2f:[{"id":"eb62e0961fe6665adb55017d02d5a1b8d0f517c234bd0171423a7d0a8cac4ac15a2a1fa8cf26f8dad826ca87b73d83c6e49df91eb87d754ad46f5e36de4f429e","href":"https://static.observableusercontent.com/files/eb62e0961fe6665adb55017d02d5a1b8d0f517c234bd0171423a7d0a8cac4ac15a2a1fa8cf26f8dad826ca87b73d83c6e49df91eb87d754ad46f5e36de4f429e","name":"clouds.nc","type":"application/octet-stream","lastModified":1710758845710.86,"size":12288},{"id":"a997e28596da16d3e731968fc994e974b1a0ac8b1873bbc10a6deb734a23be292635b2da9443f312f560f5dd9124d124d6e567670fe5538dd72573bf04b0acdb","href":"https://static.observableusercontent.com/files/a997e28596da16d3e731968fc994e974b1a0ac8b1873bbc10a6deb734a23be292635b2da9443f312f560f5dd9124d124d6e567670fe5538dd72573bf04b0acdb","name":"100-HELCOM-MORS-2018@1.nc","type":"application/octet-stream","lastModified":1710871632594.205,"size":11009380}] 2d:{"title":"Using NetCDF4 (WIP)","cells":[{"id":0,"value":"# Using NetCDF4 (WIP)","pinned":false,"hidden":false,"mode":"md"},{"id":376,"value":"## Data loading","pinned":false,"hidden":false,"mode":"md"},{"id":385,"value":"## Imports","pinned":false,"hidden":false,"mode":"md"},{"id":387,"value":"// 0.7.2\nh5 = import(\"https://cdn.observableusercontent.com/npm/h5wasm@0.4.9/+esm\").then(\n (h5) => h5.ready.then(() => h5)\n)","pinned":true,"hidden":false,"mode":"ojs"},{"id":81,"value":"## Using `h5wasm`\nRef.: https://github.com/usnistgov/h5wasm","pinned":false,"hidden":false,"mode":"md"},{"id":87,"value":"// helcom = FileAttachment(\"100-HELCOM-MORS-2018@1.nc\")\n// .arrayBuffer()\n// .then(\n// (d) => (\n// h5.FS.writeFile(\"helcom4.h5\", new Uint8Array(d)),\n// new h5.File(\"helcom4.h5\", \"r\")\n// )\n// )","pinned":true,"hidden":false,"mode":"ojs"},{"id":536,"value":"files = [FileAttachment(\"100-HELCOM-MORS-2018@1.nc\")]","pinned":true,"hidden":false,"mode":"ojs"},{"id":547,"value":"function loadNetcdf(file) {\n const fname = `${file.name.split(\".\")[0]}.h5`;\n console.log(fname);\n return file\n .arrayBuffer()\n .then(\n (d) => (\n h5.FS.writeFile(fname, new Uint8Array(d)), new h5.File(fname, \"r\")\n )\n );\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":554,"value":"helcom = loadNetcdf(files[0])","pinned":true,"hidden":false,"mode":"ojs"},{"id":424,"value":"helcom.keys()","pinned":true,"hidden":false,"mode":"ojs"},{"id":878,"value":"### Plotting geospatial coverage","pinned":false,"hidden":false,"mode":"md"},{"id":807,"value":"wellknown = require(\"https://bundle.run/wellknown@0.5.0\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":813,"value":"turf = require(\"@turf/turf@6.5\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":962,"value":"helcom.attrs","pinned":true,"hidden":false,"mode":"ojs"},{"id":701,"value":"// Geojson winding rules: https://observablehq.com/@d3/winding-order\nbbox_netcdf = turf.rewind(wellknown(helcom.attrs.geospatial_bounds.value), {\n reverse: true,\n mutate: true\n})","pinned":true,"hidden":false,"mode":"ojs"},{"id":703,"value":"world = (\n await fetch(\"https://cdn.jsdelivr.net/npm/world-atlas@2/land-50m.json\")\n).json()","pinned":true,"hidden":false,"mode":"ojs"},{"id":705,"value":"land = topojson.feature(world, world.objects.land)","pinned":true,"hidden":false,"mode":"ojs"},{"id":699,"value":"Plot.plot({\n marks: [\n Plot.geo(land, { fill: \"#edf3f7\", stroke: \"#d6dde2\" }),\n Plot.graticule(),\n Plot.geo(bbox_netcdf, {\n stroke: \"#3366cc\",\n strokeOpacity: 0.6,\n strokeWidth: 1,\n fill: \"#3366cc\",\n fillOpacity: 0.2\n })\n ],\n projection: {\n type: \"azimuthal-equal-area\",\n domain: bbox_netcdf,\n inset: 80\n },\n width: 