Add netcdf support

packages/client/src/admin/uploads/ProjectBackgroundJobContext.tsx

@@ -432,7 +432,7 @@ export default function DataUploadDropzone({
                   </h4>
                   <p className="text-sm">
                     {t(
-                      "SeaSketch currently supports vector data in GeoJSON, Shapefile (zipped), GeoTiff, and FlatGeobuf formats."
+                      "SeaSketch currently supports vector data in GeoJSON, Shapefile (zipped), GeoTiff, NetCDF and FlatGeobuf formats."
                     )}
                   </p>
                   {Boolean(state.droppedFiles) && !state.error && (

packages/spatial-uploads-handler/src/formats/netcdf.ts

@@ -0,0 +1,32 @@
+import gdal from "gdal-async";
+import { Logger } from "../logger";
+
+export async function getLayerIdentifiers(path: string, logger: Logger) {
+  const ids: string[] = [];
+  const data = await logger.exec(
+    ["gdalinfo", ["-json", path]],
+    "Problem getting layer identifiers"
+  );
+  const info = JSON.parse(data);
+  const metadata = info.metadata || {};
+  const subdatasets = metadata["SUBDATASETS"] || {};
+  for (const key in subdatasets) {
+    if (/_NAME$/.test(key)) {
+      ids.push(subdatasets[key]);
+    }
+  }
+  console.log("ids", ids);
+  return ids;
+}
+
+export async function convertToGeoTiff(
+  layerId: string,
+  outputPath: string,
+  logger: Logger
+) {
+  await logger.exec(
+    ["gdal_translate", ["-co", "COMPRESS=DEFLATE", layerId, outputPath]],
+    "Problem converting to GeoTIFF"
+  );
+  return outputPath;
+}

packages/spatial-uploads-handler/src/handleUpload.ts

@@ -17,6 +17,7 @@ import { processRasterUpload } from "./processRasterUpload";
 import { notifySlackChannel } from "./notifySlackChannel";
 import { getObject, putObject } from "./remotes";
 import { Logger } from "./logger";
+import { getLayerIdentifiers } from "./formats/netcdf";
 
 export { SpatialUploadsHandlerRequest };
 
@@ -150,6 +151,7 @@ export default async function handleUpload(
 
   const s3LogPath = `s3://${process.env.BUCKET}/${jobId}.log.txt`;
   let { name, ext, base } = path.parse(objectKey);
+
   name = sanitize(name);
   const originalName = name;
   name = `${jobId}`;
@@ -170,7 +172,7 @@ export default async function handleUpload(
   // After the environment is set up, we can start processing the file depending
   // on its type
   try {
-    if (isTif) {
+    if (isTif || ext === ".nc") {
       stats = await processRasterUpload({
         logger,
         path: workingFilePath,

packages/spatial-uploads-handler/src/processRasterUpload.ts

@@ -9,6 +9,7 @@ import { rasterInfoForBands } from "./rasterInfoForBands";
 import { Logger } from "./logger";
 import gdal from "gdal-async";
 import bbox from "@turf/bbox";
+import { convertToGeoTiff, getLayerIdentifiers } from "./formats/netcdf";
 
 export async function processRasterUpload(options: {
   logger: Logger;
@@ -41,6 +42,19 @@ export async function processRasterUpload(options: {
 
   const { ext, isCorrectProjection } = await validateInput(path, logger);
 
+  if (ext === ".nc") {
+    const layerIdentifiers = await getLayerIdentifiers(path, logger);
+    if (layerIdentifiers.length > 0) {
+      path = await convertToGeoTiff(
+        layerIdentifiers[0],
+        pathJoin(workingDirectory, jobId + ".tif"),
+        logger
+      );
+    } else {
+      throw new Error("No layers found in NetCDF file");
+    }
+  }
+
   await updateProgress("running", "analyzing");
   // Get raster stats
   const stats = await rasterInfoForBands(path);
@@ -155,12 +169,12 @@ async function validateInput(path: string, logger: Logger) {
 
   // Use rasterio to see if it is a supported file format
   const isTif = ext === ".tif" || ext === ".tiff";
-  if (!isTif) {
-    throw new Error("Only GeoTIFF files are supported");
+  if (!isTif && ext !== ".nc") {
+    throw new Error("Only GeoTIFF and NetCDF files are supported");
   }
 
   const ds = await gdal.openAsync(path);
-  if (ds.driver.description !== "GTiff") {
+  if (ds.driver.description !== "GTiff" && ds.driver.description !== "netCDF") {
     throw new Error(`Unrecognized raster driver "${ds.driver.description}"`);
   }
 

packages/spatial-uploads-handler/src/rasterInfoForBands.ts

@@ -169,7 +169,8 @@ export async function rasterInfoForBands(
     ) {
       // find a scaling factor that will represent the range of data values with
       // the full range of the encoding scheme.
-      if (range < 16_777_216) {
+      // This is useful for float values which may just be 0-1
+      if (range < 500) {
         scale = 1;
         // stretch values to fit full encoding scheme
         // Use factors of 10, e.g. 10, 100, 1000, etc.