deploy: 2a1be24

.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: db97b0df878fe9f0debb06ac1ef3a916
+config: 41873023439959888f42c846cf919dcb
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/sct_toolbox_example.ipynb

@@ -9,7 +9,7 @@
     "id": "view-in-github"
    },
    "source": [
-    "<a href=\"https://play-ashburn.neurodesk.org/v2/gh/neurodesk/example-notebooks/main?labpath=/home/jovyan/examples/example-notebooks/books/structural_imaging/sct_toolbox_example.ipynb\" target=\"_parent\"><img src=\"https://img.shields.io/badge/launch-binder-579aca.svg?logo=data:image/png;base64,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\" alt=\"Open In Binder\"/>  </a>\n",
+    "<a href=\"https://play-iowa.neurodesk.org/hub/user-redirect/lab/tree/example-notebooks/books/structural_imaging/sct_toolbox_example.ipynb\" target=\"_parent\"><img src=\"https://img.shields.io/badge/launch-binder-579aca.svg?logo=data:image/png;base64,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\" alt=\"Open In Binder\"/>  </a>\n",
     "<a href=\"https://colab.research.google.com/github/NeuroDesk/example-notebooks/blob/main/books/structural_imaging/sct_toolbox_example.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>   </a>"
    ]
   },

_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -236,11 +236,17 @@ div.body p, div.body dd, div.body li, div.body blockquote {
 a.headerlink {
     visibility: hidden;
 }
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
 
-a:visited {
-    color: #551A8B;
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
 }
 
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -328,17 +334,11 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
-
-nav.contents,
-aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
-
-nav.contents,
-aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -377,17 +377,13 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
-nav.contents > :last-child,
-aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
-nav.contents::after,
-aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -613,6 +609,25 @@ ul.simple p {
     margin-bottom: 0;
 }
 
+/* Docutils 0.17 and older (footnotes & citations) */
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+    margin-right: 0.5em;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+/* Docutils 0.18+ (footnotes & citations) */
 aside.footnote > span,
 div.citation > span {
     float: left;
@@ -637,6 +652,8 @@ div.citation > p:last-of-type:after {
     clear: both;
 }
 
+/* Footnotes & citations ends */
+
 dl.field-list {
     display: grid;
     grid-template-columns: fit-content(30%) auto;
@@ -649,6 +666,10 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
+dl.field-list > dt:after {
+    content: ":";
+}
+
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
@@ -674,16 +695,6 @@ dd {
     margin-left: 30px;
 }
 
-.sig dd {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
-.sig dl {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -752,14 +763,6 @@ abbr, acronym {
     cursor: help;
 }
 
-.translated {
-    background-color: rgba(207, 255, 207, 0.2)
-}
-
-.untranslated {
-    background-color: rgba(255, 207, 207, 0.2)
-}
-
 /* -- code displays --------------------------------------------------------- */
 
 pre {

_static/doctools.js

@@ -4,19 +4,12 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 "use strict";
 
-const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
-  "TEXTAREA",
-  "INPUT",
-  "SELECT",
-  "BUTTON",
-]);
-
 const _ready = (callback) => {
   if (document.readyState !== "loading") {
     callback();
@@ -25,11 +18,73 @@ const _ready = (callback) => {
   }
 };
 