300\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":646,"value":"helcom.attrs","pinned":true,"hidden":false,"mode":"ojs"},{"id":930,"value":"### Metadata","pinned":false,"hidden":false,"mode":"md"},{"id":596,"value":"{\n for (const property in helcom.attrs) {\n console.log(`${property}: ${helcom.attrs[property].value}`);\n }\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":672,"value":"str_sanitized = \"**MORS Environment database** has been used to collate data resulting from monitoring of environmental radioactivity in the Baltic Sea based on HELCOM Recommendation 26/3. The database is structured according to [HELCOM Guidelines on Monitoring of Radioactive Substances](https://www.helcom.fi/wp-content/uploads/2019/08/Guidelines-for-Monitoring-of-Radioactive-Substances.pdf), which specifies reporting format, database structure, data types and obligatory parameters used for reporting data under Recommendation 26/3. The database is updated and quality assured annually by HELCOM MORS EG.\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":685,"value":"sanitized_logs = \"*Remap to MARIS radionuclide names *Renaming variables to MARIS standard names., Drop variable containing only NaN or 'Not available' (id=0 in MARIS lookup tables)., Assign Detection Limit name to its id based on MARIS nomenclature., Convert data from long to wide with renamed columns., Encode time as int representing seconds since xxx, Drop row when both longitude & latitude equal 0.\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":600,"value":"function metadata(attrs) {\n let table = [];\n // \"| Heading 1 | # Title |\"\n for (const property in attrs) {\n table.push(`|${property} | ${attrs[property].value} |`);\n // console.log(`${property}: ${attrs[property].value}`);\n }\n console.log(table);\n\n return md`### Metadata \n\n| Name | Value(s) | \n| -------------- | ---------------------------------- |\n| Title | **${attrs.title.value}** |\n| Summary | ${str_sanitized}|\n| Keywords | ${attrs.keywords.value} |\n| Postprocessing logs | ${attrs.publisher_postprocess_logs.value} |\n| Publisher name | ${attrs.publisher_name.value} |\n\n`;\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":644,"value":"metadata(helcom.attrs)","pinned":false,"hidden":false,"mode":"ojs"},{"id":640,"value":"// {\n// const data = {\n// key1: \"value1\",\n// key2: \"value2\",\n// key3: \"value3\",\n// key4: \"value4\"\n// };\n\n// let html = `\n// \n// \n// \n// \n// ${Object.keys(data)\n// .map(\n// (key) => `\n// \n// \n// \n// \n// `\n// )\n// .join(\"\")}\n//

Key	Value
${key}	${data[key]}

`;\n// }","pinned":true,"hidden":false,"mode":"ojs"},{"id":616,"value":"metadata(helcom.attrs)","pinned":true,"hidden":false,"mode":"ojs"},{"id":568,"value":"helcom.attrs.title.value\n\n// .attrs.long_name.value","pinned":true,"hidden":false,"mode":"ojs"},{"id":433,"value":"helcom.get(\"biota\").keys()","pinned":true,"hidden":false,"mode":"ojs"},{"id":917,"value":"// biota, seawater, sediment\nhelcom.keys()","pinned":true,"hidden":false,"mode":"ojs"},{"id":904,"value":"helcom.get(\"biota/sample\").value.length","pinned":true,"hidden":false,"mode":"ojs"},{"id":915,"value":"helcom.get(\"seawater/sample\").value.length","pinned":true,"hidden":false,"mode":"ojs"},{"id":927,"value":"helcom.get(\"sediment/sample\").value.length","pinned":true,"hidden":false,"mode":"ojs"},{"id":480,"value":"helcom.get(\"species_t\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":472,"value":"### Getting and manipulating a variable in a group","pinned":false,"hidden":false,"mode":"md"},{"id":456,"value":"lon = helcom.get(\"biota/lon\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":465,"value":"lon.shape","pinned":true,"hidden":false,"mode":"ojs"},{"id":474,"value":"lon.attrs","pinned":true,"hidden":false,"mode":"ojs"},{"id":489,"value":"helcom.get(\"biota/lon\").metadata","pinned":true,"hidden":false,"mode":"ojs"},{"id":440,"value":"helcom.get(\"biota\").get(\"depth\").value","pinned":true,"hidden":false,"mode":"ojs"},{"id":451,"value":"helcom.get(\"biota\").get(\"area\").value[0]","pinned":true,"hidden":false,"mode":"ojs"},{"id":154,"value":"// Global individual attr\n// helcom.get_attribute(\"description\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":220,"value":"// Or all\nObject.keys(helcom.attrs).map((d) => `${d}: ${helcom.get_attribute(d)}`)","pinned":true,"hidden":false,"mode":"ojs"},{"id":94,"value":"// groups\nhelcom.keys()","pinned":true,"hidden":false,"mode":"ojs"},{"id":408,"value":"helcom.get(\"species_t\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":99,"value":"// Available variables in group\nhelcom.get(\"biota\").keys()","pinned":true,"hidden":false,"mode":"ojs"},{"id":124,"value":"helcom.get(\"biota\").get(\"cs137\").value","pinned":true,"hidden":false,"mode":"ojs"},{"id":136,"value":"// Variable attributes name\nhelcom.get(\"sediment\").get(\"cs137\").attrs.long_name.value","pinned":true,"hidden":false,"mode":"ojs"},{"id":163,"value":"// Variable attribute value\nhelcom.get(\"sediment\").get(\"cs137\").get_attribute(\"long_name\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":499,"value":"helcom.get(\"biota\").keys()","pinned":true,"hidden":false,"mode":"ojs"},{"id":505,"value":"helcom.get(\"biota\").get(\"species\").metadata[\"enum_type\"].members","pinned":true,"hidden":false,"mode":"ojs"},{"id":289,"value":"### Accessing enum types","pinned":false,"hidden":false,"mode":"md"},{"id":295,"value":"clouds = FileAttachment(\"clouds.nc\")\n .arrayBuffer()\n .then(\n (d) => (\n h5.FS.writeFile(\"clouds.h5\", new Uint8Array(d)),\n new h5.File(\"clouds.h5\", \"r\")\n )\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":336,"value":"clouds.keys()","pinned":true,"hidden":false,"mode":"ojs"},{"id":339,"value":"clouds.get(\"primary_cloud\").value","pinned":true,"hidden":false,"mode":"ojs"},{"id":348,"value":"clouds.get(\"primary_cloud\").metadata[\"enum_type\"].members","pinned":true,"hidden":false,"mode":"ojs"},{"id":357,"value":"clouds","pinned":true,"hidden":false,"mode":"ojs"},{"id":325,"value":"// fileArrayBuffer = FileAttachment(\"clouds.nc\").arrayBuffer()\n\n// netcdfFile = h5wasm.open(await fileArrayBuffer)","pinned":true,"hidden":false,"mode":"ojs"},{"id":319,"value":"// clouds\n// .get(\"clouds.nc\")\n// .arrayBuffer()\n// .then((buffer) => {\n// const h5 = new H5(buffer);\n// // const variable = h5.open(\"cloud_t\");\n\n// return variable;\n// })","pinned":true,"hidden":false,"mode":"ojs"},{"id":298,"value":"// clouds.get(\"cloud_t\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":5,"value":"## Imports","pinned":false,"hidden":false,"mode":"md"},{"id":8,"value":"hdf5 = import(\"https://cdn.observableusercontent.com/npm/jsfive@0.3.12/+esm\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":85,"value":"// 0.4.9\n// h5 = import(\"https://cdn.observableusercontent.com/npm/h5wasm@0.7.2/+esm\").then(\n// (h5) => h5.ready.then(() => h5)\n// )","pinned":true,"hidden":false,"mode":"ojs"},{"id":331,"value":"// clouds2 = FileAttachment(\"clouds.nc\")\n// .arrayBuffer()\n// .then((buffer) => h5.open(buffer))","pinned":true,"hidden":false,"mode":"ojs"},{"id":312,"value":"// import { H5 } from \"https://cdn.skypack.dev/h5wasm\"","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W2f","stdlib":"1","titling":"auto"}