{ "cells": [ { "cell_type": "markdown", "id": "ab23ab7d-347c-4968-9168-5a3c8a901533", "metadata": {}, "source": [ "# Holoviz plotting - shrinking the time range" ] }, { "cell_type": "markdown", "id": "62867e5f-8d1f-488d-98dd-1b8792b0be20", "metadata": {}, "source": [ "We've attempted to use the Holoviz package to make some interactive figures. The figures need an active python kernel to function, and so can't be inserted directly into a static webpage.\n", "\n", "In this notebook, we show some examples of creating interactive figures to highlight what can be done. At the end of the script, we build a plotting function, and bind it in a Holoviz Panel, which can then be launched as an app. This requires a separately running server to host the python functionality, and highlights the sort of possibilities that these tools can have." ] }, { "cell_type": "code", "execution_count": 1, "id": "c69ea8a8-7e25-4058-a147-ea26bd48e842", "metadata": { "tags": [] }, "outputs": [ { "data": { "application/javascript": [ "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", " var py_version = '3.2.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", " var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n", " var reloading = false;\n", " var Bokeh = root.Bokeh;\n", " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", "\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n", 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metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", " var py_version = '3.2.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", " var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n", " var reloading = true;\n", " var Bokeh = root.Bokeh;\n", " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", "\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks;\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", " if (js_modules == null) js_modules = [];\n", " if (js_exports == null) js_exports = {};\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", "\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " if (!reloading) {\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " }\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", " window._bokeh_on_load = on_load\n", "\n", " function on_error() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " var skip = [];\n", " if (window.requirejs) {\n", " window.requirejs.config({'packages': {}, 'paths': {'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n", " require([\"jspanel\"], function(jsPanel) {\n", "\twindow.jsPanel = jsPanel\n", "\ton_load()\n", " })\n", " require([\"jspanel-modal\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-tooltip\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-hint\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-layout\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-contextmenu\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-dock\"], function() {\n", "\ton_load()\n", " })\n", " require([\"gridstack\"], function(GridStack) {\n", "\twindow.GridStack = GridStack\n", "\ton_load()\n", " })\n", " require([\"notyf\"], function() {\n", "\ton_load()\n", " })\n", " root._bokeh_is_loading = css_urls.length + 9;\n", " } else {\n", " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n", " }\n", "\n", " var existing_stylesheets = []\n", " var links = document.getElementsByTagName('link')\n", " for (var i = 0; i < links.length; i++) {\n", " var link = links[i]\n", " if (link.href != null) {\n", "\texisting_stylesheets.push(link.href)\n", " }\n", " }\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " if (existing_stylesheets.indexOf(url) !== -1) {\n", "\ton_load()\n", "\tcontinue;\n", " }\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } var existing_scripts = []\n", " var scripts = document.getElementsByTagName('script')\n", " for (var i = 0; i < scripts.length; i++) {\n", " var script = scripts[i]\n", " if (script.src != null) {\n", "\texisting_scripts.push(script.src)\n", " }\n", " }\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (var i = 0; i < js_modules.length; i++) {\n", " var url = js_modules[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (const name in js_exports) {\n", " var url = js_exports[name];\n", " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " element.textContent = `\n", " import ${name} from \"${url}\"\n", " window.${name} = ${name}\n", " window._bokeh_on_load()\n", " `\n", " document.head.appendChild(element);\n", " }\n", " if (!js_urls.length && !js_modules.length) {\n", " on_load()\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " var js_urls = [];\n", " var js_modules = [];\n", " var js_exports = {};\n", " var css_urls = [];\n", " var inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {} // ensure no trailing comma for IE\n", " ];\n", "\n", " function run_inline_js() {\n", " if ((root.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " // Cache old bokeh versions\n", " if (Bokeh != undefined && !reloading) {\n", "\tvar NewBokeh = root.Bokeh;\n", "\tif (Bokeh.versions === undefined) {\n", "\t Bokeh.versions = new Map();\n", "\t}\n", "\tif (NewBokeh.version !