1325 lines
53 KiB
HTML
1325 lines
53 KiB
HTML
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<!doctype html>
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<html lang="en" class="no-js">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width,initial-scale=1">
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<link rel="shortcut icon" href="../../assets/images/favicon.png">
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<meta name="generator" content="mkdocs-1.1.2, mkdocs-material-6.1.4+insiders-1.9.0">
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<title>Add New Features - RAPIDS</title>
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<link rel="stylesheet" href="../../assets/stylesheets/main.a2a6bca7.min.css">
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<link rel="stylesheet" href="../../assets/stylesheets/palette.c308bc62.min.css">
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<link href="https://fonts.gstatic.com" rel="preconnect" crossorigin>
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<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,400,400i,700%7CRoboto+Mono&display=fallback">
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<style>body,input{font-family:"Roboto",-apple-system,BlinkMacSystemFont,Helvetica,Arial,sans-serif}code,kbd,pre{font-family:"Roboto Mono",SFMono-Regular,Consolas,Menlo,monospace}</style>
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<link rel="stylesheet" href="../../stylesheets/extra.css">
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</head>
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<body dir="ltr" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="blue">
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<script>var palette=JSON.parse(localStorage.getItem("__palette")||"{}");if(void 0!==palette.color)for(var key in palette.color)document.body.setAttribute("data-md-color-"+key,palette.color[key])</script>
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<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
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<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
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<label class="md-overlay" for="__drawer"></label>
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<div data-md-component="skip">
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<a href="#add-new-features" class="md-skip">
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Skip to content
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</a>
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</div>
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<div data-md-component="announce">
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</div>
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<header class="md-header" data-md-component="header">
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<nav class="md-header-nav md-grid" aria-label="Header">
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<a href="../.." title="RAPIDS" class="md-header-nav__button md-logo" aria-label="RAPIDS">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 01-2 2H7a2 2 0 01-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V4a2 2 0 012-2h10a2 2 0 012 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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<label class="md-header-nav__button md-icon" for="__drawer">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3V6m0 5h18v2H3v-2m0 5h18v2H3v-2z"/></svg>
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</label>
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<div class="md-header-nav__title" data-md-component="header-title">
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<div class="md-header-nav__ellipsis">
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<div class="md-header-nav__topic">
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<span class="md-ellipsis">
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RAPIDS
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</span>
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</div>
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<div class="md-header-nav__topic" data-md-component="header-topic">
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<span class="md-ellipsis">
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Add New Features
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</span>
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</div>
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</div>
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</div>
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<div class="md-header-nav__options">
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<button class="md-header-nav__button md-icon" title="Switch to light mode" aria-label="Switch to light mode" data-md-option="palette" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="blue" data-md-state="hidden">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M17 7H7a5 5 0 00-5 5 5 5 0 005 5h10a5 5 0 005-5 5 5 0 00-5-5m0 8a3 3 0 01-3-3 3 3 0 013-3 3 3 0 013 3 3 3 0 01-3 3z"/></svg>
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</button>
