├── .Rhistory ├── .gitignore ├── .readthedocs.yaml ├── LICENSE.md ├── README.md ├── docs ├── .readthedocs.yml ├── Makefile ├── _static │ ├── basic.css │ ├── css │ │ ├── badge_only.css │ │ └── theme.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── fonts │ │ ├── Inconsolata-Bold.ttf │ │ ├── Inconsolata-Regular.ttf │ │ ├── Inconsolata.ttf │ │ ├── Lato-Bold.ttf │ │ ├── Lato-Regular.ttf │ │ ├── Lato │ │ │ ├── lato-bold.eot │ │ │ ├── lato-bold.ttf │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-bolditalic.eot │ │ │ ├── lato-bolditalic.ttf │ │ │ ├── lato-bolditalic.woff │ │ │ ├── lato-bolditalic.woff2 │ │ │ ├── lato-italic.eot │ │ │ ├── lato-italic.ttf │ │ │ ├── lato-italic.woff │ │ │ ├── lato-italic.woff2 │ │ │ ├── lato-regular.eot │ │ │ ├── lato-regular.ttf │ │ │ ├── lato-regular.woff │ │ │ └── lato-regular.woff2 │ │ ├── RobotoSlab-Bold.ttf │ │ ├── RobotoSlab-Regular.ttf │ │ ├── RobotoSlab │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ └── roboto-slab-v7-regular.woff2 │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ └── fontawesome-webfont.woff2 │ ├── jquery-3.2.1.js │ ├── jquery.js │ ├── js │ │ ├── modernizr.min.js │ │ └── theme.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── underscore-1.3.1.js │ └── underscore.js ├── changelog.rst ├── conf.py ├── index.rst ├── intro.rst ├── make.bat ├── mneflow_api.rst ├── models.rst └── requirements.txt ├── examples ├── .ipynb ├── continuous_example.py ├── mneflow_example_tf2.ipynb ├── mneflow_save_restore.ipynb ├── own_graph_example.ipynb ├── regression_example.ipynb └── sequence_data_example.ipynb ├── mneflow ├── __init__.py ├── data.py ├── layers.py ├── models.py └── utils.py ├── py3ml.yml ├── requirements.txt ├── scripts └── basic_example.py └── setup.py /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zubara/mneflow/92ee4f85c27427c869116ab6a1c9693b5da8089e/.Rhistory -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *.pyo 3 | scripts/* 4 | docs/_build/* 5 | examples/*.py 6 | examples/.ipynb_checkpoints/ 7 | build 8 | datasets 9 | dist 10 | tests 11 | mneflow.egg-info 12 | tfr 13 | -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | version: 2 6 | 7 | build: 8 | os: "ubuntu-22.04" 9 | tools: 10 | python: "3.8" 11 | 12 | python: 13 | install: 14 | - requirements: docs/requirements.txt 15 | - method: pip 16 | path: . 17 | 18 | sphinx: 19 | configuration: docs/conf.py -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2019, Ivan Zubarev 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | 1. Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | 2. Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | 3. Neither the name of the copyright holder nor the names of its 17 | contributors may be used to endorse or promote products derived from 18 | this software without specific prior written permission. 19 | 20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 30 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # MNEflow 2 | Neural networks for EEG-MEG decoding with MNE-python and Tensorflow. 3 | 4 | # Installation 5 | ``` 6 | pip install mneflow 7 | ``` 8 | 9 | # Dependencies 10 | 11 | - tensorflow >= 2.1.0 12 | - mne > 0.24.0 13 | 14 | # Documentation 15 | 16 | API reference is avalable in the [Documentation](https://mneflow.readthedocs.io/en/latest/). 17 | 18 | Also check the [example notebooks](https://mneflow.readthedocs.io/en/latest/intro.html#examples). 19 | 20 | # References 21 | Zubarev I, Vranou G, Parkkonen L. MNEflow: Neural networks for EEG/MEG decoding and interpretation [link](https://www.sciencedirect.com/science/article/pii/S2352711021001795) 22 | 23 | When using the implemented models please cite: 24 | 25 | ### for LF-CNN or VAR-CNN 26 | Zubarev I, Zetter R, Halme HL, Parkkonen L. Adaptive neural network classifier for decoding MEG signals. Neuroimage. 2019 May 4;197:425-434. [link](https://www.sciencedirect.com/science/article/pii/S1053811919303544?via%3Dihub) 27 | 28 | ``` 29 | @article{Zubarev2019AdaptiveSignals., 30 | title = {{Adaptive neural network classifier for decoding MEG signals.