Merge pull request #386 from wearepal/soil-component

Soil component with WRB Classifications

app/javascript/projects/modelling/components/index.ts

@@ -36,6 +36,7 @@ import { ORValComponent } from "./orval_component"
 import { IMDComponent } from "./imd_component"
 import { HedgerowComponent } from "./hedgerow_component"
 import { ProjectPermissions } from "../../project_editor"
+import { SoilComponent } from "./soil_component"
 
 export interface ProjectProperties {
   extent: Extent
@@ -75,6 +76,7 @@ export function createDefaultComponents(saveMapLayer: SaveMapLayer, saveModel: S
       new CROMEComponent(extent, zoom, mask, maskLayer, maskCQL),
       new ATIComponent(extent, zoom, mask, maskLayer, maskCQL),
       new DesignationsComponent(extent, zoom, mask, maskLayer, maskCQL),
+      new SoilComponent(projectProps),
 
       // Outputs
       new MapLayerComponent(saveMapLayer),

app/javascript/projects/modelling/components/soil_component.ts

@@ -0,0 +1,257 @@
+import { BaseComponent } from "./base_component"
+import { NodeData, WorkerInputs, WorkerOutputs } from 'rete/types/core/data'
+import { Input, Node, Output, Socket } from 'rete'
+import { ProjectProperties } from "."
+import { Extent } from "ol/extent"
+import { booleanDataSocket, categoricalDataSocket, numericDataSocket } from "../socket_types"
+import { createXYZ } from "ol/tilegrid"
+import { retrieveISRICData } from "../model_retrieval"
+import { CategoricalTileGrid, NumericTileGrid } from "../tile_grid"
+import { TypedArray } from "d3"
+import { maskFromExtentAndShape } from "../bounding_box"
+import { SelectControl, SelectControlOptions } from "../controls/select"
+
+const ERBSoilTypes = [
+    "Acrisols",
+    "Albeluvisols",
+    "Alisols",
+    "Andosols",
+    "Arenosols",
+    "Calcisols",
+    "Cambisols",
+    "Chernozems",
+    "Cryosols",
+    "Durisols",
+    "Ferralsols",
+    "Fluvisols",
+    "Gleysols",
+    "Gypsisols",
+    "Histosols",
+    "Kastanozems",
+    "Leptosols",
+    "Lixisols",
+    "Luvisols",
+    "Nitisols",
+    "Phaeozems",
+    "Planosols",
+    "Plinthosols",
+    "Podzols",
+    "Regosols",
+    "Solonchaks",
+    "Solonetz",
+    "Stagnosols",
+    "Umbrisols",
+    "Vertisols"
+]
+
+interface SoilGridOptions {
+    SCOId : number
+    name : string
+    map: string
+    coverageId: string
+    outputSocket: Socket
+}
+
+const SoilGrids : SelectControlOptions[] = [
+    { id: 0, name: 'WRB (most probable)'},
+    { id: 1, name: 'WRB (probability)' }
+]
+
+const SoilGridOptions : SoilGridOptions[] = [
+    {
+        SCOId: 0,
+        name: 'All',
+        map: 'wrb',
+        coverageId: 'MostProbable',
+        outputSocket: categoricalDataSocket
+    }
+]
+
+ERBSoilTypes.forEach((soilType, index) => {
+    SoilGridOptions.push({
+        SCOId: 0,
+        name: soilType,
+        map: 'wrb',
+        coverageId: 'MostProbable',
+        outputSocket: booleanDataSocket
+    })
+    SoilGridOptions.push({
+        SCOId: 1,
+        name: soilType,
+        map: 'wrb',
+        coverageId: soilType,
+        outputSocket: numericDataSocket
+
+    })
+})
+
+async function renderCategoricalData(extent: Extent, zoom: number, maskMode: boolean, maskLayer: string, maskCQL: string) {
+
+    const tileGrid = createXYZ()
+    const mask = await maskFromExtentAndShape(extent, zoom, maskLayer, maskCQL, maskMode)
+    const outputTileRange = tileGrid.getTileRangeForExtentAndZ(extent, zoom)
+
+    const geotiff = await retrieveISRICData(extent, 'MostProbable', 'wrb', outputTileRange)
+
+
+    const rasters = await geotiff.readRasters({ bbox: extent, width: outputTileRange.getWidth(), height: outputTileRange.getHeight() })
+    const image = await geotiff.getImage()
+
+
+    const result = new CategoricalTileGrid(
+        zoom,
+        outputTileRange.minX,
+        outputTileRange.minY,
+        outputTileRange.getWidth(),
+        outputTileRange.getHeight()
+    )
+
+    for (let i = 0; i < (rasters[0] as TypedArray).length; i++) {
+
+        let x = (outputTileRange.minX + i % image.getWidth())
+        let y = (outputTileRange.minY + Math.floor(i / image.getWidth()))
+        result.set(x, y, mask.get(x, y) ? rasters[0][i]+1 : 255)
+
+    }
+
+    result.setLabels(new Map(ERBSoilTypes.map((soilType, index) => [index+1, soilType])))
+
+    return result
+}
+
+async function renderNumericData(extent: Extent, zoom: number, maskMode: boolean, maskLayer: string, maskCQL: string, map: string, coverageId: string) {