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<button class="md-header-nav__button md-icon" title="Switch to dark mode" aria-label="Switch to dark mode" data-md-option="palette" data-md-color-scheme="slate" data-md-color-primary="blue" data-md-color-accent="blue" data-md-state="hidden">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M7 10a2 2 0 012 2 2 2 0 01-2 2 2 2 0 01-2-2 2 2 0 012-2m10-3a5 5 0 015 5 5 5 0 01-5 5H7a5 5 0 01-5-5 5 5 0 015-5h10M7 9a3 3 0 00-3 3 3 3 0 003 3h10a3 3 0 003-3 3 3 0 00-3-3H7z"/></svg>
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</button>
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</div>
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<label class="md-header-nav__button md-icon" for="__search">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0116 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 019.5 16 6.5 6.5 0 013 9.5 6.5 6.5 0 019.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5z"/></svg>
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</label>
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<div class="md-search" data-md-component="search" role="dialog">
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<label class="md-search__overlay" for="__search"></label>
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<div class="md-search__inner" role="search">
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<form class="md-search__form" name="search">
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<input type="text" class="md-search__input" name="query" aria-label="Search" placeholder="Search" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false" data-md-component="search-query" data-md-state="active">
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<label class="md-search__icon md-icon" for="__search">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0116 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 019.5 16 6.5 6.5 0 013 9.5 6.5 6.5 0 019.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5z"/></svg>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11h12z"/></svg>
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</label>
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<button type="reset" class="md-search__icon md-icon" aria-label="Clear" data-md-component="search-reset" tabindex="-1">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 6.41L17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12 19 6.41z"/></svg>
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</button>
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<div class="md-search__suggest" data-md-component="search-suggest"></div>
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</form>
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<div class="md-search__output">
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<div class="md-search__scrollwrap" data-md-scrollfix>
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<div class="md-search-result" data-md-component="search-result">
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<div class="md-search-result__meta">
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Initializing search
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</div>
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<ol class="md-search-result__list"></ol>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div class="md-header-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05L244 40.45a28.87 28.87 0 00-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 01-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 000 40.81l195.61 195.6a28.86 28.86 0 0040.8 0l194.69-194.69a28.86 28.86 0 000-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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</div>
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</nav>
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</header>
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<div class="md-container" data-md-component="container">
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<main class="md-main" data-md-component="main">
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<div class="md-main__inner md-grid">
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<div class="md-sidebar md-sidebar--primary" data-md-component="navigation" >
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<div class="md-sidebar__scrollwrap">
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<div class="md-sidebar__inner">
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<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
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<label class="md-nav__title" for="__drawer">
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<a href="../.." title="RAPIDS" class="md-nav__button md-logo" aria-label="RAPIDS">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 01-2 2H7a2 2 0 01-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V4a2 2 0 012-2h10a2 2 0 012 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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</a>
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RAPIDS
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</label>
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<div class="md-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source">