}}, 31 | year = {2019}, 32 | journal = {NeuroImage}, 33 | author = {Zubarev, Ivan and Zetter, Rasmus and Halme, Hanna-Leena and Parkkonen, Lauri}, 34 | month = {5}, 35 | pages = {425--434}, 36 | volume = {197}, 37 | url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811919303544 http://www.ncbi.nlm.nih.gov/pubmed/31059799}, 38 | doi = {10.1016/j.neuroimage.2019.04.068}, 39 | issn = {1095-9572}, 40 | pmid = {31059799}, 41 | keywords = {Brain–computer interface, Convolutional neural network, Magnetoencephalography} 42 | } 43 | ``` 44 | 45 | ### for EEGNet 46 | ``` 47 | @article{Lawhern2018, 48 | author={Vernon J Lawhern and Amelia J Solon and Nicholas R Waytowich and Stephen M Gordon and Chou P Hung and Brent J Lance}, 49 | title={EEGNet: a compact convolutional neural network for EEG-based brain–computer interfaces}, 50 | journal={Journal of Neural Engineering}, 51 | volume={15}, 52 | number={5}, 53 | pages={056013}, 54 | url={http://stacks.iop.org/1741-2552/15/i=5/a=056013}, 55 | year={2018} 56 | } 57 | ``` 58 | 59 | 60 | ### for FBCSP-ShallowNet and Deep4 61 | ``` 62 | @article{Schirrmeister2017DeepVisualization, 63 | title = {{Deep learning with convolutional neural networks for EEG decoding and visualization}}, 64 | year = {2017}, 65 | journal = {Human Brain Mapping}, 66 | author = {Schirrmeister, Robin Tibor and Springenberg, Jost Tobias and Fiederer, Lukas Dominique Josef and Glasstetter, Martin and Eggensperger, Katharina and Tangermann, Michael and Hutter, Frank and Burgard, Wolfram and Ball, Tonio}, 67 | number = {11}, 68 | month = {11}, 69 | pages = {5391--5420}, 70 | volume = {38}, 71 | url = {http://doi.wiley.com/10.1002/hbm.23730}, 72 | doi = {10.1002/hbm.23730}, 73 | issn = {10659471}, 74 | keywords = {EEG analysis, brain, brain mapping, computer interface, electroencephalography, end‐to‐end learning, machine interface, machine learning, model interpretability} 75 | }``` 76 | -------------------------------------------------------------------------------- /docs/.readthedocs.yml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | # Required 6 | version: 2 7 | 8 | # Build documentation in the docs/ directory with Sphinx 9 | sphinx: 10 | configuration: docs/conf.py 11 | 12 | # Optionally build your docs in additional formats such as PDF 13 | formats: 14 | - pdf 15 | 16 | # Optionally set the version of Python and requirements required to build your docs 17 | python: 18 | version: 3.7 19 | install: 20 | - requirements: docs/requirements.txt 21 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SOURCEDIR = . 8 | BUILDDIR = _build 9 | 10 | # Put it first so that "make" without argument is like "make help". 11 | help: 12 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 13 | 14 | .PHONY: help Makefile 15 | 16 | # Catch-all target: route all unknown targets to Sphinx using the new 17 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 18 | %: Makefile 19 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /docs/_static/basic.css: -------------------------------------------------------------------------------- 1 | /* 2 | * basic.css 3 | * ~~~~~~~~~ 4 | * 5 | * Sphinx stylesheet -- basic theme. 6 | * 7 | * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. 8 | * :license: BSD, see LICENSE for details. 9 | * 10 | */ 11 | 12 | /* -- main layout ----------------------------------------------------------- */ 13 | 14 | div.clearer { 15 | clear: both; 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16 | 17 | /** 18 | * make the code below compatible with browsers without 19 | * an installed firebug like debugger 20 | if (!window.console || !console.firebug) { 21 | var names = ["log", "debug", "info", "warn", "error", "assert", "dir", 22 | "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", 23 | "profile", "profileEnd"]; 24 | window.console = {}; 25 | for (var i = 0; i < names.length; ++i) 26 | window.console[names[i]] = function() {}; 27 | } 28 | */ 29 | 30 | /** 31 | * small helper function to urldecode strings 32 | */ 33 | jQuery.urldecode = function(x) { 34 | return decodeURIComponent(x).replace(/\+/g, ' '); 35 | }; 36 | 37 | /** 38 | * small helper function to urlencode strings 39 | */ 40 | jQuery.urlencode = encodeURIComponent; 41 | 42 | /** 43 | * This function returns the parsed url parameters of the 44 | * current request. Multiple values per key are supported, 45 | * it will always return arrays of strings for the value parts. 