+
+    const tileGrid = createXYZ()
+    const mask = await maskFromExtentAndShape(extent, zoom, maskLayer, maskCQL, maskMode)
+    const outputTileRange = tileGrid.getTileRangeForExtentAndZ(extent, zoom)
+
+    const geotiff = await retrieveISRICData(extent, coverageId, map, outputTileRange)
+
+    const rasters = await geotiff.readRasters({ bbox: extent, width: outputTileRange.getWidth(), height: outputTileRange.getHeight() })
+    const image = await geotiff.getImage()
+
+    const result = new NumericTileGrid(
+        zoom,
+        outputTileRange.minX,
+        outputTileRange.minY,
+        outputTileRange.getWidth(),
+        outputTileRange.getHeight()
+    )
+
+    for (let i = 0; i < (rasters[0] as TypedArray).length; i++) {
+
+        let x = (outputTileRange.minX + i % image.getWidth())
+        let y = (outputTileRange.minY + Math.floor(i / image.getWidth()))
+
+        const value = rasters[0][i]
+        result.set(x, y, mask.get(x, y) ? (value === 255 ? NaN : value) : NaN)
+
+    }
+
+    return result
+}
+
+export class SoilComponent extends BaseComponent {
+    projectZoom: number
+    projectExtent: Extent
+    maskMode: boolean
+    maskLayer: string
+    maskCQL: string
+
+
+    constructor(projectProps: ProjectProperties) {
+        super("ISRIC Soil Data")
+        this.category = "Inputs"
+        this.projectZoom = projectProps.zoom
+        this.projectExtent = projectProps.extent
+        this.maskMode = projectProps.mask
+        this.maskLayer = projectProps.maskLayer
+        this.maskCQL = projectProps.maskCQL
+    }
+
+    changeOutputs(node: Node) {
+
+        node.getConnections().forEach(c => {
+            if (c.output.node !== node) {
+                this.editor?.removeConnection(c)
+            }
+        })
+        node.getConnections().forEach(c => this.editor?.removeConnection(c))
+
+        Array.from(node.outputs.values()).forEach(output => node.removeOutput(output))
+
+        this.updateOutputs(node)
+
+    }
+
+    updateOutputs(node: Node) {
+
+        const soilgridId = node.data.soilgridId || 0
+        // TODO - add outputs based on soilgridId
+        const soilGridOpts = SoilGridOptions.filter(opt => opt.SCOId == soilgridId)
+        soilGridOpts.forEach(
+            opt => node.addOutput(new Output(`${opt.name}-${opt.map}`, opt.name, opt.outputSocket))
+        )
+        node.update()
+
+    }
+
+    async builder(node: Node) {
+
+        node.meta.toolTip = "Data from ISRIC SoilGrids API."
+        node.meta.toolTipLink = "https://www.isric.org/"
+
+        node.addControl(
+            new SelectControl(
+                this.editor,
+                'soilgridId',
+                () => SoilGrids,
+                () => this.changeOutputs(node),
+                'Soil Grid'
+            )
+        )
+
+        this.updateOutputs(node)
+
+    }
+
+
+    async worker(node: NodeData, inputs: WorkerInputs, outputs: WorkerOutputs, ...args: unknown[]) {
+
+        const soilgridId = node.data.soilgridId || 0
+        const soilGrid = SoilGrids.find(opt => opt.id == soilgridId)
+        const soilGridOpts = SoilGridOptions.filter(opt => opt.SCOId == soilgridId)
+        let catData: CategoricalTileGrid | undefined = undefined
+
+        const promises = soilGridOpts.filter(
+            opt => node.outputs[`${opt.name}-${opt.map}`].connections.length > 0
+        ).map(async opt => {
+            if(soilGrid?.name == 'WRB (most probable)') {
+
+                if(!catData) {
+                    catData = await renderCategoricalData(this.projectExtent, this.projectZoom, this.maskMode, this.maskLayer, this.maskCQL)
+                }
+
+                switch(opt.name) {
+                    case 'All':
+                        outputs[`${opt.name}-${opt.map}`] = catData
+                        break
+                    default:
+                        outputs[`${opt.name}-${opt.map}`] = catData?.getBoolFromLabel(opt.name)
+                        break
+                }
+
+            }else{
+
+                outputs[`${opt.name}-${opt.map}`] = await renderNumericData(this.projectExtent, this.projectZoom, this.maskMode, this.maskLayer, this.maskCQL, opt.map, opt.coverageId)
+
+            }
+        })
+
+        await Promise.all(promises)
+
+        //outputs["WRB"] = await renderCategoricalData(this.projectExtent, this.projectZoom, this.maskMode, this.maskLayer, this.maskCQL)
+
+    }
+
+}