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<div class="md-source__icon md-icon">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M439.55 236.05L244 40.45a28.87 28.87 0 00-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 01-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 000 40.81l195.61 195.6a28.86 28.86 0 0040.8 0l194.69-194.69a28.86 28.86 0 000-40.81z"/></svg>
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</div>
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<div class="md-source__repository">
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carissalow/rapids
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</div>
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</a>
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</div>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../.." class="md-nav__link">
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Home
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</a>
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-2" type="checkbox" id="nav-2" >
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<label class="md-nav__link" for="nav-2">
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Setup
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Setup" data-md-level="1">
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<label class="md-nav__title" for="nav-2">
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<span class="md-nav__icon md-icon"></span>
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Setup
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../file-structure/" class="md-nav__link">
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File Structure
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../setup/installation/" class="md-nav__link">
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Installation
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../setup/configuration/" class="md-nav__link">
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Configuration
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../setup/execution/" class="md-nav__link">
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Execution
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</a>
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-3" type="checkbox" id="nav-3" >
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<label class="md-nav__link" for="nav-3">
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Example Workflows
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Example Workflows" data-md-level="1">
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<label class="md-nav__title" for="nav-3">
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<span class="md-nav__icon md-icon"></span>
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Example Workflows
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../workflow-examples/minimal/" class="md-nav__link">
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Minimal
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</a>
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-4" type="checkbox" id="nav-4" checked>
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<label class="md-nav__link" for="nav-4">
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Behavioral Features
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Behavioral Features" data-md-level="1">
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<label class="md-nav__title" for="nav-4">
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<span class="md-nav__icon md-icon"></span>
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Behavioral Features
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../feature-introduction/" class="md-nav__link">
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Introduction
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</a>
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</li>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="nav-4-2" type="checkbox" id="nav-4-2" >
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<label class="md-nav__link" for="nav-4-2">
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Phone
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Phone" data-md-level="2">
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<label class="md-nav__title" for="nav-4-2">
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<span class="md-nav__icon md-icon"></span>
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Phone
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Phone Accelerometer
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Phone Activity Recognition
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Phone Battery
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20.71 7.04c.39-.39.39-1.04 0-1.41l-2.34-2.34c-.37-.39-1.02-.39-1.41 0l-1.84 1.83 3.75 3.75M3 17.25V21h3.75L17.81 9.93l-3.75-3.75L3 17.25z"/></svg>
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<h1 id="add-new-features">Add New Features<a class="headerlink" href="#add-new-features" title="Permanent link">¶</a></h1>
|
|
<div class="admonition hint">
|
|
<p class="admonition-title">Hint</p>
|
|