== Bokeh.version) {\n", "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n", "\t}\n", "\troot.Bokeh = Bokeh;\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " }\n", " root._bokeh_is_initializing = false\n", " }\n", "\n", " function load_or_wait() {\n", " // Implement a backoff loop that tries to ensure we do not load multiple\n", " // versions of Bokeh and its dependencies at the same time.\n", " // In recent versions we use the root._bokeh_is_initializing flag\n", " // to determine whether there is an ongoing attempt to initialize\n", " // bokeh, however for backward compatibility we also try to ensure\n", " // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n", " // before older versions are fully initialized.\n", " if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n", " root._bokeh_is_initializing = false;\n", " root._bokeh_onload_callbacks = undefined;\n", " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", " load_or_wait();\n", " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", " setTimeout(load_or_wait, 100);\n", " } else {\n", " Bokeh = root.Bokeh;\n", " bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", " root._bokeh_is_initializing = true\n", " root._bokeh_onload_callbacks = []\n", " if (!reloading && (!bokeh_loaded || is_dev)) {\n", "\troot.Bokeh = undefined;\n", " }\n", " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", "\trun_inline_js();\n", " });\n", " }\n", " }\n", " // Give older versions of the autoload script a head-start to ensure\n", " // they initialize before we start loading newer version.\n", " setTimeout(load_or_wait, 100)\n", "}(window));" ], "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.2.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n var reloading = true;\n var Bokeh = root.Bokeh;\n var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n require([\"jspanel\"], function(jsPanel) {\n\twindow.jsPanel = jsPanel\n\ton_load()\n })\n require([\"jspanel-modal\"], function() {\n\ton_load()\n })\n require([\"jspanel-tooltip\"], function() {\n\ton_load()\n })\n require([\"jspanel-hint\"], function() {\n\ton_load()\n })\n require([\"jspanel-layout\"], function() {\n\ton_load()\n })\n require([\"jspanel-contextmenu\"], function() {\n\ton_load()\n })\n require([\"jspanel-dock\"], function() {\n\ton_load()\n })\n require([\"gridstack\"], function(GridStack) {\n\twindow.GridStack = GridStack\n\ton_load()\n })\n require([\"notyf\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 9;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.2.1/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.1/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n var url = js_exports[name];\n if (skip.indexOf(url) >= 0 || root[name] != null) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async = false;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n element.textContent = `\n import ${name} from \"${url}\"\n window.${name} = ${name}\n window._bokeh_on_load()\n `\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n var js_urls = [];\n var js_modules = [];\n var js_exports = {};\n var css_urls = [];\n var inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n\tvar NewBokeh = root.Bokeh;\n\tif (Bokeh.versions === undefined) {\n\t Bokeh.versions = new Map();\n\t}\n\tif (NewBokeh.version !== Bokeh.version) {\n\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n\t}\n\troot.Bokeh = Bokeh;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the 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handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import erddapy\n", "from erddapy import ERDDAP\n", "import numpy as np\n", "import pandas as pd\n", "import xarray as xr\n", "import datetime\n", "\n", "import matplotlib\n", "from matplotlib import pyplot as plt\n", "\n", "import pathlib\n", "\n", "import holoviews as hv\n", "import hvplot.pandas # noqa\n", "import hvplot.xarray\n", "import panel as pn\n", "\n", "\n", "pn.extension(template='material')" ] }, { "cell_type": "code", "execution_count": 2, "id": "ec619abf-30e3-4658-a8d0-541d19ded668", "metadata": { "tags": [] }, "outputs": [], "source": [ "def get_erddap_data(erddap_url, dataset, data_protocol=\"griddap\", variables=None, constraints=None):\n", " \"\"\"\n", " Function: get_erddap_data\n", " This function uses the erddapy python library to access data from ERDDAP servers,\n", " and to return it to users in convenient formats for python users.\n", " Data can be pulled from \"tabledap\" or \"griddap\" formats, with different\n", " output types, depending on the dap type.\n", " \n", " Inputs:\n", " erddap_url - The url address of the erddap server to pull data from\n", " variables - The selected variables within the dataset.\n", " data_protocol - The erddap data protocol for the chosen dataset.\n", " Options include \"tabledap\" or \"griddap\"\n", " The default option is given as \"griddap\"\n", " dataset - The ID for the relevant dataset on the erddap server\n", " If no variables are given, it is assumed that all variables\n", " will be pulled.\n", " constraints - These are set by the user to help restrict the data pull\n", " to only the area and timeframe of interest.\n", " If no constraints are given, all data in a dataset is pulled.\n", " Constraints should be given as a dictionary, where\n", " each entry is a bound and/or selection of a specific axis variable\n", " Exs. {\"longitude<=\": \"min(longitude)+10\", \"longitude>=\": \"0\"}\n", " {\"longitude=\": \"140\", \"time>=\": \"max(time)-30\"}\n", " \n", " Outputs:\n", " erddap_data - This variable contains the pulled data from the erddap server.