Applying GIS, Data Vis. and Deep Learning to environmental science and nuclear emergency responses
Public
Edited
Apr 11, 2024
// 0.7.2
h5 = import("https://cdn.observableusercontent.com/npm/h5wasm@0.4.9/+esm").then(
(h5) => h5.ready.then(() => h5)
)
// helcom = FileAttachment("100-HELCOM-MORS-2018@1.nc")
// .arrayBuffer()
// .then(
// (d) => (
// h5.FS.writeFile("helcom4.h5", new Uint8Array(d)),
// new h5.File("helcom4.h5", "r")
// )
// )
files = [FileAttachment("100-HELCOM-MORS-2018@1.nc")]
function loadNetcdf(file) {
const fname = `${file.name.split(".")[0]}.h5`;
console.log(fname);
return file
.arrayBuffer()
.then(
(d) => (
h5.FS.writeFile(fname, new Uint8Array(d)), new h5.File(fname, "r")
)
);
}
helcom = loadNetcdf(files[0])
helcom.keys()
wellknown = require("https://bundle.run/wellknown@0.5.0")
turf = require("@turf/turf@6.5")
helcom.attrs
// Geojson winding rules: https://observablehq.com/@d3/winding-order
bbox_netcdf = turf.rewind(wellknown(helcom.attrs.geospatial_bounds.value), {
reverse: true,
mutate: true
})
world = (
await fetch("https://cdn.jsdelivr.net/npm/world-atlas@2/land-50m.json")
).json()
land = topojson.feature(world, world.objects.land)
helcom.attrs
{
for (const property in helcom.attrs) {
console.log(`${property}: ${helcom.attrs[property].value}`);
}
}
str_sanitized = "**MORS Environment database** has been used to collate data resulting from monitoring of environmental radioactivity in the Baltic Sea based on HELCOM Recommendation 26/3. The database is structured according to [HELCOM Guidelines on Monitoring of Radioactive Substances](https://www.helcom.fi/wp-content/uploads/2019/08/Guidelines-for-Monitoring-of-Radioactive-Substances.pdf), which specifies reporting format, database structure, data types and obligatory parameters used for reporting data under Recommendation 26/3. The database is updated and quality assured annually by HELCOM MORS EG."
sanitized_logs = "*Remap to MARIS radionuclide names *Renaming variables to MARIS standard names., Drop variable containing only NaN or 'Not available' (id=0 in MARIS lookup tables)., Assign Detection Limit name to its id based on MARIS nomenclature., Convert data from long to wide with renamed columns., Encode time as int representing seconds since xxx, Drop row when both longitude & latitude equal 0."
function metadata(attrs) {
let table = [];
// "| Heading 1 | # Title |"
for (const property in attrs) {
table.push(`|${property} | ${attrs[property].value} |`);
// console.log(`${property}: ${attrs[property].value}`);
}
console.log(table);
return md`### Metadata
| Name | Value(s) |
| -------------- | ---------------------------------- |
| Title | **${attrs.title.value}** |
| Summary | ${str_sanitized}|
| Keywords | ${attrs.keywords.value} |
| Postprocessing logs | ${attrs.publisher_postprocess_logs.value} |
| Publisher name | ${attrs.publisher_name.value} |
`;
}
// {
// const data = {
// key1: "value1",
// key2: "value2",
// key3: "value3",
// key4: "value4"
// };
// let html = `<table>
// <tr>
// <th>Key</th>
// <th>Value</th>
// </tr>
// ${Object.keys(data)
// .map(
// (key) => `
// <tr>
// <td>${key}</td>
// <td>${data[key]}</td>
// </tr>
// `
// )
// .join("")}
// </table>`;
// }
metadata(helcom.attrs)
helcom.attrs.title.value
// .attrs.long_name.value
helcom.get("biota").keys()
// biota, seawater, sediment
helcom.keys()
helcom.get("biota/sample").value.length
helcom.get("seawater/sample").value.length
helcom.get("sediment/sample").value.length
helcom.get("species_t")
lon = helcom.get("biota/lon")
lon.shape
lon.attrs
helcom.get("biota/lon").metadata
helcom.get("biota").get("depth").value
helcom.get("biota").get("area").value[0]
// Global individual attr
// helcom.get_attribute("description")
// Or all
Object.keys(helcom.attrs).map((d) => `${d}: ${helcom.get_attribute(d)}`)
// groups
helcom.keys()
helcom.get("species_t")
// Available variables in group
helcom.get("biota").keys()
helcom.get("biota").get("cs137").value
// Variable attributes name
helcom.get("sediment").get("cs137").attrs.long_name.value
// Variable attribute value
helcom.get("sediment").get("cs137").get_attribute("long_name")
helcom.get("biota").keys()
helcom.get("biota").get("species").metadata["enum_type"].members
clouds.keys()
clouds.get("primary_cloud").value
clouds.get("primary_cloud").metadata["enum_type"].members
clouds
// fileArrayBuffer = FileAttachment("clouds.nc").arrayBuffer()
// netcdfFile = h5wasm.open(await fileArrayBuffer)
// clouds
// .get("clouds.nc")
// .arrayBuffer()
// .then((buffer) => {
// const h5 = new H5(buffer);
// // const variable = h5.open("cloud_t");
// return variable;
// })
// clouds.get("cloud_t")
// 0.4.9
// h5 = import("https://cdn.observableusercontent.com/npm/h5wasm@0.7.2/+esm").then(
// (h5) => h5.ready.then(() => h5)
// )
// clouds2 = FileAttachment("clouds.nc")
// .arrayBuffer()
// .then((buffer) => h5.open(buffer))
// import { H5 } from "https://cdn.skypack.dev/h5wasm"
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