<p>We recommend reading the <a href="../feature-introduction/">Behavioral Features Introduction</a> before reading this page</p>
|
|
</div>
|
|
<div class="admonition hint">
|
|
<p class="admonition-title">Hint</p>
|
|
<p>You won’t have to deal with time zones, dates, times, data cleaning or preprocessing. The data that RAPIDS pipes to your feature extraction code is ready to process.</p>
|
|
</div>
|
|
<h2 id="new-features-for-existing-sensors">New Features for Existing Sensors<a class="headerlink" href="#new-features-for-existing-sensors" title="Permanent link">¶</a></h2>
|
|
<p>You can add new features to any existing sensors (see list below) by adding a new provider in three steps:</p>
|
|
<ol>
|
|
<li><a href="#modify-the-configyaml-file">Modify</a> the <code>config.yaml</code> file </li>
|
|
<li><a href="#create-a-provider-folder-script-and-function">Create</a> a provider folder, script and function</li>
|
|
<li><a href="#implement-your-feature-extraction-code">Implement</a> your features extraction code</li>
|
|
</ol>
|
|
<p>As a tutorial, we will add a new provider for <code>PHONE_ACCELEROMETER</code> called <code>VEGA</code> that extracts <code>feature1</code>, <code>feature2</code>, <code>feature3</code> in Python and that it requires a parameter from the user called <code>MY_PARAMETER</code>.</p>
|
|
<details class="info"><summary>Existing Sensors</summary><p>An existing sensor is any of the phone or Fitbit sensors with a configuration entry in <code>config.yaml</code>:</p>
|
|
<ul>
|
|
<li>Phone Accelerometer</li>
|
|
<li>Phone Activity Recognition</li>
|
|
<li>Phone Applications Foreground</li>
|
|
<li>Phone Battery</li>
|
|
<li>Phone Bluetooth</li>
|
|
<li>Phone Calls</li>
|
|
<li>Phone Conversation</li>
|
|
<li>Phone Data Yield</li>
|
|
<li>Phone Light</li>
|
|
<li>Phone Locations</li>
|
|
<li>Phone Messages</li>
|
|
<li>Phone Screen</li>
|
|
<li>Phone WiFI Connected</li>
|
|
<li>Phone WiFI Visible</li>
|
|
<li>Fitbit Heart Rate Summary</li>
|
|
<li>Fitbit Heart Rate Intraday</li>
|
|
<li>Fitbit Sleep Summary</li>
|
|
<li>Fitbit Steps Summary</li>
|
|
<li>Fitbit Steps Intraday</li>
|
|
</ul>
|
|
</details>
|
|
<h3 id="modify-the-configyaml-file">Modify the <code>config.yaml</code> file<a class="headerlink" href="#modify-the-configyaml-file" title="Permanent link">¶</a></h3>
|
|
<p>In this step you need to add your provider configuration section under the relevant sensor in <code>config.yaml</code>. See our example for our tutorial’s <code>VEGA</code> provider for <code>PHONE_ACCELEROMETER</code>:</p>
|
|
<details class="example"><summary>Example configuration for a new accelerometer provider <code>VEGA</code></summary><div class="highlight"><pre><span></span><code><span class="nt">PHONE_ACCELEROMETER</span><span class="p">:</span>
|
|
<span class="nt">TABLE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">accelerometer</span>
|
|
<span class="nt">PROVIDERS</span><span class="p">:</span>
|
|
<span class="nt">RAPIDS</span><span class="p">:</span>
|
|
<span class="nt">COMPUTE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
|
|
<span class="l l-Scalar l-Scalar-Plain">...</span>
|
|
|
|
<span class="nt">PANDA</span><span class="p">:</span>
|
|
<span class="nt">COMPUTE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
|
|
<span class="l l-Scalar l-Scalar-Plain">...</span>
|
|
<span class="nt">VEGA</span><span class="p">:</span>
|
|
<span class="nt">COMPUTE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
|
|
<span class="nt">FEATURES</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"feature1"</span><span class="p p-Indicator">,</span> <span class="s">"feature2"</span><span class="p p-Indicator">,</span> <span class="s">"feature3"</span><span class="p p-Indicator">]</span>
|
|
<span class="nt">MY_PARAMTER</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">a_string</span>
|
|
<span class="nt">SRC_FOLDER</span><span class="p">:</span> <span class="s">"vega"</span>
|
|
<span class="nt">SRC_LANGUAGE</span><span class="p">:</span> <span class="s">"python"</span>
|
|
</code></pre></div>
|
|
</details>
|
|
<table>
|
|
<thead>
|
|
<tr>
|
|
<th>Key </th>
|
|
<th>Description</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td><code>[COMPUTE]</code></td>
|
|
<td>Flag to activate/deactivate your provider</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>[FEATURES]</code></td>
|
|
<td>List of features your provider supports. Your provider code should only return the features on this list</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>[MY_PARAMTER]</code></td>
|
|
<td>An arbitrary parameter that our example provider <code>VEGA</code> needs. This can be a boolean, integer, float, string or an array of any of such types.</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>[SRC_LANGUAGE]</code></td>
|
|
<td>The programming language of your provider script, it can be <code>python</code> or <code>r</code>, in our example <code>python</code></td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>[SRC_FOLDER]</code></td>
|
|
<td>The name of your provider in lower case, in our example <code>vega</code> (this will be the name of your folder in the next step)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<h3 id="create-a-provider-folder-script-and-function">Create a provider folder, script and function<a class="headerlink" href="#create-a-provider-folder-script-and-function" title="Permanent link">¶</a></h3>
