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b/_sources/index.rst.txt @@ -0,0 +1,101 @@ +.. vbjax documentation master file, created by + sphinx-quickstart on Tue Dec 5 11:11:08 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +*********************************** +Welcome to vbjax's documentation! +*********************************** + +Introduction +############ +`vbjax` is a Jax-based package for working with virtual brain style models. + +Installation +############ + +Installs with `pip install "vbjax"`, but you can use the source, + +.. code-block:: bash + + git clone https://github.com/ins-amu/vbjax + cd vbjax + pip install .[dev] + + +The primary additional dependency of vbjax is +[JAX](github.com/google/jax), which itself depends only on +NumPy, SciPy & opt-einsum, so it should be safe to add to your +existing projects. + +gee pee you +------------ + +**CUDA** + +If you have a CUDA-enabled GPU, you install the requisite dependencies like so + +.. code-block:: bash + + pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html + + +**M1/M2** 🍎 + +On newer Apple machines w/ M1 or M2 GPUs, JAX supports using the GPU experimentally +by installing just two extra packages: + +.. code-block:: bash + + pip install ml-dtypes==0.2.0 jax-metal + + +About a third of vbjax tests fail due to absence of certain operations like n-dim +scatter/gather & FFTs, and it may not be faster because these CPUs already have +excellent memory bandwidth & latency hiding. + +**CUDA** 🐳 + +*BUT* because GPU software stack versions make aligning stars look like child's play, +container images are available and auto-built w/ +[GitHub Actions](.github/workflows/docker-image.yml), so you can use w/ Docker + +.. code-block:: bash + + docker run --rm -it ghcr.io/ins-amu/vbjax:main python3 -c 'import vbjax; print(vbjax.__version__)' + + +The images are built on Nvidia runtime images, so `--gpus all` is enough +for Jax to discover the GPU(s). + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + +Tutorial +######## + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + tutorial + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + +Modules +######## + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + modules + diff --git a/_sources/modules.rst.txt b/_sources/modules.rst.txt new file mode 100644 index 0000000..79a7fdf --- /dev/null +++ b/_sources/modules.rst.txt @@ -0,0 +1,66 @@ +neural_mass +----------- + +.. automodule:: vbjax.neural_mass + :members: + :undoc-members: + :show-inheritance: + +monitor +-------- + +.. automodule:: vbjax.monitor + :members: + :undoc-members: + :show-inheritance: + +loops +----- + +.. automodule:: vbjax.loops + :members: + :undoc-members: + :show-inheritance: + +connectome +---------- + +.. automodule:: vbjax.connectome + :members: + :undoc-members: + :show-inheritance: + +layers +------ + +.. automodule:: vbjax.layers + :members: + :undoc-members: + :show-inheritance: + + + + +sparse +------ + +.. automodule:: vbjax.sparse + :members: + :undoc-members: + :show-inheritance: + +util +---- + +.. automodule:: vbjax.util + :members: + :undoc-members: + :show-inheritance: + +shtlc +----- + +.. automodule:: vbjax.shtlc + :members: + :undoc-members: + :show-inheritance: diff --git a/_sources/tutorial.rst.txt b/_sources/tutorial.rst.txt new file mode 100644 index 0000000..3a5efeb --- /dev/null +++ b/_sources/tutorial.rst.txt @@ -0,0 +1,7 @@ +Examples +======== + +.. automodule:: 00_intro + +.. automodule:: 01_sweep + diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, 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center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +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; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 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caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, 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b/_static/doctools.js new file mode 100644 index 0000000..d06a71d --- /dev/null +++ b/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2023 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(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + 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+ switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 0000000..44860e8 --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '0.1.dev1+gb4f27ec', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 0000000000000000000000000000000000000000..a858a410e4faa62ce324d814e4b816fff83a6fb3 GIT binary patch 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* :copyright: Copyright 2007-2023 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 */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = 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for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) 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." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + 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; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // 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([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.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; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // 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 }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // 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]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * 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))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + 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 SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + 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( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * 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")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..ffc526d --- /dev/null +++ b/genindex.html @@ -0,0 +1,574 @@ + + + + + + + Index — vbjax 0.1.dev1+gb4f27ec documentation + + + + + + + + + + + +
+
+
+
+ + +