46 | */ 47 | jQuery.getQueryParameters = function(s) { 48 | if (typeof s === 'undefined') 49 | s = document.location.search; 50 | var parts = s.substr(s.indexOf('?') + 1).split('&'); 51 | var result = {}; 52 | for (var i = 0; i < parts.length; i++) { 53 | var tmp = parts[i].split('=', 2); 54 | var key = jQuery.urldecode(tmp[0]); 55 | var value = jQuery.urldecode(tmp[1]); 56 | if (key in result) 57 | result[key].push(value); 58 | else 59 | result[key] = [value]; 60 | } 61 | return result; 62 | }; 63 | 64 | /** 65 | * highlight a given string on a jquery object by wrapping it in 66 | * span elements with the given class name. 67 | */ 68 | jQuery.fn.highlightText = function(text, className) { 69 | function highlight(node, addItems) { 70 | if (node.nodeType === 3) { 71 | var val = node.nodeValue; 72 | var pos = val.toLowerCase().indexOf(text); 73 | if (pos >= 0 && 74 | !jQuery(node.parentNode).hasClass(className) && 75 | !jQuery(node.parentNode).hasClass("nohighlight")) { 76 | var span; 77 | var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); 78 | if (isInSVG) { 79 | span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); 80 | } else { 81 | span = document.createElement("span"); 82 | span.className = className; 83 | } 84 | span.appendChild(document.createTextNode(val.substr(pos, text.length))); 85 | node.parentNode.insertBefore(span, node.parentNode.insertBefore( 86 | document.createTextNode(val.substr(pos + text.length)), 87 | node.nextSibling)); 88 | node.nodeValue = val.substr(0, pos); 89 | if (isInSVG) { 90 | var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); 91 | var bbox = node.parentElement.getBBox(); 92 | rect.x.baseVal.value = bbox.x; 93 | rect.y.baseVal.value = bbox.y; 94 | rect.width.baseVal.value = bbox.width; 95 | rect.height.baseVal.value = bbox.height; 96 | rect.setAttribute('class', className); 97 | addItems.push({ 98 | "parent": node.parentNode, 99 | "target": rect}); 100 | } 101 | } 102 | } 103 | else if (!jQuery(node).is("button, select, textarea")) { 104 | jQuery.each(node.childNodes, function() { 105 | highlight(this, addItems); 106 | }); 107 | } 108 | } 109 | var addItems = []; 110 | var result = this.each(function() { 111 | highlight(this, addItems); 112 | }); 113 | for (var i = 0; i < addItems.length; ++i) { 114 | jQuery(addItems[i].parent).before(addItems[i].target); 115 | } 116 | return result; 117 | }; 118 | 119 | /* 120 | * backward compatibility for jQuery.browser 121 | * This will be supported until firefox bug is fixed. 122 | */ 123 | if (!jQuery.browser) { 124 | jQuery.uaMatch = function(ua) { 125 | ua = ua.toLowerCase(); 126 | 127 | var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || 128 | /(webkit)[ \/]([\w.]+)/.exec(ua) || 129 | /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || 130 | /(msie) ([\w.]+)/.exec(ua) || 131 | ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || 132 | []; 133 | 134 | return { 135 | browser: match[ 1 ] || "", 136 | version: match[ 2 ] || "0" 137 | }; 138 | }; 139 | jQuery.browser = {}; 140 | jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; 141 | } 142 | 143 | /** 144 | * Small JavaScript module for the documentation. 