|
|
<p>In this step you need to add a folder, script and function for your provider.</p>
|
|
<ol>
|
|
<li>Create your provider <strong>folder</strong> under <code>src/feature/DEVICE_SENSOR/YOUR_PROVIDER</code>, in our example <code>src/feature/phone_accelerometer/vega</code> (same as <code>[SRC_FOLDER]</code> in the step above).</li>
|
|
<li>Create your provider <strong>script</strong> inside your provider folder, it can be a Python file called <code>main.py</code> or an R file called <code>main.R</code>.</li>
|
|
<li>
|
|
<p>Add your provider <strong>function</strong> in your provider script. The name of such function should be <code>[providername]_features</code>, in our example <code>vega_features</code></p>
|
|
<div class="admonition info">
|
|
<p class="admonition-title">Python function</p>
|
|
<div class="highlight"><pre><span></span><code><span class="k">def</span> <span class="p">[</span><span class="n">providername</span><span class="p">]</span><span class="n">_features</span><span class="p">(</span><span class="n">sensor_data_files</span><span class="p">,</span> <span class="n">day_segment</span><span class="p">,</span> <span class="n">provider</span><span class="p">,</span> <span class="n">filter_data_by_segment</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
|
|
</code></pre></div>
|
|
</div>
|
|
<div class="admonition info">
|
|
<p class="admonition-title">R function</p>
|
|
<div class="highlight"><pre><span></span><code><span class="p">[</span><span class="n">providername</span><span class="p">]</span>_<span class="n">features</span> <span class="o"><-</span> <span class="nf">function</span><span class="p">(</span><span class="n">sensor_data</span><span class="p">,</span> <span class="n">day_segment</span><span class="p">,</span> <span class="n">provider</span><span class="p">)</span>
|
|
</code></pre></div>
|
|
</div>
|
|
</li>
|
|
</ol>
|
|
<h3 id="implement-your-feature-extraction-code">Implement your feature extraction code<a class="headerlink" href="#implement-your-feature-extraction-code" title="Permanent link">¶</a></h3>
|
|
<p>The provider function that you created in the step above will receive the following parameters:</p>
|
|
<table>
|
|
<thead>
|
|
<tr>
|
|
<th>Parameter </th>
|
|
<th>Description</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td><code>sensor_data_files</code></td>
|
|
<td>Path to the CSV file containing the data of a single participant. This data has been cleaned and preprocessed. Your function will be automatically called for each participant in your study (in the <code>[PIDS]</code> array in <code>config.yaml</code>)</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>day_segment</code></td>
|
|
<td>The label of the day segment that should be processed.</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>provider</code></td>
|
|
<td>The parameters you configured for your provider in <code>config.yaml</code> will be available in this variable as a dictionary in Python or a list in R. In our example this dictionary contains <code>{MY_PARAMETER:"a_string"}</code></td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>filter_data_by_segment</code></td>
|
|
<td>Python only. A function that you will use to filter your data. In R this function is already available in the environment.</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>*args</code></td>
|
|
<td>Python only. Not used for now</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>**kwargs</code></td>
|
|
<td>Python only. Not used for now</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>The code to extract your behavioral features should be implemented in your provider function and in general terms it will have three stages:</p>
|
|
<details class="info"><summary>1. Read a participant’s data by loading the CSV data stored in the file pointed by <code>sensor_data_files</code></summary><div class="highlight"><pre><span></span><code><span class="n">acc_data</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">sensor_data_files</span><span class="p">[</span><span class="s2">"sensor_data"</span><span class="p">])</span>
|
|
</code></pre></div>
|
|
<p>Note that phone’s battery, screen, and activity recognition data is given as episodes instead of event rows (for example, start and end timestamps of the periods the phone screen was on)</p>
|
|
</details>
|
|
<details class="info"><summary>2. Filter your data to process only those rows that belong to <code>day_segment</code></summary><p>This step is only one line of code, but to undersand why we need it, keep reading.
|
|
<div class="highlight"><pre><span></span><code><span class="n">acc_data</span> <span class="o">=</span> <span class="n">filter_data_by_segment</span><span class="p">(</span><span class="n">acc_data</span><span class="p">,</span> <span class="n">day_segment</span><span class="p">)</span>
|
|
</code></pre></div></p>
|
|
<p>You should use the <code>filter_data_by_segment()</code> function to process and group those rows that belong to each of the <a href="../../setup/configuration/#day-segments">day segments RAPIDS could be configured with</a>.</p>
|
|
