From f1271b441a87a2585f4c6a76d619028bdfd27cc9 Mon Sep 17 00:00:00 2001 From: blowekamp Date: Mon, 24 Jun 2024 11:59:25 +0000 Subject: [PATCH] Automatic Update Mon Jun 24 11:59:25 UTC 2024 --- _static/basic.css | 2 +- _static/classic.css | 2 +- _static/doctools.js | 2 +- _static/documentation_options.js | 2 +- _static/language_data.js | 4 +- _static/searchtools.js | 165 ++++++++++++++++++++----------- _static/sidebar.js | 2 +- api.html | 16 +-- commandline.html | 16 +-- genindex.html | 16 +-- index.html | 19 ++-- objects.inv | Bin 746 -> 746 bytes py-modindex.html | 16 +-- search.html | 22 ++--- searchindex.js | 2 +- 15 files changed, 165 insertions(+), 121 deletions(-) diff --git a/_static/basic.css b/_static/basic.css index 30fee9d..f316efc 100644 --- a/_static/basic.css +++ b/_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. * */ diff --git a/_static/classic.css b/_static/classic.css index 9ad992b..5530147 100644 --- a/_static/classic.css +++ b/_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. * */ diff --git a/_static/doctools.js b/_static/doctools.js index d06a71d..4d67807 100644 --- a/_static/doctools.js +++ b/_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. * */ diff --git a/_static/documentation_options.js b/_static/documentation_options.js index e47970c..a52ba6e 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.5.2.dev8', + VERSION: '0.5.2.dev9', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/_static/language_data.js b/_static/language_data.js index 250f566..367b8ed 100644 --- a/_static/language_data.js +++ b/_static/language_data.js @@ -5,7 +5,7 @@ * 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. * */ @@ -13,7 +13,7 @@ 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 diff --git a/_static/searchtools.js b/_static/searchtools.js index 7918c3f..92da3f8 100644 --- a/_static/searchtools.js +++ b/_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(); diff --git a/_static/sidebar.js b/_static/sidebar.js index c5e2692..f28c206 100644 --- a/_static/sidebar.js +++ b/_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. * */ diff --git a/api.html b/api.html index 1ce9f13..02f0433 100644 --- a/api.html +++ b/api.html @@ -5,12 +5,12 @@ - API — sitk-ibex 0.5.2.dev8 documentation + API — sitk-ibex 0.5.2.dev9 documentation - + - - + + @@ -29,7 +29,7 @@

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    • diff --git a/index.html b/index.html index ac1bfb8..24d6b4a 100644 --- a/index.html +++ b/index.html @@ -5,12 +5,12 @@ - Welcome to sitk-ibex’s documentation! — sitk-ibex 0.5.2.dev8 documentation + Welcome to sitk-ibex’s documentation! — sitk-ibex 0.5.2.dev9 documentation - + - - + + @@ -29,7 +29,7 @@

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    • @@ -66,7 +66,8 @@

    SITK-IBEX: Aligning images acquired with the IBEX microscopy imaging techniq

    Build Status

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    The Python module is distributed on PyPI - The Python Package Index. The package can be installed by running:

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    • diff --git a/objects.inv b/objects.inv index d90d350d3f88fe638deca7dab6628a67c6932354..ee2d8bf9c25314c07355e0db7cc46ff60dc687f5 100644 GIT binary patch delta 12 TcmaFG`igae8>8h$_r**AAo>K1 delta 12 TcmaFG`igae8>7WW_r**AAoT=` diff --git a/py-modindex.html b/py-modindex.html index 03358ed..a8c01c5 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -4,12 +4,12 @@ - Python Module Index — sitk-ibex 0.5.2.dev8 documentation + Python Module Index — sitk-ibex 0.5.2.dev9 documentation - + - - + + @@ -27,7 +27,7 @@

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    • diff --git a/search.html b/search.html index d592f26..e4afb26 100644 --- a/search.html +++ b/search.html @@ -4,21 +4,22 @@ - Search — sitk-ibex 0.5.2.dev8 documentation + Search — sitk-ibex 0.5.2.dev9 documentation - + - - + + - - + + + @@ -65,10 +66,7 @@

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    • diff --git a/searchindex.js b/searchindex.js index 23acdfb..591f757 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api", "commandline", "index"], "filenames": ["api.rst", "commandline.rst", "index.rst"], "titles": ["API", "Command Line Interface", "Welcome to sitk-ibex\u2019s documentation!"], "terms": {"sitkibex": [0, 2], "registr": [0, 2], "fixed_imag": [0, 1], "imag": [0, 1], "moving_imag": [0, 1], "do_fft_initi": 0, "true": [0, 1], "do_affine2d": 0, "fals": [0, 1], "do_affine3d": 0, "ignore_spac": 0, "sigma": [0, 1], "1": [0, 1], "0": [0, 1, 2], "auto_mask": 0, "samples_per_paramet": [0, 1], "5000": [0, 1], "expand": 0, "none": 0, "transform": [0, 1, 2], "robust": [0, 2], "multi": [0, 1, 2], "phase": [0, 2], "panel": [0, 2], "confoc": 0, "microscopi": 0, "The": [0, 1, 2], "fix": [0, 1, 2], "move": [0, 1, 2], "ar": [0, 2], "expect": 0, "same": 0, "molecular": 0, "label": [0, 2], "region": 0, "avail": [0, 1, 2], "fft": 0, "initi": 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