diff --git a/.buildinfo b/.buildinfo index 9c7e58f5..f2ebd0a8 100644 --- a/.buildinfo +++ b/.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: 27c7f503f98a773a1024679d78694c25 +config: 2b084f06778b34a90407f4a793f89995 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/.doctrees/cli.doctree b/.doctrees/cli.doctree index 0173f24a..9242bc01 100644 Binary files a/.doctrees/cli.doctree and b/.doctrees/cli.doctree differ diff --git a/.doctrees/cutting.doctree b/.doctrees/cutting.doctree index 7b406d63..4b9341d6 100644 Binary files a/.doctrees/cutting.doctree and b/.doctrees/cutting.doctree differ diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index dee765a4..c1787e20 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree index d7b246df..7089fef1 100644 Binary files a/.doctrees/index.doctree and b/.doctrees/index.doctree differ diff --git a/.doctrees/math_ref.doctree b/.doctrees/math_ref.doctree index 842dfecd..f0145d1a 100644 Binary files a/.doctrees/math_ref.doctree and b/.doctrees/math_ref.doctree differ diff --git a/.doctrees/quickstart.doctree b/.doctrees/quickstart.doctree index d1c8ae8f..29c70dde 100644 Binary files a/.doctrees/quickstart.doctree and b/.doctrees/quickstart.doctree differ diff --git a/.doctrees/slicing.doctree b/.doctrees/slicing.doctree index d952b1ae..9baa6b81 100644 Binary files a/.doctrees/slicing.doctree and b/.doctrees/slicing.doctree differ diff --git a/_static/basic.css b/_static/basic.css index 30fee9d0..f316efcb 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/doctools.js b/_static/doctools.js index d06a71d7..4d67807d 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/language_data.js b/_static/language_data.js index 250f5665..367b8ed8 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 7918c3fa..92da3f8b 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/sphinxdoc.css b/_static/sphinxdoc.css index 1e9ffe0a..b03830b4 100644 --- a/_static/sphinxdoc.css +++ b/_static/sphinxdoc.css @@ -5,7 +5,7 @@ * Sphinx stylesheet -- sphinxdoc theme. Originally created by * Armin Ronacher for Werkzeug. * - * :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/cli.html b/cli.html index 381091df..0b7f8571 100644 --- a/cli.html +++ b/cli.html @@ -7,9 +7,9 @@ 4. Command Line Interface — MSlice 2.9 documentation - + - + @@ -242,7 +242,7 @@

This Page

rel="nofollow">Show Source - + @@ -274,7 +274,7 @@

Navigation

\ No newline at end of file diff --git a/cutting.html b/cutting.html index c17f4079..aeed115c 100644 --- a/cutting.html +++ b/cutting.html @@ -7,9 +7,9 @@ 2. Taking Cuts — MSlice 2.9 documentation - + - + @@ -73,14 +73,16 @@

2. Taking CutsKeep. To make a Kept figure Current again (for example to use Plot Over), click Make Current. See Keep / Make Current for more details.

-_images/cut_options.png +_images/cut_options.png +

You can edit the axes limits, scale and titles by double-clicking on the relevant axis in the plot window. Clicking on each plot line will also allow you to change its colour and symbol. These functionalities are also accessible from the options button (the cog symbol) in the plot figure toolbar.

2.2. Overplotting powder lines

-_images/powder_lines.png +_images/powder_lines.png +

To help with a “first look” data analysis, MSlice can overplot on the cuts the positions of powder reflections from common sample environment materials (Aluminium, Copper, Niobium and Tantalum). These functionalities may be accessed from the Information menu option as shown above.

@@ -90,7 +92,8 @@

2.2. Overplotting powder lines

2.3. Converting intensity information in displayed data in cuts

-_images/intensity_chi_cut.png +_images/intensity_chi_cut.png +

In addition to displaying the cut data as S(Q, \omega), the cut figure window can also display the data with intensity information converted.