Index

+ +
+ A + | B + | C + | D + | E + | G + | H + | I + | J + | K + | M + | N + | R + | S + | T + | U + | V + | X + | Y + +
+

A

+ + + +
+ +

B

+ + + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

E

+ + + +
+ +

G

+ + +
+ +

H

+ + +
+ +

I

+ + + +
+ +

J

+ + + +
+ +

K

+ + + +
+ +

M

+ + + +
+ +

N

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + + +
+ +

U

+ + +
+ +

V

+ + + +
    +
  • + vbjax.monitor + +
    • +
  • + vbjax.neural_mass + +
    • +
  • + vbjax.shtlc + +
    • +
  • + vbjax.sparse + +
    • +
  • + vbjax.util + +
    • +
+ +

X

+ + +
+ +

Y

+ + + +
+ + + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..265d9fb --- /dev/null +++ b/index.html @@ -0,0 +1,266 @@ + + + + + + + + Welcome to vbjax’s documentation! — vbjax 0.1.dev1+gb4f27ec documentation + + + + + + + + + + + + +
+
+
+
+ +
+

Welcome to vbjax’s documentation!

+
+

Introduction

+

vbjax is a Jax-based package for working with virtual brain style models.

+
+
+

Installation

+

Installs with pip install "vbjax", but you can use the source,

+
git clone https://github.com/ins-amu/vbjax
+cd vbjax
+pip install .[dev]
+
+
+

The primary additional dependency of vbjax is +[JAX](github.com/google/jax), which itself depends only on +NumPy, SciPy & opt-einsum, so it should be safe to add to your +existing projects.

+
+

gee pee you

+

CUDA

+

If you have a CUDA-enabled GPU, you install the requisite dependencies like so

+
pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+
+
+

M1/M2 🍎

+

On newer Apple machines w/ M1 or M2 GPUs, JAX supports using the GPU experimentally +by installing just two extra packages:

+
pip install ml-dtypes==0.2.0 jax-metal
+
+
+

About a third of vbjax tests fail due to absence of certain operations like n-dim +scatter/gather & FFTs, and it may not be faster because these CPUs already have +excellent memory bandwidth & latency hiding.

+

CUDA 🐳

+

BUT because GPU software stack versions make aligning stars look like child’s play, +container images are available and auto-built w/ +[GitHub Actions](.github/workflows/docker-image.yml), so you can use w/ Docker

+
docker run --rm -it ghcr.io/ins-amu/vbjax:main python3 -c 'import vbjax; print(vbjax.__version__)'
+
+
+

The images are built on Nvidia runtime images, so --gpus all is enough +for Jax to discover the GPU(s).

+
+
+
+
+
+

Tutorial

+
+

Contents:

+ +
+ +
+
+

Modules

+
+

Contents:

+ +
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/modules.html b/modules.html new file mode 100644 index 0000000..72dafda --- /dev/null +++ b/modules.html @@ -0,0 +1,1184 @@ + + + + + + + + neural_mass — vbjax 0.1.dev1+gb4f27ec documentation + + + + + + + + + + + + +
+
+
+
+ +
+

