Merge pull request #450 from wearepal/natmap-soil

NATMAP Soil carbon data in model view & permissions

app/javascript/controllers/projects_controller.tsx

@@ -14,6 +14,7 @@ export default class extends Controller {
     projectDefraHedgerowPermission: Boolean,
     projectKewRgb25cmPermission: Boolean,
     projectKewSamplesPermission: Boolean,
+    projectNatmapSoilPermission: Boolean,
     projectExtents: Array,
     backButtonPath: String,
     dbModels: Object
@@ -26,6 +27,7 @@ export default class extends Controller {
   declare readonly projectDefraHedgerowPermissionValue: boolean
   declare readonly projectKewRgb25cmPermissionValue: boolean
   declare readonly projectKewSamplesPermissionValue: boolean
+  declare readonly projectNatmapSoilPermissionValue: boolean
   declare readonly projectExtentsValue: Array<any>
   declare readonly backButtonPathValue: string
   declare readonly dbModelsValue: DBModels
@@ -43,7 +45,8 @@ export default class extends Controller {
           { 
             DefraHedgerows: this.projectDefraHedgerowPermissionValue,
             KewRgb25cm: this.projectKewRgb25cmPermissionValue,
-            KewSamples: this.projectKewSamplesPermissionValue
+            KewSamples: this.projectKewSamplesPermissionValue,
+            NATMAPSoil: this.projectNatmapSoilPermissionValue
           }
         }
         teamExtents={this.projectExtentsValue as TeamExtentData[]}

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

@@ -40,6 +40,7 @@ import { SoilComponent } from "./soil_component"
 import { SegmentComponent } from "./segment_component"
 import { KewSamplesComponent } from "./kew_samples_component"
 import { InterpolationComponent } from "./interpolation_component"
+import { NatmapSoilComponent } from "./natmap_soil_component"
 
 export interface ProjectProperties {
   extent: Extent
@@ -58,6 +59,7 @@ export function createDefaultComponents(saveMapLayer: SaveMapLayer, saveModel: S
     // Team permissions restrict some components. Add them here.
     if (permissions.DefraHedgerows) restrictedComponents.push(new HedgerowComponent(projectProps))
     if (permissions.KewSamples) restrictedComponents.push(new KewSamplesComponent(projectProps))
+    if (permissions.NATMAPSoil) restrictedComponents.push(new NatmapSoilComponent(projectProps))
 
