Automatic Update

Fri May 31 18:32:52 UTC 2024

_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/classic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- classic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_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 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 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, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer

_static/searchtools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
       .then((data) => {
         if (data)
           listItem.appendChild(
-            Search.makeSearchSummary(data, searchTerms)
+            Search.makeSearchSummary(data, searchTerms, anchor)
           );
         // highlight search terms in the summary
         if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
@@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => {
     );
   else
     Search.status.innerText = _(
-      `Search finished, found ${resultCount} page(s) matching the search query.`
-    );
+      "Search finished, found ${resultCount} page(s) matching the search query."
+    ).replace('${resultCount}', resultCount);
 };
 const _displayNextItem = (
   results,
@@ -137,6 +137,22 @@ const _displayNextItem = (
   // search finished, update title and status message
   else _finishSearch(resultCount);
 };
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+  const leftScore = a[4];
+  const rightScore = b[4];
+  if (leftScore === rightScore) {
+    // same score: sort alphabetically
+    const leftTitle = a[1].toLowerCase();
+    const rightTitle = b[1].toLowerCase();
+    if (leftTitle === rightTitle) return 0;
+    return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+  }
+  return leftScore > rightScore ? 1 : -1;
+};
 
 /**
  * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
@@ -160,13 +176,26 @@ const Search = {
   _queued_query: null,
   _pulse_status: -1,
 
-  htmlToText: (htmlString) => {
+  htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
+    for (const removalQuery of [".headerlinks", "script", "style"]) {
+      htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+    }
+    if (anchor) {
+      const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+      if (anchorContent) return anchorContent.textContent;
+
+      console.warn(
+        `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+      );
+    }
+
+    // if anchor not specified or not found, fall back to main content
     const docContent = htmlElement.querySelector('[role="main"]');
-    if (docContent !== undefined) return docContent.textContent;
+    if (docContent) return docContent.textContent;
+
     console.warn(
-      "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
+      "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
     );
     return "";
   },
@@ -239,16 +268,7 @@ const Search = {
     else Search.deferQuery(query);
   },
 
-  /**
-   * execute search (requires search index to be loaded)
-   */
-  query: (query) => {
-    const filenames = Search._index.filenames;
-    const docNames = Search._index.docnames;
-    const titles = Search._index.titles;
-    const allTitles = Search._index.alltitles;
-    const indexEntries = Search._index.indexentries;
-
+  _parseQuery: (query) => {
     // stem the search terms and add them to the correct list
     const stemmer = new Stemmer();
     const searchTerms = new Set();
@@ -284,16 +304,32 @@ const Search = {
     // console.info("required: ", [...searchTerms]);
     // console.info("excluded: ", [...excludedTerms]);
 
-    // array of [docname, title, anchor, descr, score, filename]
-    let results = [];
+    return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+    const allTitles = Search._index.alltitles;
+    const indexEntries = Search._index.indexentries;
+
+    // Collect multiple result groups to be sorted separately and then ordered.
+    // Each is an array of [docname, title, anchor, descr, score, filename].
+    const normalResults = [];
+    const nonMainIndexResults = [];
+
     _removeChildren(document.getElementById("search-progress"));
 
-    const queryLower = query.toLowerCase();
+    const queryLower = query.toLowerCase().trim();
     for (const [title, foundTitles] of Object.entries(allTitles)) {
-      if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
+      if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
           let score = Math.round(100 * queryLower.length / title.length)
-          results.push([
+          normalResults.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
@@ -308,46 +344,47 @@ const Search = {
     // search for explicit entries in index directives
     for (const [entry, foundEntries] of Object.entries(indexEntries)) {
       if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
-        for (const [file, id] of foundEntries) {
-          let score = Math.round(100 * queryLower.length / entry.length)
-          results.push([
+        for (const [file, id, isMain] of foundEntries) {
+          const score = Math.round(100 * queryLower.length / entry.length);
+          const result = [
             docNames[file],
             titles[file],
             id ? "#" + id : "",
             null,
             score,
             filenames[file],
-          ]);
+          ];
+          if (isMain) {
+            normalResults.push(result);
+          } else {
+            nonMainIndexResults.push(result);
+          }
         }
       }
     }
 
     // lookup as object
     objectTerms.forEach((term) =>
-      results.push(...Search.performObjectSearch(term, objectTerms))
+      normalResults.push(...Search.performObjectSearch(term, objectTerms))
     );
 
     // lookup as search terms in fulltext
-    results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+    normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
 
     // let the scorer override scores with a custom scoring function
-    if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
-
-    // now sort the results by score (in opposite order of appearance, since the
-    // display function below uses pop() to retrieve items) and then
-    // alphabetically
-    results.sort((a, b) => {
-      const leftScore = a[4];
-      const rightScore = b[4];
-      if (leftScore === rightScore) {
-        // same score: sort alphabetically
-        const leftTitle = a[1].toLowerCase();
-        const rightTitle = b[1].toLowerCase();
-        if (leftTitle === rightTitle) return 0;
-        return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
-      }
-      return leftScore > rightScore ? 1 : -1;
-    });
+    if (Scorer.score) {
+      normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+      nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+    }
+
+    // Sort each group of results by score and then alphabetically by name.
+    normalResults.sort(_orderResultsByScoreThenName);
+    nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+    // Combine the result groups in (reverse) order.
+    // Non-main index entries are typically arbitrary cross-references,
+    // so display them after other results.
+    let results = [...nonMainIndexResults, ...normalResults];
 