neural_mass

+
+
+class JRTheta(A, B, a, b, v0, nu_max, r, J, a_1, a_2, a_3, a_4, mu, I)
+

Bases: tuple

+
+
+A
+

Alias for field number 0

+
+ +
+
+B
+

Alias for field number 1

+
+ +
+
+I
+

Alias for field number 13

+
+ +
+
+J
+

Alias for field number 7

+
+ +
+
+a
+

Alias for field number 2

+
+ +
+
+a_1
+

Alias for field number 8

+
+ +
+
+a_2
+

Alias for field number 9

+
+ +
+
+a_3
+

Alias for field number 10

+
+ +
+
+a_4
+

Alias for field number 11

+
+ +
+
+b
+

Alias for field number 3

+
+ +
+
+mu
+

Alias for field number 12

+
+ +
+
+nu_max
+

Alias for field number 5

+
+ +
+
+r
+

Alias for field number 6

+
+ +
+
+v0
+

Alias for field number 4

+
+ +
+ +
+
+class JRState(y0, y1, y2, y3, y4, y5)
+

Bases: tuple

+
+
+y0
+

Alias for field number 0

+
+ +
+
+y1
+

Alias for field number 1

+
+ +
+
+y2
+

Alias for field number 2

+
+ +
+
+y3
+

Alias for field number 3

+
+ +
+
+y4
+

Alias for field number 4

+
+ +
+
+y5
+

Alias for field number 5

+
+ +
+ +
+
+jr_dfun(ys, c, p)
+
+ +
+
+class BVEPTheta(tau0, I1, x0)
+

Bases: tuple

+
+
+I1
+

Alias for field number 1

+
+ +
+
+tau0
+

Alias for field number 0

+
+ +
+
+x0
+

Alias for field number 2

+
+ +
+ +
+
+bvep_dfun(ys, c, p: BVEPTheta)
+
+ +
+
+class MPRTheta(tau, I, Delta, J, eta, cr, cv)
+

Bases: tuple

+
+
+Delta
+

Alias for field number 2

+
+ +
+
+I
+

Alias for field number 1

+
+ +
+
+J
+

Alias for field number 3

+
+ +
+
+cr
+

Alias for field number 5

+
+ +
+
+cv
+

Alias for field number 6

+
+ +
+
+eta
+

Alias for field number 4

+
+ +
+
+tau
+

Alias for field number 0

+
+ +
+ +
+
+class MPRState(r, V)
+

Bases: tuple

+
+
+V
+

Alias for field number 1

+
+ +
+
+r
+

Alias for field number 0

+
+ +
+ +
+
+mpr_dfun(ys, c, p)
+
+ +
+
+mpr_r_positive(rv, _)
+
+ +
+
+class BOLDTheta(tau_s, tau_f, tau_o, alpha, te, v0, e0, epsilon, nu_0, r_0, recip_tau_s, recip_tau_f, recip_tau_o, recip_alpha, recip_e0, k1, k2, k3)
+

Bases: tuple

+
+
+alpha
+

Alias for field number 3

+
+ +
+
+e0
+

Alias for field number 6

+
+ +
+
+epsilon
+

Alias for field number 7

+
+ +
+
+k1
+

Alias for field number 15

+
+ +
+
+k2
+

Alias for field number 16

+
+ +
+
+k3
+

Alias for field number 17

+
+ +
+
+nu_0
+

Alias for field number 8

+
+ +
+
+r_0
+

Alias for field number 9

+
+ +
+
+recip_alpha
+

Alias for field number 13

+
+ +
+
+recip_e0
+

Alias for field number 14

+
+ +
+
+recip_tau_f
+

Alias for field number 11

+
+ +
+
+recip_tau_o
+

Alias for field number 12

+
+ +
+
+recip_tau_s
+

Alias for field number 10

+
+ +
+
+tau_f
+

Alias for field number 1

+
+ +
+
+tau_o
+

Alias for field number 2

+
+ +
+
+tau_s
+

Alias for field number 0

+
+ +
+
+te
+

Alias for field number 4

+
+ +
+
+v0
+

Alias for field number 5

+
+ +
+ +
+
+compute_bold_theta(tau_s=0.65, tau_f=0.41, tau_o=0.98, alpha=0.32, te=0.04, v0=4.0, e0=0.4, epsilon=0.5, nu_0=40.3, r_0=25.0)
+
+ +
+
+bold_dfun(sfvq, x, p: BOLDTheta)
+
+ +
+
+class DCMTheta(A, B, C)
+

Bases: tuple

+
+
+A
+

Alias for field number 0

+
+ +
+
+B
+

Alias for field number 1

+
+ +
+
+C
+

Alias for field number 2

+
+ +
+ +
+
+dcm_dfun(x, u, p: DCMTheta)
+

Implements the classical bilinear DCM +dot{x} = (A + sum_j u_j B_j ) x + C u

+
+ +
+
+DopaTheta
+

alias of dopaTheta

+
+ +
+
+class DopaState(r, V, u, Sa, Sg, Dp)
+

Bases: tuple

+
+
+Dp
+

Alias for field number 5

+
+ +
+
+Sa
+

Alias for field number 3

+
+ +
+
+Sg
+

Alias for field number 4

+
+ +
+
+V
+

Alias for field number 1

+
+ +
+
+r
+

Alias for field number 0

+
+ +
+
+u
+

Alias for field number 2

+
+ +
+ +
+
+dopa_dfun(y, cy, p: dopaTheta)
+

Adaptive QIF model with dopamine modulation.