145 | */ 146 | var Documentation = { 147 | 148 | init : function() { 149 | this.fixFirefoxAnchorBug(); 150 | this.highlightSearchWords(); 151 | this.initIndexTable(); 152 | if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) { 153 | this.initOnKeyListeners(); 154 | } 155 | }, 156 | 157 | /** 158 | * i18n support 159 | */ 160 | TRANSLATIONS : {}, 161 | PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; }, 162 | LOCALE : 'unknown', 163 | 164 | // gettext and ngettext don't access this so that the functions 165 | // can safely bound to a different name (_ = Documentation.gettext) 166 | gettext : function(string) { 167 | var translated = Documentation.TRANSLATIONS[string]; 168 | if (typeof translated === 'undefined') 169 | return string; 170 | return (typeof translated === 'string') ? translated : translated[0]; 171 | }, 172 | 173 | ngettext : function(singular, plural, n) { 174 | var translated = Documentation.TRANSLATIONS[singular]; 175 | if (typeof translated === 'undefined') 176 | return (n == 1) ? singular : plural; 177 | return translated[Documentation.PLURALEXPR(n)]; 178 | }, 179 | 180 | addTranslations : function(catalog) { 181 | for (var key in catalog.messages) 182 | this.TRANSLATIONS[key] = catalog.messages[key]; 183 | this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); 184 | this.LOCALE = catalog.locale; 185 | }, 186 | 187 | /** 188 | * add context elements like header anchor links 189 | */ 190 | addContextElements : function() { 191 | $('div[id] > :header:first').each(function() { 192 | $('\u00B6'). 193 | attr('href', '#' + this.id). 194 | attr('title', _('Permalink to this headline')). 195 | appendTo(this); 196 | }); 197 | $('dt[id]').each(function() { 198 | $('\u00B6'). 199 | attr('href', '#' + this.id). 200 | attr('title', _('Permalink to this definition')). 201 | appendTo(this); 202 | }); 203 | }, 204 | 205 | /** 206 | * workaround a firefox stupidity 207 | * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075 208 | */ 209 | fixFirefoxAnchorBug : function() { 210 | if (document.location.hash && $.browser.mozilla) 211 | window.setTimeout(function() { 212 | document.location.href += ''; 213 | }, 10); 214 | }, 215 | 216 | /** 217 | * highlight the search words provided in the url in the text 218 | */ 219 | highlightSearchWords : function() { 220 | var params = $.getQueryParameters(); 221 | var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; 222 | if (terms.length) { 223 | var body = $('div.body'); 224 | if (!body.length) { 225 | body = $('body'); 226 | } 227 | window.setTimeout(function() { 228 | $.each(terms, function() { 229 | body.highlightText(this.toLowerCase(), 'highlighted'); 230 | }); 231 | }, 10); 232 | $('

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

') 234 | .appendTo($('#searchbox')); 235 | } 236 | }, 237 | 238 | /** 239 | * init the domain index toggle buttons 240 | */ 241 | initIndexTable : function() { 242 | var togglers = $('img.toggler').click(function() { 243 | var src = $(this).attr('src'); 244 | var idnum = $(this).attr('id').substr(7); 245 | $('tr.cg-' + idnum).toggle(); 246 | if (src.substr(-9) === 'minus.png') 247 | $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); 248 | else 249 | $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); 250 | }).css('display', ''); 251 | if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { 252 | togglers.click(); 253 | } 254 | }, 255 | 256 | /** 257 | * helper function to hide the search marks again 258 | */ 259 | hideSearchWords : function() { 260 | $('#searchbox .highlight-link').fadeOut(300); 261 | $('span.highlighted').removeClass('highlighted'); 262 | }, 263 | 264 | /** 265 | * make the url absolute 266 | */ 267 | makeURL : function(relativeURL) { 268 | return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; 269 | }, 270 | 271 | /** 272 | * get the current relative url 273 | */ 274 | getCurrentURL : function() { 275 | var path = document.location.pathname; 276 | var parts = path.split(/\//); 277 | $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { 278 | if (this === '..') 