     // Freely available components here.
     const components : BaseComponent[] = [

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

@@ -0,0 +1,220 @@
+import { NodeData, WorkerInputs, WorkerOutputs } from "rete/types/core/data"
+import { ProjectProperties } from "."
+import { Node, Output, Socket } from "rete"
+import { BaseComponent } from "./base_component"
+import { SelectControlOptions } from "../controls/select"
+import { numericDataSocket } from "../socket_types"
+import { retrieveWFSData } from "../model_retrieval"
+import { Feature } from "ol"
+import { Geometry } from "ol/geom"
+import { BooleanTileGrid, NumericTileGrid } from "../tile_grid"
+import { createXYZ } from "ol/tilegrid"
+import { maskFromExtentAndShape } from "../bounding_box"
+
+interface NatmapSoilOptions extends SelectControlOptions {
+    key: string
+    socket: Socket
+    unit: string
+}
+
+const natmap_outputs : NatmapSoilOptions[] = [
+    {
+        id: 0,
+        name: 'Min Carbon stock 0-10cm (kg/m²)',
+        key: 'MIN_STK_10',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 1,
+        name: 'Max Carbon stock 0-10cm (kg/m²)',
+        key: 'MAX_STK_10',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 2,
+        name: 'Min Carbon stock 0-15cm (kg/m²)',
+        key: 'MIN_STK_15',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 3,
+        name: 'Max Carbon stock 0-15cm (kg/m²)',
+        key: 'MAX_STK_15',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 4,
+        name: 'Min Carbon stock 0-30cm (kg/m²)',
+        key: 'MIN_STK_30',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 5,
+        name: 'Max Carbon stock 0-30cm (kg/m²)',
+        key: 'MAX_STK_30',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 6,
+        name: 'Average Carbon stock 0-30cm (kg/m²)',
+        key: 'AV_STK_30',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 7,
+        name: 'Average Carbon stock 30-100cm (kg/m²)',
+        key: 'AV_STK_100',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 8,
+        name: 'Average Carbon stock 100-150cm (kg/m²)',
+        key: 'AV_STK_150',
+        socket: numericDataSocket,
+        unit: 'kg/m^2'
+    },
+    {
+        id: 9,
+        name: 'Average Organic Carbon 0-30cm (%)',
+        key: 'AV_OC_30',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 10,
+        name: 'Min Organic Carbon 0-30cm (%)',
+        key: 'MIN_OC_30',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 11,
+        name: 'Max Organic Carbon 0-30cm (%)',
+        key: 'MAX_OC_30',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 12,
+        name: 'Average Organic Carbon 30-100cm (%)',
+        key: 'AV_OC_100',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 13,
+        name: 'Min Organic Carbon 30-100cm (%)',
+        key: 'MIN_OC_100',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 14,
+        name: 'Max Organic Carbon 30-100cm (%)',
+        key: 'MAX_OC_100',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 15,
+        name: 'Average Organic Carbon 100-150cm (%)',
+        key: 'AV_OC_150',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 16,
+        name: 'Min Organic Carbon 100-150cm (%)',
+        key: 'MIN_OC_150',
+        socket: numericDataSocket,
+        unit: '%'
+    },
+    {
+        id: 17,
+        name: 'Max Organic Carbon 100-150cm (%)',
+        key: 'MAX_OC_150',
+        socket: numericDataSocket,
+        unit: '%'
+    }
+
+]
+
+function applyFeaturesToGrid(features: Feature<Geometry>[], projectProps: ProjectProperties, prop: string, mask: BooleanTileGrid) : NumericTileGrid {
+
+    const tileGrid = createXYZ()
+    const outputTileRange = tileGrid.getTileRangeForExtentAndZ(projectProps.extent, projectProps.zoom)
+    const grid = new NumericTileGrid(
+        projectProps.zoom,
+        outputTileRange.minX,
+        outputTileRange.minY,
+        outputTileRange.getWidth(),
+        outputTileRange.getHeight()
+    )
+
+    for (let feature of features) {
+
+        const geom = feature.getGeometry()
+        if (geom === undefined) { continue }
+
+        const val = feature.get(prop)
+        if (val === undefined) { continue }
+
+        const featureTileRange = tileGrid.getTileRangeForExtentAndZ(
+            geom.getExtent(),
+            projectProps.zoom
+        )
+
+        grid.iterateOverTileRange(featureTileRange, (x, y) => {
+                const center = tileGrid.getTileCoordCenter([projectProps.zoom, x, y])
+
+                if (geom.intersectsCoordinate(center)) {
+                    grid.set(x, y, mask.get(x, y) ? val : NaN)
+                }
+            }
+        )
+    }
+
+    return grid
+}
+
+export class NatmapSoilComponent extends BaseComponent {
+    projectProps: ProjectProperties
+    cachedFeatures: Feature<Geometry>[]
+    cachedOutputs: Map<string, NumericTileGrid>
+
+    constructor(projectProps: ProjectProperties) {
+        super("NATMAP Soil")
+        this.category = "Inputs"
+        this.projectProps = projectProps
+        this.cachedFeatures = []
+        this.cachedOutputs = new Map()
+    }
+
+    async builder(node: Node) {
+        natmap_outputs.forEach(opt => {
+            node.addOutput(new Output(opt.key, opt.name, opt.socket))
+        })
+    }
+
+    async worker(node: NodeData, inputs: WorkerInputs, outputs: WorkerOutputs, ...args: unknown[]) {
+
+        this.cachedFeatures = this.cachedFeatures.length === 0 ? await retrieveWFSData('cranfield_soil:NATMAPcarbon', this.projectProps) : this.cachedFeatures
+
+        const mask = await maskFromExtentAndShape(this.projectProps.extent, this.projectProps.zoom, this.projectProps.maskLayer, this.projectProps.maskCQL, this.projectProps.mask)
+
+        natmap_outputs.filter(opt => node.outputs[opt.key].connections.length > 0).forEach(opt => {
+            const res = this.cachedOutputs.has(opt.key) ? this.cachedOutputs.get(opt.key) : applyFeaturesToGrid(this.cachedFeatures, this.projectProps, opt.key, mask)
+            this.cachedOutputs.set(opt.key, res as NumericTileGrid)
+            outputs[opt.key] = res
+        })
+
+    }
+}