+
+ +
+
+dopa_net_dfun(y, p)
+

Canonical form for network of dopa nodes.

+
+ +
+
+dopa_r_positive(y, _)
+
+ +
+
+dopa_gfun_mulr(y, p)
+

Provide a multiplicative r, additive V gfun.

+
+ +
+
+dopa_gfun_add(y, p)
+

Provides an additive noise gfun.

+
+ +
+
+

monitor

+
+
+make_offline(step_fn, sample_fn, *args)
+

Compute monitor samples in an offline or batch fashion.

+
+ +
+
+make_timeavg(shape)
+

Make a time average monitor.

+
+ +
+
+compute_sarvas_gain(q, r, o, att, Ds=0, Dc=0) → Array
+
+ +
+
+make_gain(gain, shape=None)
+

Make a gain-matrix monitor suitable for sEEG, EEG & MEG.

+
+ +
+
+make_bold(shape, dt, p: BOLDTheta)
+

Make a BOLD fMRI monitor.

+
+ +
+
+make_cov(shape)
+
+ +
+
+make_fc(shape)
+
+ +
+
+make_fft(shape, period)
+
+ +
+
+

loops

+

Functions for building time stepping loops.

+
+
+heun_step(x, dfun, dt, *args, add=0, adhoc=None, return_euler=False)
+

Use a Heun scheme to step state with a right hand sides dfun(.) +and additional forcing term add.

+
+ +
+
+make_sde(dt, dfun, gfun, adhoc=None, return_euler=False, unroll=10)
+

Use a stochastic Heun scheme to integrate autonomous stochastic +differential equations (SDEs).

+
+
Parameters:
+
+
dtfloat

Time step

+
+
dfunfunction

Function of the form dfun(x, p) that computes drift coefficients of +the stochastic differential equation.

+
+
gfunfunction or float

Function of the form gfun(x, p) that computes diffusion coefficients +of the stochastic differential equation. If a numerical value is +provided, this is used as a constant diffusion coefficient for additive +linear SDE.

+
+
adhocfunction or None

Function of the form f(x, p) that allows making adhoc corrections +to states after a step.

+
+
return_euler: bool, default False

Return solution with local Euler estimates.

+
+
unroll: int, default 10

Force unrolls the time stepping loop.

+
+
+
+
Returns:
+
+
stepfunction

Function of the form step(x, z_t, p) that takes one step in time +according to the Heun scheme.

+
+
loopfunction

Function of the form loop(x0, zs, p) that iteratively calls step +for all z.

+
+
+
+
+

Notes

+

In both cases, a Jax compatible parameter set p is provided, either an array +or some pytree compatible structure.

+

Note that the integrator does not sample normally distributed noise, so this +must be provided by the user.

+
>>> import vbjax as vb
+>>> _, sde = vb.make_sde(1.0, lambda x, p: -x, 0.1)
+>>> sde(1.0, vb.randn(4), None)
+Array([ 0.5093468 ,  0.30794007,  0.07600437, -0.03876263], dtype=float32)
+
+
+
+ +
+
+make_ode(dt, dfun, adhoc=None)
+

Use a Heun scheme to integrate autonomous ordinary differential +equations (ODEs).

+
+
Parameters:
+
+
dtfloat

Time step

+
+
dfunfunction

Function of the form dfun(x, p) that computes derivatives of the +ordinary differential equations.

+
+
adhocfunction or None

Function of the form f(x, p) that allows making adhoc corrections +to states after a step.

+
+
+
+
Returns:
+
+
stepfunction

Function of the form step(x, t, p) that takes one step in time +according to the Heun scheme.

+
+
loopfunction

Function of the form loop(x0, ts, p) that iteratively calls step +for all time steps ts.

+
+
+
+
+

Notes

+

In both cases, a Jax compatible parameter set p is provided, either an array +or some pytree compatible structure.