279 | parts.pop(); 280 | }); 281 | var url = parts.join('/'); 282 | return path.substring(url.lastIndexOf('/') + 1, path.length - 1); 283 | }, 284 | 285 | initOnKeyListeners: function() { 286 | $(document).keyup(function(event) { 287 | var activeElementType = document.activeElement.tagName; 288 | // don't navigate when in search box or textarea 289 | if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') { 290 | switch (event.keyCode) { 291 | case 37: // left 292 | var prevHref = $('link[rel="prev"]').prop('href'); 293 | if (prevHref) { 294 | window.location.href = prevHref; 295 | return false; 296 | } 297 | case 39: // right 298 | var nextHref = $('link[rel="next"]').prop('href'); 299 | if (nextHref) { 300 | window.location.href = nextHref; 301 | return false; 302 | } 303 | } 304 | } 305 | }); 306 | } 307 | }; 308 | 309 | // quick alias for translations 310 | _ = Documentation.gettext; 311 | 312 | $(document).ready(function() { 313 | Documentation.init(); 314 | }); 315 | -------------------------------------------------------------------------------- /docs/_static/documentation_options.js: -------------------------------------------------------------------------------- 1 | var DOCUMENTATION_OPTIONS = { 2 | URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), 3 | VERSION: '0.2.0', 4 | LANGUAGE: 'None', 5 | COLLAPSE_INDEX: false, 6 | FILE_SUFFIX: '.html', 7 | HAS_SOURCE: true, 8 | SOURCELINK_SUFFIX: '.txt', 9 | NAVIGATION_WITH_KEYS: false 10 | }; -------------------------------------------------------------------------------- /docs/_static/file.png: 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147 | if (re.test(w)) { 148 | var fp = re.exec(w); 149 | stem = fp[1]; 150 | suffix = fp[2]; 151 | re = new RegExp(mgr0); 152 | if (re.test(stem)) 153 | w = stem + step3list[suffix]; 154 | } 155 | 156 | // Step 4 157 | re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; 158 | re2 = /^(.+?)(s|t)(ion)$/; 159 | if (re.test(w)) { 160 | var fp = re.exec(w); 161 | stem = fp[1]; 162 | re = new RegExp(mgr1); 163 | if (re.test(stem)) 164 | w = stem; 165 | } 166 | else if (re2.test(w)) { 167 | var fp = re2.exec(w); 168 | stem = fp[1] + fp[2]; 169 | re2 = new RegExp(mgr1); 170 | if (re2.test(stem)) 171 | w = stem; 172 | } 173 | 174 | // Step 5 175 | re = /^(.+?)e$/; 176 | if (re.test(w)) { 177 | var fp = re.exec(w); 178 | stem = fp[1]; 179 | re = new RegExp(mgr1); 180 | re2 = new RegExp(meq1); 181 | re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); 182 | if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) 183 | w = stem; 184 | } 185 | re = /ll$/; 186 | re2 = new RegExp(mgr1); 187 | if (re.test(w) && re2.test(w)) { 188 | re = /.$/; 189 | w = w.replace(re,""); 190 | } 191 | 192 | // and turn initial Y back to y 193 | if (firstch == "y") 194 | w = firstch.toLowerCase() + w.substr(1); 195 | return w; 196 | } 197 | } 198 | 199 | 200 | 201 | 202 | 203 | var splitChars = (function() { 204 | var result = {}; 205 | var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, 206 | 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, 207 | 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, 208 | 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, 209 | 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, 210 | 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, 211 | 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, 212 | 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, 213 | 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, 214 | 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; 215 | var i, j, start, end; 216 | for (i = 0; i < singles.length; i++) { 217 | result[singles[i]] = true; 218 | } 219 | var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], 220 | [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], 221 | [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], 222 | [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], 223 | [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], 224 | [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], 225 | [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], 226 | [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], 227 | [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], 228 | [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], 229 | [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], 230 | [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], 231 | [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], 232 | [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], 233 | [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], 234 | [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], 235 | [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], 236 | [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], 237 | [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], 238 | [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], 239 | [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], 240 | [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], 241 | [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], 242 | [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], 243 | [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], 244 | [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], 245 | [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], 246 | [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], 247 | [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], 248 | [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], 249 | [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], 250 | [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], 251 | [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], 252 | [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], 253 | [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], 254 | [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], 255 | [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], 256 | [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], 257 | [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], 258 | [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], 259 | [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], 260 | [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], 261 | [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], 262 | [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], 263 | [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], 264 | [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], 265 | [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], 266 | [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], 267 | [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; 268 | for (i = 0; i < ranges.length; i++) { 269 | start = ranges[i][0]; 270 | end = ranges[i][1]; 271 | for (j = start; j <= end; j++) { 272 | result[j] = true; 273 | } 274 | } 275 | return result; 276 | })(); 277 | 278 | function splitQuery(query) { 279 | var result = []; 280 | var start = -1; 281 | for (var i = 0; i < query.length; i++) { 282 | if (splitChars[query.charCodeAt(i)]) { 283 | if (start !== -1) { 284 | result.push(query.slice(start, i)); 285 | start = -1; 286 | } 287 | } else if (start === -1) { 288 | start = i; 289 | } 290 | } 291 | if (start !== -1) { 292 | result.push(query.slice(start)); 293 | } 294 | return result; 295 | } 296 | 297 | 298 | -------------------------------------------------------------------------------- /docs/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zubara/mneflow/92ee4f85c27427c869116ab6a1c9693b5da8089e/docs/_static/minus.png -------------------------------------------------------------------------------- /docs/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zubara/mneflow/92ee4f85c27427c869116ab6a1c9693b5da8089e/docs/_static/plus.png -------------------------------------------------------------------------------- /docs/_static/pygments.css: -------------------------------------------------------------------------------- 1 | pre { line-height: 125%; margin: 0; } 2 | td.linenos pre { color: #000000; background-color: #f0f0f0; padding: 0 5px 0 5px; } 3 | span.linenos { color: #000000; background-color: #f0f0f0; padding: 0 5px 0 5px; } 4 | td.linenos pre.special { color: #000000; background-color: #ffffc0; padding: 0 5px 0 5px; } 5 | span.linenos.special { color: #000000; background-color: #ffffc0; padding: 0 5px 0 5px; } 6 | .highlight .hll { background-color: #ffffcc } 7 | .highlight { background: #f8f8f8; } 8 | .highlight .c { color: #408080; font-style: italic } /* Comment */ 9 | .highlight .err { border: 1px solid #FF0000 } /* Error */ 10 | .highlight .k { color: #008000; font-weight: bold } /* Keyword */ 11 | .highlight .o { color: #666666 } /* Operator */ 12 | .highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */ 13 | .highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */ 14 | .highlight .cp { color: #BC7A00 } /* Comment.Preproc */ 15 | .highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */ 16 | .highlight .c1 { color: #408080; 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23 | }, 24 | */ 25 | 26 | // query matches the full name of an object 27 | objNameMatch: 11, 28 | // or matches in the last dotted part of the object name 29 | objPartialMatch: 6, 30 | // Additive scores depending on the priority of the object 31 | objPrio: {0: 15, // used to be importantResults 32 | 1: 5, // used to be objectResults 33 | 2: -5}, // used to be unimportantResults 34 | // Used when the priority is not in the mapping. 35 | objPrioDefault: 0, 36 | 37 | // query found in title 38 | title: 15, 39 | partialTitle: 7, 40 | // query found in terms 41 | term: 5, 42 | partialTerm: 2 43 | }; 44 | } 45 | 46 | if (!splitQuery) { 47 | function splitQuery(query) { 48 | return query.split(/\s+/); 49 | } 50 | } 51 | 52 | /** 53 | * Search Module 54 | */ 55 | var Search = { 56 | 57 | _index : null, 58 | _queued_query : null, 59 | _pulse_status : -1, 60 | 61 | htmlToText : function(htmlString) { 62 | var htmlElement = document.createElement('span'); 63 | htmlElement.innerHTML = htmlString; 64 | $(htmlElement).find('.headerlink').remove(); 65 | docContent = $(htmlElement).find('[role=main]')[0]; 66 | return docContent.textContent || docContent.innerText; 67 | }, 68 | 69 | init : function() { 70 | var params = $.getQueryParameters(); 71 | if (params.q) { 72 | var query = params.q[0]; 73 | $('input[name="q"]')[0].value = query; 74 | this.performSearch(query); 75 | } 76 | }, 77 | 78 | loadIndex : function(url) { 79 | $.ajax({type: "GET", url: url, data: null, 80 | dataType: "script", cache: true, 81 | complete: function(jqxhr, textstatus) { 82 | if (textstatus != "success") { 83 | document.getElementById("searchindexloader").src = url; 84 | } 85 | }}); 86 | }, 87 | 88 | setIndex : function(index) { 89 | var q; 90 | this._index = index; 91 | if ((q = this._queued_query) !== null) { 92 | this._queued_query = null; 93 | Search.query(q); 94 | } 95 | }, 96 | 97 | hasIndex : function() { 98 | return this._index !== null; 99 | }, 100 | 101 | deferQuery : function(query) { 102 | this._queued_query = query; 103 | }, 104 | 105 | stopPulse : function() { 106 | this._pulse_status = 0; 107 | }, 108 | 109 | startPulse : function() { 110 | if (this._pulse_status >= 0) 111 | return; 112 | function pulse() { 113 | var i; 114 | Search._pulse_status = (Search._pulse_status + 1) % 4; 115 | var dotString = ''; 116 | for (i = 0; i < Search._pulse_status; i++) 117 | dotString += '.'; 118 | Search.dots.text(dotString); 119 | if (Search._pulse_status > -1) 120 | window.setTimeout(pulse, 500); 121 | } 122 | pulse(); 123 | }, 124 | 125 | /** 126 | * perform a search for something (or wait until index is loaded) 127 | */ 128 | performSearch : function(query) { 129 | // create the required interface elements 130 | this.out = $('#search-results'); 131 | this.title = $('

' + _('Searching') + '

').appendTo(this.out); 132 | this.dots = $('').appendTo(this.title); 133 | this.status = $('

 

').appendTo(this.out); 134 | this.output = $('