app/javascript/projects/modelling/model_retrieval.ts

@@ -3,6 +3,30 @@
 import * as GeoTIFF from 'geotiff/dist-browser/geotiff'
 import { Extent } from 'ol/extent'
 import { bboxFromExtent } from './bounding_box'
+import { ProjectProperties } from './components'
+import { GeoJSON } from "ol/format"
+import { Geometry } from 'ol/geom'
+import { Feature } from 'ol'
+
+export async function retrieveWFSData(source: string, projectProps: ProjectProperties) : Promise<Feature<Geometry>[]> {
+
+    const response = await fetch(
+        "https://landscapes.wearepal.ai/geoserver/wfs?" +
+        new URLSearchParams(
+          {
+            outputFormat: 'application/json',
+            request: 'GetFeature',
+            typeName: source,
+            srsName: 'EPSG:3857',
+            bbox : bboxFromExtent(projectProps.extent),
+          }
+        )
+    )
+
+    const features = new GeoJSON().readFeatures(await response.json())
+
+    return features
+}
 
 // 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) {

app/javascript/projects/modelling/tile_grid.ts

@@ -3,6 +3,7 @@ import { Extent } from "ol/extent"
 import { createXYZ } from "ol/tilegrid"
 import { registerSerializer } from "threads"
 import { getMedianCellSize } from "./components/cell_area_component"
+import { TileRange } from "ol"
 
 function validateZoom(zoom: number) {
   if (!(
@@ -244,12 +245,30 @@ export class NumericTileGrid extends TileGrid {
   }
 
   iterate(callback: (x: number, y: number, value: number) => void) {
+
     const { x, y, width, height } = this
     for (let i = x; i < x + width; i++) {
       for (let j = y; j < y + height; j++) {
         callback(i, j, this.get(i, j))
       }
     }
+
+  }
+
+  iterateOverTileRange(range: TileRange, callback: (x: number, y: number, value: number) => void) {
+
+    const { x, y, width, height } = this
+    const minX = Math.max(x, range.minX)
+    const maxX = Math.min(x + width, range.maxX)
+    const minY = Math.max(y, range.minY)
+    const maxY = Math.min(y + height, range.maxY)
+
+    for (let i = minX; i < maxX; i++) {
+      for (let j = minY; j < maxY; j++) {
+        callback(i, j, this.get(i, j))
+      }
+    }
+
   }
 
   get(x: number, y: number, zoom = this.zoom): number {

app/javascript/projects/project_editor.tsx

@@ -25,6 +25,7 @@ export interface ProjectPermissions {
   DefraHedgerows: boolean
   KewRgb25cm: boolean
   KewSamples: boolean
+  NATMAPSoil: boolean
 }
 
 export interface TeamExtentData {

app/models/project.rb

@@ -72,6 +72,14 @@ def kew_samples_permission
     tp ? tp.enabled : false
   end
 
+  def natmap_soil_permission
+    p = Permission.find_by(name: 'natmap_soil')
+    return false unless p
+
+    tp = team.team_permissions.find_by(permission: p)
+    tp ? tp.enabled : false
+  end
+
   def extents
     team_extents = Extent.where(team_id: team.id).to_json
   end

app/views/projects/show.html.erb

@@ -7,6 +7,7 @@
   data-projects-project-defra-hedgerow-permission-value="<%= @project.defra_hedgerow_permission %>"
   data-projects-project-kew-rgb25cm-permission-value="<%= @project.kew_rgb25cm_permission %>"
   data-projects-project-kew-samples-permission-value="<%= @project.kew_samples_permission %>"
+  data-projects-project-natmap-soil-permission-value="<%= @project.natmap_soil_permission %>"
   data-projects-project-extents-value="<%= @project.extents %>"
   data-projects-back-button-path-value="<%= team_projects_path(@project.team) %>"
   data-projects-db-models-value="<%= render partial: "defs", formats: [:json] %>"

db/migrate/20241121163637_add_natmap_permission.rb

@@ -0,0 +1,9 @@
+class AddNatmapPermission < ActiveRecord::Migration[6.1]
+  def change
+    permission = Permission.find_or_create_by(name: 'natmap_soil')
+
+    Team.all.each do |team|
+      TeamPermission.find_or_create_by(team: team, permission: permission, enabled: false)
+    end
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2024_10_21_150643) do
+ActiveRecord::Schema.define(version: 2024_11_21_163637) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"