The different options available are:

@@ -188,7 +191,7 @@

This Page

rel="nofollow">Show Source - + @@ -220,7 +223,7 @@

Navigation

\ No newline at end of file diff --git a/genindex.html b/genindex.html index f22e1b7e..40b863e8 100644 --- a/genindex.html +++ b/genindex.html @@ -6,9 +6,9 @@ Index — MSlice 2.9 documentation - + - + @@ -43,7 +43,7 @@

Index

@@ -69,7 +69,7 @@

Navigation

\ No newline at end of file diff --git a/index.html b/index.html index 3ca4d296..ad41ce15 100644 --- a/index.html +++ b/index.html @@ -7,9 +7,9 @@ MSlice for Mantid — MSlice 2.9 documentation - + - + @@ -114,7 +114,7 @@

This Page

rel="nofollow">Show Source - + @@ -143,7 +143,7 @@

Navigation

\ No newline at end of file diff --git a/math_ref.html b/math_ref.html index cb887bbe..90960fb5 100644 --- a/math_ref.html +++ b/math_ref.html @@ -7,9 +7,9 @@ 5. Mathematical Reference — MSlice 2.9 documentation - + - + @@ -230,7 +230,7 @@

This Page

rel="nofollow">Show Source - + @@ -259,7 +259,7 @@

Navigation

\ No newline at end of file diff --git a/quickstart.html b/quickstart.html index 191b2c67..ae5133e3 100644 --- a/quickstart.html +++ b/quickstart.html @@ -7,9 +7,9 @@ 1. Quick Start — MSlice 2.9 documentation - + - + @@ -61,7 +61,8 @@

1.1. Starting MSlice

1.2. Loading Data

-_images/load_tab.png +_images/load_tab.png +

The GUI is divided into three main tabs, a Data Loading tab which shows the filesystem and allows the user to load reduced data files, a Workspace Manager which handles the loaded data, and a Plots tab which provides an easy way to interact with all currently open plots. To reach a particular data folder you can either @@ -97,21 +98,24 @@

1.2. Loading Data

1.4. Plotting a Slice

-_images/data_tab.png +_images/data_tab.png +

Once the Slice tab is enabled (either directly for loaded non-PSD data, or after calculating projections for PSD data) you can click Display to show a 2D slice of the data. The default values of the limits of the data and step sizes are taken from the input data file. You can change these values and replot. Note that there is a minimum step size which is 1/100 of the default step size which is to ensure that the program does not run out of memory for very small step sizes (which have large number of points). For step sizes smaller than the data step size, some pixels will contain no data and will appear empty (white) in the 2D slice. For more details see Slicing from the GUI.

-_images/slice_intensity.png +_images/slice_intensity.png +

Once the slice is displayed (in a separate window), double clicking on the plot or colorbar axes will allow you to change the plot limits, and whether to use a linear or logarithmic axis. Double clicking on the plot or axes titles will allow you to edit them. Both changing the limits and titles can be done using the options menu accessible from the toolbar.

1.5. Interactive Cuts

-_images/interactive_cuts.png +_images/interactive_cuts.png +

From the slice window, you can also select an Interactive Cut which will allow you to select a region of data to integrate into a 1D and dynamically change this region and the corresponding cut. Clicking Interactive Cut will change the cursor to a cross-hair. You should then select a rectangular region in the 2D slice, after which a separate @@ -128,14 +132,16 @@

1.4. Plotting a Slice

1.6. Plotting a Cut

-_images/cut_q.png +_images/cut_q.png +

Instead of an interactive cut, you can use the main GUI to specify more specific limits and step sizes for cuts. This will also allow you to overplot multiple cuts from the same dataset with different integration ranges, or from different datasets. To overplot multiple ranges, you can also use the width parameter. This splits in specified integration ranges into chunks of the widths specified. For example, if from is 0 and to is 10 and width is 3, Mslice will plot 4 cuts which integrate over [0,3], [3,6], [6,9] and [9,10] respectively.

-_images/multi_cut.png +_images/multi_cut.png +

To overplot multiple datasets, you can select multiple workspaces in the left pane (using Shift or Ctrl) and then give common limits, step sizes and integration range, and click Plot. For more details see Cutting from the GUI.

@@ -161,7 +167,8 @@

1.8. Manipulating WorkspacesAdd. A new workspace named after the first selected workspace with _sum appended will be created.