+
>>> import vbjax as vb, jax.numpy as np
+>>> _, ode = vb.make_ode(1.0, lambda x, p: -x)
+>>> ode(1.0, np.r_[:4], None)
+Array([0.5   , 0.25  , 0.125 , 0.0625], dtype=float32, weak_type=True)
+
+
+
+ +
+
+make_dde(dt, nh, dfun, unroll=10, adhoc=None)
+

Invokes make_sdde w/ gfun 0.

+
+ +
+
+make_sdde(dt, nh, dfun, gfun, unroll=1, zero_delays=False, adhoc=None)
+

Use a stochastic Heun scheme to integrate autonomous +stochastic delay differential equations (SDEs).

+
+
Parameters:
+
+
dtfloat

Time step

+
+
nhint

Maximum delay in time steps.

+
+
dfunfunction

Function of the form dfun(xt, x, t, p) that computes drift coefficients of +the stochastic differential equation.

+
+
gfunfunction or float

Function of the form gfun(x, p) that computes diffusion coefficients +of the stochastic differential equation. If a numerical value is +provided, this is used as a constant diffusion coefficient for additive +linear SDE.

+
+
adhocfunction or None

Function of the form f(x,p) that allows making adhoc corrections after +each step.

+
+
+
+
Returns:
+
+
stepfunction

Function of the form step((x_t,t), z_t, p) that takes one step in time +according to the Heun scheme.

+
+
loopfunction

Function of the form loop((xs, t), p) that iteratively calls step +for each xs[nh:] and starting time index t.

+
+
+
+
+

Notes

+
    +

  • A Jax compatible parameter set p is provided, either an array +or some pytree compatible structure.

    • +

  • The integrator does not sample normally distributed noise, so this +must be provided by the user.

    • +

  • The history buffer passed to the user functions, on the corrector +stage of the Heun method, does not contain the predictor stage, for +performance reasons, unless zero_delays is set to True. +A good compromise can be to set all zero delays to dt.

    • +
+
>>> import vbjax as vb, jax.numpy as np
+>>> _, sdde = vb.make_sdde(1.0, 2, lambda xt, x, t, p: -xt[t-2], 0.0)
+>>> x,t = sdde(np.ones(6)+10, None)
+>>> x
+Array([ 11.,  11.,  11.,   0., -11., -22.], dtype=float32)
+
+
+
+ +
+
+make_continuation(run_chunk, chunk_len, max_lag, n_from, n_svar, stochastic=True)
+

Helper function to lower memory usage for longer simulations with time delays. +WIP

+

Takes a function

+
+

run_chunk(buf, params) -> (buf, chunk_states)

+
+

and returns another

+
+

continue_chunk(buf, params, rng_key) -> (buf, chunk_states)

+
+

The continue_chunk function wraps run_chunk and manages +moving the latest states to the first part of buf and filling +the rest with samples from N(0,1) if required.

+
+ +
+
+

connectome

+

Utilities for connectomes.

+
+
+make_conn_latent_mvnorm(SCs, nc=10, return_full=False)
+

Make a latent multivariate normal distribution over connectomes.

+
+
Parameters:
+
+
SCs(nconn, n, n) array

Array of connectomes in a given parcellation.

+
+
ncint, optional

Number of components to use for the latent space.

+
+
return_full: bool, optional

Whether or not to return extra information on the SVD.

+
+
+
+
Returns:
+
+
u_mean(nc, ), array_like

Mean of distribution in latent space.

+
+
u_cov(nc, nc), array_like

Covariance of distribution in latent space.

+
+
xfmfunction

Maps latent vector to full connectome.

+
+
u_cov(nc, nc) array

Covariance of the multivariate normal. Returned if return_full=True.

+
+
u(nconn, nconn) array

Left singular vectors corresponding to connectomes embedded. +Returned if return_full=True.

+
+
s(nconn) array

Singular values. Returned if return_full=True.

+
+
vt(nconn, n*n) array

Right singular vectors. Returned if return_full=True.

+
+
nconfint

Number of confusions induced by dimensionality reduction. +Returned if return_full=True.