<p>Let’s understand the <code>filter_data_by_segment()</code> function with an example. A RAPIDS user can extract features on any arbitrary <a href="../../setup/configuration/#day-segments">day segment</a>. A day segment is a period of time that has a label and one or more instances. For example, the user (or you) could have requested features on a daily, weekly, and week-end basis for <code>p01</code>. The labels are arbritrary and the instances depend on the days a participant was monitored for: </p>
|
|
<ul>
|
|
<li>the daily segment could be named <code>my_days</code> and if <code>p01</code> was monitored for 14 days, it would have 14 instances</li>
|
|
<li>the weekly segment could be named <code>my_weeks</code> and if <code>p01</code> was monitored for 14 days, it would have 2 instances.</li>
|
|
<li>the weekend segment could be named <code>my_weekends</code> and if <code>p01</code> was monitored for 14 days, it would have 2 instances.</li>
|
|
</ul>
|
|
<p>For this example, RAPIDS will call your provider function three times for <code>p01</code>, once where <code>day_segment</code> is <code>my_days</code>, once where <code>day_segment</code> is <code>my_weeks</code> and once where <code>day_segment</code> is <code>my_weekends</code>. In this example not every row in <code>p01</code>‘s data needs to take part in the feature computation for either segment <strong>and</strong> the rows need to be grouped differently. </p>
|
|
<p>Thus <code>filter_data_by_segment()</code> comes in handy, it will return a data frame that contains the rows that were logged during a day segment plus an extra column called <code>local_segment</code>. This new column will have as many unique values as day segment instances exist (14, 2, and 2 for our <code>p01</code>‘s <code>my_days</code>, <code>my_weeks</code>, and <code>my_weekends</code> examples). After filtering, <strong>you should group the data frame by this column and compute any desired features</strong>, for example:</p>
|
|
<div class="highlight"><pre><span></span><code><span class="n">acc_features</span><span class="p">[</span><span class="s2">"maxmagnitude"</span><span class="p">]</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s2">"local_segment"</span><span class="p">])[</span><span class="s2">"magnitude"</span><span class="p">]</span><span class="o">.</span><span class="n">max</span><span class="p">()</span>
|
|
</code></pre></div>
|
|
<p>The reason RAPIDS does not filter the participant’s data set for you is because your code might need to compute something based on a participant’s complete dataset before computing their features. For example, you might want to identify the number that called a participant the most throughout the study before computing a feature with the number of calls the participant received from this number.</p>
|
|
</details>
|
|
<details class="info"><summary>3. Return a data frame with your features</summary><p>After filtering, grouping your data, and computing your features, your provider function should return a data frame that has:</p>
|
|
<ul>
|
|
<li>One row per day segment instance (e.g. 14 our <code>p01</code>‘s <code>my_days</code> example)</li>
|
|
<li>The <code>local_segment</code> column added by <code>filter_data_by_segment()</code></li>
|
|
<li>One column per feature. By convention the name of your features should only contain letters or numbers (<code>feature1</code>). RAPIDS will automatically add the right sensor and provider prefix (<code>phone_accelerometr_vega_</code>)</li>
|
|
</ul>
|
|
</details>
|
|
<details class="example"><summary><code>PHONE_ACCELEROMETER</code> Provider Example</summary><p>For your reference, this a short example of our own provider (<code>RAPIDS</code>) for <code>PHONE_ACCELEROMETER</code> that computes five acceleration features</p>
|
|
<div class="highlight"><pre><span></span><code><span class="k">def</span> <span class="nf">rapids_features</span><span class="p">(</span><span class="n">sensor_data_files</span><span class="p">,</span> <span class="n">day_segment</span><span class="p">,</span> <span class="n">provider</span><span class="p">,</span> <span class="n">filter_data_by_segment</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
|
|
|
|
<span class="n">acc_data</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">sensor_data_files</span><span class="p">[</span><span class="s2">"sensor_data"</span><span class="p">])</span>
|
|
<span class="n">requested_features</span> <span class="o">=</span> <span class="n">provider</span><span class="p">[</span><span class="s2">"FEATURES"</span><span class="p">]</span>
|
|
<span class="c1"># name of the features this function can compute</span>
|
|
<span class="n">base_features_names</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"maxmagnitude"</span><span class="p">,</span> <span class="s2">"minmagnitude"</span><span class="p">,</span> <span class="s2">"avgmagnitude"</span><span class="p">,</span> <span class="s2">"medianmagnitude"</span><span class="p">,</span> <span class="s2">"stdmagnitude"</span><span class="p">]</span>
|
|
<span class="c1"># the subset of requested features this function can compute</span>
|
|
<span class="n">features_to_compute</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">requested_features</span><span class="p">)</span> <span class="o">&</span> <span class="nb">set</span><span class="p">(</span><span class="n">base_features_names</span><span class="p">))</span>