+/**
+ * highlight a given string on a node by wrapping it in
+ * span elements with the given class name.
+ */
+const _highlight = (node, addItems, text, className) => {
+  if (node.nodeType === Node.TEXT_NODE) {
+    const val = node.nodeValue;
+    const parent = node.parentNode;
+    const pos = val.toLowerCase().indexOf(text);
+    if (
+      pos >= 0 &&
+      !parent.classList.contains(className) &&
+      !parent.classList.contains("nohighlight")
+    ) {
+      let span;
+
+      const closestNode = parent.closest("body, svg, foreignObject");
+      const isInSVG = closestNode && closestNode.matches("svg");
+      if (isInSVG) {
+        span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+      } else {
+        span = document.createElement("span");
+        span.classList.add(className);
+      }
+
+      span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      parent.insertBefore(
+        span,
+        parent.insertBefore(
+          document.createTextNode(val.substr(pos + text.length)),
+          node.nextSibling
+        )
+      );
+      node.nodeValue = val.substr(0, pos);
+
+      if (isInSVG) {
+        const rect = document.createElementNS(
+          "http://www.w3.org/2000/svg",
+          "rect"
+        );
+        const bbox = parent.getBBox();
+        rect.x.baseVal.value = bbox.x;
+        rect.y.baseVal.value = bbox.y;
+        rect.width.baseVal.value = bbox.width;
+        rect.height.baseVal.value = bbox.height;
+        rect.setAttribute("class", className);
+        addItems.push({ parent: parent, target: rect });
+      }
+    }
+  } else if (node.matches && !node.matches("button, select, textarea")) {
+    node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
+  }
+};
+const _highlightText = (thisNode, text, className) => {
+  let addItems = [];
+  _highlight(thisNode, addItems, text, className);
+  addItems.forEach((obj) =>
+    obj.parent.insertAdjacentElement("beforebegin", obj.target)
+  );
+};
+
 /**
  * Small JavaScript module for the documentation.
  */
 const Documentation = {
   init: () => {
+    Documentation.highlightSearchWords();
     Documentation.initDomainIndexTable();
     Documentation.initOnKeyListeners();
   },
@@ -71,6 +126,51 @@ const Documentation = {
     Documentation.LOCALE = catalog.locale;
   },
 
+  /**
+   * highlight the search words provided in the url in the text
+   */
+  highlightSearchWords: () => {
+    const highlight =
+      new URLSearchParams(window.location.search).get("highlight") || "";
+    const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
+    if (terms.length === 0) return; // nothing to do
+
+    // There should never be more than one element matching "div.body"
+    const divBody = document.querySelectorAll("div.body");
+    const body = divBody.length ? divBody[0] : document.querySelector("body");
+    window.setTimeout(() => {
+      terms.forEach((term) => _highlightText(body, term, "highlighted"));
+    }, 10);
+
+    const searchBox = document.getElementById("searchbox");
+    if (searchBox === null) return;
+    searchBox.appendChild(
+      document
+        .createRange()
+        .createContextualFragment(
+          '<p class="highlight-link">' +
+            '<a href="javascript:Documentation.hideSearchWords()">' +
+            Documentation.gettext("Hide Search Matches") +
+            "</a></p>"
+        )
+    );
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords: () => {
+    document
+      .querySelectorAll("#searchbox .highlight-link")
+      .forEach((el) => el.remove());
+    document
+      .querySelectorAll("span.highlighted")
+      .forEach((el) => el.classList.remove("highlighted"));
+    const url = new URL(window.location);
+    url.searchParams.delete("highlight");
+    window.history.replaceState({}, "", url);
+  },
+
   /**
    * helper function to focus on search bar
    */
@@ -110,11 +210,15 @@ const Documentation = {
     )
       return;
 
+    const blacklistedElements = new Set([
+      "TEXTAREA",
+      "INPUT",
+      "SELECT",
+      "BUTTON",
+    ]);
     document.addEventListener("keydown", (event) => {
-      // bail for input elements
-      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
-      // bail with special keys
-      if (event.altKey || event.ctrlKey || event.metaKey) return;
+      if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements
+      if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys
 
       if (!event.shiftKey) {
         switch (event.key) {
@@ -136,6 +240,10 @@ const Documentation = {
               event.preventDefault();
             }
             break;
+          case "Escape":
+            if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+            Documentation.hideSearchWords();
+            event.preventDefault();
         }
       }
 

_static/documentation_options.js

@@ -1,4 +1,5 @@
-const DOCUMENTATION_OPTIONS = {
+var DOCUMENTATION_OPTIONS = {
+    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
     VERSION: '',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
@@ -9,5 +10,5 @@ const DOCUMENTATION_OPTIONS = {
     SOURCELINK_SUFFIX: '',
     NAVIGATION_WITH_KEYS: false,
     SHOW_SEARCH_SUMMARY: true,
-    ENABLE_SEARCH_SHORTCUTS: true,
+    ENABLE_SEARCH_SHORTCUTS: false,
 };

_static/language_data.js

@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, if available */
+/* Non-minified version is copied as a separate JS file, is available */
 
 /**
  * Porter Stemmer