+
+
+
+
+
+ +
+
+

layers

+
+
+make_dense_layers(in_dim, latent_dims=[10], out_dim=None, init_scl=0.1, extra_in=0, act_fn=<PjitFunction of <function leaky_relu>>, key=Array([ 0, 42], dtype=uint32))
+

Make a dense neural network with the given latent layer sizes.

+
+ +
+
+

sparse

+
+
+make_spmv(A, is_symmetric=False, use_scipy=False)
+

Make a closure for a general sparse matrix-vector multiplication.

+
+
Parameters:
+
+
Ascipy.sparse.csr_matrix

Constant sparse matrix.

+
+
is_symmetricbool, optional, default False

Whether matrix is symmetric.

+
+
use_scipy: bool, optional, default False

Use scipy.

+
+
+
+
Returns:
+
+
spmvfunction

Function implementing spase matrix vector multiply with +support for gradients in Jax.

+
+
+
+
+
+ +
+
+csr_to_jax_bcoo(A: csr_matrix)
+

Convert CSR format to batched COO format.

+
+ +
+
+make_sg_spmv(A: csr_matrix, use_pmap=False, sharding: PositionalSharding = None)
+

Make a SpMV kernel w/ generic scatter-gather operations.

+
+ +
+
+

util

+
+
+to_np(x: Array) → ndarray
+
+ +
+
+to_jax(x: ndarray)
+

Move NumPy array to JAX via DLPack.

+
+ +
+
+tuple_meshgrid(tup)
+

Applies meshgrid to arrays in a named tuple.

+
+ +
+
+tuple_ravel(tup)
+

Flatten arrays in fields of tuple.

+
+ +
+
+tuple_shard(tup, n)
+

Shard arrays in fields of tuple.

+
+ +
+
+

shtlc

+

SHT based local coupling functions.

+
+
+make_grid_shtns(lmax, nlat, nlon, D)
+

Create shtns object and grid as in make_grid.

+
+ +
+
+make_lm(lmax: int)
+
+ +
+
+make_grid(nlat, nlon)
+

Create grid for SHT, phi latitude, theta longitude.

+
+ +
+
+grid_pairwise_distance(theta, phi)
+

Compute pairwise distances on grid. Memory intensive for large grids.

+
+ +
+
+randn_relaxed(sht)
+

For shtns sht return random spatial array captured by sht.

+
+ +
+
+kernel_diff(D, l)
+

Compute diffusion kernel, l in shtns order.

+
+ +
+
+kernel_dist_origin(theta, phi)
+

Compute distance to origin on grid.

+
+ +
+
+kernel_sh_normalized(sht, k)
+
+ +
+
+kernel_laplace(sht, theta, phi, size)
+

Compute spatial & spectral coefficients for Laplacian kernel.

+
+ +
+
+kernel_gaussian(sht, theta, phi, size)
+

Compute spatial & spectral coefficients for Gaussian kernel.

+
+ +
+
+kernel_mexican_hat(sht, theta, phi, size)
+

Compute spatial & spectral coefficients for Mexican hat kernel.

+
+ +
+
+kernel_conv_prep(sht, k)
+

Prepares evaluated kernel for SHT convolution.

+
+ +
+
+kernel_estimate_shtns(sht, k, x0)
+

Estimate effective kernel for kernel k with state x0 for shtns object sht.

+
+ +
+
+make_shtdiff_np(lmax, nlat, nlon, D, return_L=False, np=<module 'numpy' from '/opt/hostedtoolcache/Python/3.12.2/x64/lib/python3.12/site-packages/numpy/__init__.py'>)
+

Construct SHT diff implementation in plain NumPy.

+
+ +
+
+make_shtdiff(nlat, lmax=None, nlon=None, D=0.0004, return_L=False)
+

Construct SHT diff implementation with Jax.