|
|
|
|
<span class="n">acc_features</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">"local_segment"</span><span class="p">]</span> <span class="o">+</span> <span class="n">features_to_compute</span><span class="p">)</span>
|
|
<span class="k">if</span> <span class="ow">not</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">empty</span><span class="p">:</span>
|
|
<span class="n">acc_data</span> <span class="o">=</span> <span class="n">filter_data_by_segment</span><span class="p">(</span><span class="n">acc_data</span><span class="p">,</span> <span class="n">day_segment</span><span class="p">)</span>
|
|
|
|
<span class="k">if</span> <span class="ow">not</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">empty</span><span class="p">:</span>
|
|
<span class="n">acc_features</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">()</span>
|
|
<span class="c1"># get magnitude related features: magnitude = sqrt(x^2+y^2+z^2)</span>
|
|
<span class="n">magnitude</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">row</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s2">"double_values_0"</span><span class="p">]</span> <span class="o">**</span> <span class="mi">2</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s2">"double_values_1"</span><span class="p">]</span> <span class="o">**</span> <span class="mi">2</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s2">"double_values_2"</span><span class="p">]</span> <span class="o">**</span> <span class="mi">2</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
|
|
<span class="n">acc_data</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">magnitude</span> <span class="o">=</span> <span class="n">magnitude</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
|
|
|
|
<span class="k">if</span> <span class="s2">"maxmagnitude"</span> <span class="ow">in</span> <span class="n">features_to_compute</span><span class="p">:</span>
|
|
<span class="n">acc_features</span><span class="p">[</span><span class="s2">"maxmagnitude"</span><span class="p">]</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s2">"local_segment"</span><span class="p">])[</span><span class="s2">"magnitude"</span><span class="p">]</span><span class="o">.</span><span class="n">max</span><span class="p">()</span>
|
|
<span class="k">if</span> <span class="s2">"minmagnitude"</span> <span class="ow">in</span> <span class="n">features_to_compute</span><span class="p">:</span>
|
|
<span class="n">acc_features</span><span class="p">[</span><span class="s2">"minmagnitude"</span><span class="p">]</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s2">"local_segment"</span><span class="p">])[</span><span class="s2">"magnitude"</span><span class="p">]</span><span class="o">.</span><span class="n">min</span><span class="p">()</span>
|
|
<span class="k">if</span> <span class="s2">"avgmagnitude"</span> <span class="ow">in</span> <span class="n">features_to_compute</span><span class="p">:</span>
|
|
<span class="n">acc_features</span><span class="p">[</span><span class="s2">"avgmagnitude"</span><span class="p">]</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s2">"local_segment"</span><span class="p">])[</span><span class="s2">"magnitude"</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
|
|
<span class="k">if</span> <span class="s2">"medianmagnitude"</span> <span class="ow">in</span> <span class="n">features_to_compute</span><span class="p">:</span>
|
|
<span class="n">acc_features</span><span class="p">[</span><span class="s2">"medianmagnitude"</span><span class="p">]</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s2">"local_segment"</span><span class="p">])[</span><span class="s2">"magnitude"</span><span class="p">]</span><span class="o">.</span><span class="n">median</span><span class="p">()</span>
|
|
<span class="k">if</span> <span class="s2">"stdmagnitude"</span> <span class="ow">in</span> <span class="n">features_to_compute</span><span class="p">:</span>
|
|
<span class="n">acc_features</span><span class="p">[</span><span class="s2">"stdmagnitude"</span><span class="p">]</span> <span class="o">=</span> <span class="n">acc_data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s2">"local_segment"</span><span class="p">])[</span><span class="s2">"magnitude"</span><span class="p">]</span><span class="o">.</span><span class="n">std</span><span class="p">()</span>
|
|
|
|
<span class="n">acc_features</span> <span class="o">=</span> <span class="n">acc_features</span><span class="o">.</span><span class="n">reset_index</span><span class="p">()</span>
|
|
|
|
<span class="k">return</span> <span class="n">acc_features</span>
|
|
</code></pre></div>
|
|
</details>
|
|
<h2 id="new-features-for-non-existing-sensors">New Features for Non-Existing Sensors<a class="headerlink" href="#new-features-for-non-existing-sensors" title="Permanent link">¶</a></h2>
|
|
<p>If you want to add features for a device or a sensor that we do not support at the moment (those that do not appear in the <code>"Existing Sensors"</code> list above), <a href="../../team">contact us</a> or request it on <a href="http://awareframework.com:3000/">Slack</a> and we can add the necessary code so you can follow the instructions above.</p>
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