-_images/subtract_dialog.png +_images/subtract_dialog.png +

To subtract a background dataset from sample dataset(s), first select one or more sample workspace(s). Then click Subtract. A dialog will appear asking you to select the background dataset to subtract and optionally allow you to specify a self-shielding factor. This self-shielding factor is applied to the background dataset first before it @@ -171,7 +178,8 @@

1.8. Manipulating Workspaces1.00. Clicking Ok will produce two subtracted workspaces, MAR28237_Ei10.00meV_subtracted and MAR28236_Ei10.00meV_subtracted. The subtracted dataset can be sliced or cut as usual.

-_images/subtract_slice.png +_images/subtract_slice.png +

1.9. Energy transfer units

@@ -232,7 +240,7 @@

This Page

rel="nofollow">Show Source - + @@ -264,7 +272,7 @@

Navigation

\ No newline at end of file diff --git a/search.html b/search.html index f2f3256b..5b34e7ad 100644 --- a/search.html +++ b/search.html @@ -6,17 +6,18 @@ Search — MSlice 2.9 documentation - + - + - - + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js index 91c36d5c..ae3f1163 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["cli", "cutting", "index", "math_ref", "quickstart", "slicing"], "filenames": ["cli.rst", "cutting.rst", "index.rst", "math_ref.rst", "quickstart.rst", "slicing.rst"], "titles": ["4. Command Line Interface", "2. Taking Cuts", "MSlice for Mantid", "5. Mathematical Reference", "1. Quick Start", "3. 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Command Line Interface", "2. Taking Cuts", "MSlice for Mantid", "5. Mathematical Reference", "1. Quick Start", "3. Taking Slices"], "titleterms": {"A": 3, "algebra": 0, "algorithm": [1, 3], "command": 0, "convert": [1, 5], "current": 4, "cut": [0, 1, 3, 4], "data": [1, 4, 5], "displai": [1, 5], "energi": 4, "exampl": 0, "file": 5, "from": [1, 5], "gener": 0, "gui": [1, 5], "inform": [1, 5], "intens": [1, 5], "interact": 4, "interfac": 0, "keep": 4, "line": [0, 1, 5], "load": [0, 4], "make": 4, "manipul": [0, 4], "mantid": 2, "mathemat": 3, "matplotlib": 0, "mode": 4, "mslice": [0, 2, 4], "non": [3, 4], "note": 3, "overplot": [1, 5], "plot": [0, 4], "powder": [1, 5], "psd": [3, 4], "quick": 4, "recoil": 5, "refer": 3, "region": 3, "save": [1, 5], "script": 0, "seri": 0, "slice": [0, 3, 4, 5], "specif": 0, "start": 4, "take": [1, 5], "transfer": 4, "two": 3, "unit": [3, 4], "us": 0, "valid": 3, "workspac": [0, 4]}}) \ No newline at end of file diff --git a/slicing.html b/slicing.html index cc56dc5d..44fbfb3a 100644 --- a/slicing.html +++ b/slicing.html @@ -7,9 +7,9 @@ 3. Taking Slices — MSlice 2.9 documentation - + - + @@ -67,8 +67,10 @@

3. Taking Slices

3.2. Overplotting recoil and powder lines

-_images/recoil.png -_images/powder_lines1.png +_images/recoil.png + +_images/powder_lines1.png +

To help with a “first look” data analysis, MSlice can overplot on the 2D slices the recoil lines of light nuclei (Hydrogen 1H, Deuterium 2H, Helium and 4He are implemented but a user defined Z is also available), and the positions of powder reflections from common sample environment materials (Aluminium, Copper, @@ -79,7 +81,8 @@

3.2. Overplotting recoil and powder line

3.3. Converting intensity information in displayed data in slices

-_images/intensity_chi.png +_images/intensity_chi.png +

In addition to displaying the data as S(Q, \omega), the slice figure window can also display the data with the Bose factor corrected, as the dynamical susceptibility \chi''(Q, \omega) or as the density of states. For these options, the sample temperature must be given. This can either be specified as a log key, if the sample @@ -155,7 +158,7 @@

This Page

rel="nofollow">Show Source - + @@ -187,7 +190,7 @@

Navigation

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