     // remove duplicate search results
     // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
@@ -361,7 +398,12 @@ const Search = {
       return acc;
     }, []);
 
-    results = results.reverse();
+    return results.reverse();
+  },
+
+  query: (query) => {
+    const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+    const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
 
     // for debugging
     //Search.lastresults = results.slice();  // a copy
@@ -466,14 +508,18 @@ const Search = {
       // add support for partial matches
       if (word.length > 2) {
         const escapedWord = _escapeRegExp(word);
-        Object.keys(terms).forEach((term) => {
-          if (term.match(escapedWord) && !terms[word])
-            arr.push({ files: terms[term], score: Scorer.partialTerm });
-        });
-        Object.keys(titleTerms).forEach((term) => {
-          if (term.match(escapedWord) && !titleTerms[word])
-            arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
-        });
+        if (!terms.hasOwnProperty(word)) {
+          Object.keys(terms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: terms[term], score: Scorer.partialTerm });
+          });
+        }
+        if (!titleTerms.hasOwnProperty(word)) {
+          Object.keys(titleTerms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+          });
+        }
       }
 
       // no match but word was a required one
@@ -496,9 +542,8 @@ const Search = {
 
       // create the mapping
       files.forEach((file) => {
-        if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
-          fileMap.get(file).push(word);
-        else fileMap.set(file, [word]);
+        if (!fileMap.has(file)) fileMap.set(file, [word]);
+        else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
       });
     });
 
@@ -549,8 +594,8 @@ const Search = {
    * search summary for a given text. keywords is a list
    * of stemmed words.
    */
-  makeSearchSummary: (htmlText, keywords) => {
-    const text = Search.htmlToText(htmlText);
+  makeSearchSummary: (htmlText, keywords, anchor) => {
+    const text = Search.htmlToText(htmlText, anchor);
     if (text === "") return null;
 
     const textLower = text.toLowerCase();

_static/sidebar.js

@@ -16,7 +16,7 @@
  * Once the browser is closed the cookie is deleted and the position
  * reset to the default (expanded).
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

api.html

@@ -7,10 +7,10 @@
 
     <title>API &#8212; tomojs-pytools  documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
-    <link rel="stylesheet" type="text/css" href="_static/classic.css?v=514cf933" />
+    <link rel="stylesheet" type="text/css" href="_static/classic.css?v=def86cc0" />
 
     <script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=888ff710"></script>
+    <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
 
     <link rel="index" title="Index" href="genindex.html" />
@@ -285,6 +285,21 @@ <h3>Navigation</h3>
 </dd></dl>
 
 <dl class="py function" id="module-pytools.meta">
+<dt class="sig sig-object py" id="pytools.meta.is_16bit">
+<span class="sig-prename descclassname"><span class="pre">pytools.meta.</span></span><span class="sig-name descname"><span class="pre">is_16bit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="headerlink" href="#pytools.meta.is_16bit" title="Link to this definition">¶</a></dt>
+<dd><p>Read an image file header to inspect meta-data.</p>
+<p>Supported file formats include TIFF, and others supported by SimpleITK and the Insight toolkit.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>file_path</strong> – The path to an image file.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the pixel type is a 16-bit integer (signed or unsigned), False otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
 <dt class="sig sig-object py" id="pytools.meta.is_int16">
 <span class="sig-prename descclassname"><span class="pre">pytools.meta.</span></span><span class="sig-name descname"><span class="pre">is_int16</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="headerlink" href="#pytools.meta.is_int16" title="Link to this definition">¶</a></dt>
 <dd><p>Read an image file header to inspect meta-data.</p>
@@ -451,6 +466,7 @@ <h3><a href="index.html">Table of Contents</a></h3>
 </li>
 <li><a class="reference internal" href="#pytools.visual_min_max"><code class="docutils literal notranslate"><span class="pre">visual_min_max()</span></code></a></li>
 <li><a class="reference internal" href="#pytools.zarr_extract_2d"><code class="docutils literal notranslate"><span class="pre">zarr_extract_2d()</span></code></a></li>
+<li><a class="reference internal" href="#pytools.meta.is_16bit"><code class="docutils literal notranslate"><span class="pre">is_16bit()</span></code></a></li>
 <li><a class="reference internal" href="#pytools.meta.is_int16"><code class="docutils literal notranslate"><span class="pre">is_int16()</span></code></a></li>
 <li><a class="reference internal" href="#pytools.utils.zarr.bin_shrink"><code class="docutils literal notranslate"><span class="pre">bin_shrink()</span></code></a></li>
 <li><a class="reference internal" href="#pytools.utils.zarr.build_pyramid"><code class="docutils literal notranslate"><span class="pre">build_pyramid()</span></code></a></li>
@@ -478,15 +494,15 @@ <h3>This Page</h3>
             rel="nofollow">Show Source</a></li>
     </ul>
    </div>
-<div id="searchbox" style="display: none" role="search">
+<search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="search.html" method="get">
       <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
-</div>
+</search>
 <script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
@@ -510,7 +526,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2022, Bradley Lowekamp.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
     </div>
   </body>
 </html>