app/javascript/projects/modelling/model_retrieval.ts

@@ -4,6 +4,7 @@ import * as GeoTIFF from 'geotiff/dist-browser/geotiff'
 import { Extent } from 'ol/extent'
 import { bboxFromExtent } from './bounding_box'
 
+// Returns a GeoTIFF object from a WMS server. Useful for some categorical/boolean data but may be susceptible to data loss. Fatest option usually
 export async function retrieveModelData(extent: Extent, source: string, tileRange: any, style?: string) {
 
     // Uses WMS server: Returns data between 0 and 255
@@ -39,6 +40,7 @@ export async function retrieveModelData(extent: Extent, source: string, tileRang
 
 }
 
+// Returns a GeoTIFF object from a WCS server. Useful for continuous data but may be slower.
 export async function retrieveModelDataWCS(extent: Extent, source: string, tileRange: any) {
 
     // Uses WCS server: Returns raw data
@@ -68,4 +70,33 @@ export async function retrieveModelDataWCS(extent: Extent, source: string, tileR
     const tiff = await GeoTIFF.fromArrayBuffer(arrayBuffer)
 
     return tiff
+}
+
+// For interaction with ISRIC SoilGrids API
+export async function retrieveISRICData(extent: Extent, coverageId: string, map: string, tileRange: any) {
+
+    const server = `https://maps.isric.org/mapserv?map=/map/${map}.map&`
+    const [width, height] = [tileRange.getWidth(), tileRange.getHeight()]
+    const response = await fetch(
+        server + new URLSearchParams(
+            {
+                service: 'WCS',
+                version: '1.0.0',
+                request: 'GetCoverage',
+                COVERAGE: coverageId,
+                FORMAT: 'GEOTIFF_INT16',
+                WIDTH: width,
+                HEIGHT: height,
+                CRS: 'EPSG:3857',
+                RESPONSE_CRS: 'EPSG:3857',
+                BBOX: extent.toString()
+            }
+        )
+    )
+
+    const arrayBuffer = await response.arrayBuffer()
+    const tiff = await GeoTIFF.fromArrayBuffer(arrayBuffer)
+
+    return tiff
+
 }

app/javascript/projects/modelling/tile_grid.ts

@@ -390,6 +390,22 @@ export class CategoricalTileGrid extends TileGrid {
     this.minMax = [0, this.labels.size]
   }
 
+  getBoolFromLabel(label: string): BooleanTileGrid {
+
+    const boolGrid = new BooleanTileGrid(this.zoom, this.x, this.y, this.width, this.height)
+
+    const key = Array.from(this.labels).find(([key, value]) => value === label)?.[0]
+
+    this.iterate((x, y, value) => {
+      if (value === key) {
+        boolGrid.set(x, y, true)
+      }
+    })
+
+    return boolGrid
+
+  }
+
   getMinMax() {
     if (this.minMax == null) {
       //no labels given.