\n", " If the data_protocol is \"griddap\", then erddap_data is an xarray dataset\n", " If the data_protocol is \"tabledap\", then erddap_data is a pandas dataframe\n", " \"\"\"\n", " \n", " import erddapy\n", " from erddapy import ERDDAP\n", " import pandas as pd\n", " import xarray\n", " \n", " \n", " ############################################\n", " # Set-up the connection to the ERDDAP server\n", " ############################################\n", " \n", " # Connect to the erddap server\n", " e = ERDDAP(server=erddap_url, protocol=data_protocol, response='csv')\n", " \n", " # Identify the dataset of interest\n", " e.dataset_id = dataset\n", " \n", " \n", " #########################################\n", " # Pull the data, based upon protocol type\n", " #########################################\n", " \n", " # GRIDDAP Protocol\n", " if data_protocol == \"griddap\":\n", " \n", " # Initialize the connection\n", " e.griddap_initialize()\n", "\n", " # Update the constraints\n", " if constraints is not None:\n", " e.constraints.update(constraints)\n", " e.griddap_initialize()\n", " \n", " # Update the selection of the variables\n", " if variables is not None:\n", " e.variables = variables\n", "\n", " erddap_data = e.to_xarray()\n", " \n", " # TABLEDAP Protocol\n", " elif data_protocol == \"tabledap\":\n", "\n", " # Update the constraints\n", " if constraints is not None:\n", " e.constraints = constraints\n", " \n", " # Update the selection of the variables\n", " if variables is not None:\n", " e.variables = variables\n", " \n", " erddap_data = e.to_pandas()\n", " \n", " # Invalid protocol given\n", " else:\n", " print('Invalid ERDDAP protocol. Given protocol is: ' + data_protocol)\n", " print('Valid protocols include \"griddap\" or \"tabledap\". Please restart and try again with a valid protocol')\n", " erddap_data = None\n", " \n", " \n", " #############################\n", " return erddap_data" ] }, { "cell_type": "markdown", "id": "7758cdee-61f2-4880-9a9f-fae4f8c6041f", "metadata": { "tags": [] }, "source": [ "# Load in data from the ERDDAP server" ] }, { "cell_type": "markdown", "id": "af82699a-160f-4350-902d-024d0fd61f32", "metadata": { "tags": [] }, "source": [ "First, we need to get some data. To do this, we can download data from the NANOOS buoy near Hansville, WA. The data is a gridded product of individual CTD casts taken for the last 10+ years on a near-daily basis." ] }, { "cell_type": "code", "execution_count": 3, "id": "2da6d7e2-c858-4636-bd8b-1bfe5a704b29", "metadata": { "tags": [] }, "outputs": [], "source": [ "nwem_url = 'http://nwem.apl.washington.edu/erddap'\n", "\n", "nwem_dataset = 'orca3_L3_depthgridded_025'\n", "\n", "variables = [\"sea_water_temperature\",\n", " \"sea_water_practical_salinity\",\n", " \"mass_concentration_of_oxygen_in_sea_water\"]\n", "\n", "constraints = {\"cast_start_time>=\":datetime.datetime(2016,1,1).strftime('%Y-%m-%dT%H:%M:%SZ')}\n", "#constraints = {\"cast_start_time>=\": \"max(cast_start_time)-365\"}\n", "\n", "nwem_grid = get_erddap_data(nwem_url, nwem_dataset, \n", " variables=variables, \n", " constraints=constraints,\n", " data_protocol=\"griddap\")" ] }, { "cell_type": "markdown", "id": "a97901d1-35f9-43af-b741-1234e450040e", "metadata": {}, "source": [ "# Create a slider to move between individual casts" ] }, { "cell_type": "markdown", "id": "d30ff148-3978-41dc-b386-abbfcf98e8a7", "metadata": {}, "source": [ "Next, we can create an interactive plot, where we can show the sea surface temperature for individual casts." ] }, { "cell_type": "code", "execution_count": 4, "id": "9b5f047a-dcd0-42f8-80f0-72b3f6f258c3", "metadata": { "tags": [] }, "outputs": [ { "data": {}, "metadata": {}, "output_type": "display_data" }, { "data": {}, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.holoviews_exec.v0+json": "", "text/html": [ "
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\n", "" ], "text/plain": [ "Row\n", " [0] Markdown(str)\n", " [1] Matplotlib(Figure)" ] }, "execution_count": 6, "metadata": { "application/vnd.holoviews_exec.v0+json": { "id": "79b18223-6aff-4217-afb7-afee135207bf" } }, "output_type": "execute_result" } ], "source": [ "# Create an interactive xarray\n", "nwem_interactive = nwem_grid.interactive()\n", "\n", "# Create a date slider widget\n", "date_slider = pn.widgets.DateRangeSlider(name='Earliest Date', \n", " start=datetime.datetime(2016,1,1), \n", " end=datetime.datetime(2023,1,1), \n", " value=(datetime.datetime(2017,1,1),\n", " datetime.datetime(2020,1,1))).servable(target='sidebar')\n", "\n", "\n", "# Use a matplotlib panel pane to \n", "# plot the time range, using the interactive array\n", "# and the date slider\n", "mpl = pn.pane.Matplotlib(\n", " pn.bind(plot_timerange, nwem_interactive, date_slider)\n", ")\n", "\n", "pn.Row(\n", " 'Buoy data', mpl\n", ").servable(target='main')" ] }, { "cell_type": "markdown", "id": "af36d029-ef27-4378-a8df-8194dc5e91ea", "metadata": {}, "source": [ "To test out the app, we can click the \"Preview with Panel\" button in the notebook ribbon at the top (it's next to the code/markdown dropdown menu)" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.16" } }, "nbformat": 4, "nbformat_minor": 5 }