3.1. Visualize Results</a></li>
+<li class="toctree-l3"><a class="reference internal" href="notebooks/generate_cutting_mask_svg.html#Export-to-XML">3.3.2. Export to XML</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">4. py-lmd Modules</a><ul>
@@ -613,7 +618,7 @@ <h3><span class="section-number">4.1.3. </span>SegmentationLoader<a class="heade
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="notebooks/generate_xml_from_qupath_export.html" class="btn btn-neutral float-left" title="3.2. Generate cutting XML from exported results from QUPath" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="notebooks/generate_cutting_mask_svg.html" class="btn btn-neutral float-left" title="3.3. Convert SVG graphic into LMD excision instructions" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
     </div>
 
   <hr/>

diff --git a/docs/html/pages/notebooks/generate_cutting_mask_svg.html b/docs/html/pages/notebooks/generate_cutting_mask_svg.html