+
+ +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000000000000000000000000000000000000..c6f8c3938cd144e52e020318733a62854c10ecff GIT binary patch literal 1039 zcmV+q1n~PKAX9K?X>NERX>N99Zgg*Qc_4OWa&u{KZXhxWBOp+6Z)#;@bUGk*VrpS{ z3L_v^WpZQrV+tc6RA^-&a%F8{X>Md?av*PJAarPH zb0B7EY-J#6b0A}HZE$jBb8}^6Aa!$TZf78RY-wUH3V7PB+0Aa_HV_B!yPrZudkqmM zyO+H+n>{3G(4bjtkHlCUOWg1aB&FJW+Slmo^+_sOR$>+CI7VgJE;)fucVtLZ}$ZMNp;>C440)y1m+4-yuhQI6lGfs8Io+dCiaSZv$5 zI&1H$^?AA1ItKO_Q$g?qrci}0p?oc|AkOX!9UMR@Rtk%a zCzzy2XrZy*>Fi^{q#wnw#%$>F5CyS^BpcAKD01rP#v4UoweJaPTT{?B6BKbe{B~=! zLxRlOBJ|BN>9C7nq=i)ScRNwy=J(%jKew1+^tBlaElGQI0!(NR8gh<$Gc2Xj3V6xm zA!#%H@yRuw*F1j3C$n{w3Ao&Yns)KLQnGBuWzEK_jMs*Ua4u3@avAn@3 zki~n_+W7M6k#volow!?bV#jG?^;_&H{PyDmWz;hhzcMn#4F`XuU?1Qq!?eCihC4fP z8#uAz33$9=@h>bLS-KBA*9r8wMnCKA2F%;|lU!6%({kL3lvMq;uJ99i1s)Mir`Y{?zkizaF% z1L*jdPAHX58C+eGD4sDoG~=L0s z16@iQDA@*r0n#*E-02#eY#|eLYUTI_2aNuPs>Dwl)5BUJq4Fs{P-Bb9@Ue6;ojU1? zmTv^7oQ!B-w|F`O#8mP=ZUUlCQD!fPBXU!FUlMj4VIxzpJpnFOUDl>xWMgwNjcIxP z5iC7PQ~NF$9R4<`UA}xzV1yn`u}Uq(A7(Y^v{SgNQdS=fY=)eRbu}M7w5#sMkE_>a z%GYC~lNNuXsmC|G*;j{d{PX?qR1M8Ki!L8tPyVzTqW>o;>@VgYrcw{nd7Cni-91e` z9YJ++yIP%8`a#6wKDWbcoFyfMShweJIyRZ7>GwxyaFx3}T=2o1c56O1wf?jNJDh^F J`WGr~55W?*@Dl(4 literal 0 HcmV?d00001 diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 0000000..9824320 --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,137 @@ + + + + + + + Python Module Index — vbjax 0.1.dev1+gb4f27ec documentation + + + + + + + + + + + + + + +
+
+
+
+ + +

Python Module Index

+ +
+ v +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
+ v
+ vbjax +
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    + vbjax.monitor +
    + vbjax.neural_mass +
    + vbjax.shtlc +
    + vbjax.sparse +
    + vbjax.util +
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..e2f02f9 --- /dev/null +++ b/search.html @@ -0,0 +1,101 @@ + + + + + + + Search — vbjax 0.1.dev1+gb4f27ec documentation + + + + + + + + + + + + + + + + + +
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+ + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..691b62c --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["index", "modules", "tutorial"], "filenames": ["index.rst", "modules.rst", "tutorial.rst"], "titles": ["Welcome to vbjax\u2019s documentation!", "neural_mass", "Examples"], "terms": {"i": [0, 1], "jax": [0, 1], "base": [0, 1], "packag": [0, 1], "work": 0, "virtual": 0, "brain": 0, "style": 0, "model": [0, 1], "pip": 0, "can": [0, 1], "us": [0, 1], "sourc": 0, "git": 0, "clone": 0, "http": 0, "github": 0, "com": 0, "ins": 0, "amu": 0, "cd": 0, "dev": 0, "The": [0, 1], "primari": 0, "addit": [0, 1], "depend": 0, "googl": 0, "which": 0, "itself": 0, "onli": 0, "numpi": [0, 1], "scipi": [0, 1], "opt": [0, 1], "einsum": 0, "so": [0, 1], "should": 0, "safe": 0, "add": [0, 1], "your": 0, "exist": 0, "project": 0, "cuda": 0, "If": [0, 1], "have": 0, "enabl": 0, "gpu": 0, "requisit": 0, 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Examples

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