BII pipeline

GEO-BON · Oct 17, 2024 · 31338d6 · 31338d6
1 parent 09b0462
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Showing 4 changed files with 83 additions and 27 deletions.
diff --git a/pipelines/BII.json b/pipelines/BII.json
@@ -26,8 +26,8 @@
       "id": "16",
       "type": "output",
       "position": {
-        "x": 1009,
-        "y": 164
+        "x": 1060,
+        "y": 110
       },
       "data": {
         "label": "Output"
@@ -54,6 +54,28 @@
       "data": {
         "label": "Output"
       }
+    },
+    {
+      "id": "19",
+      "type": "io",
+      "position": {
+        "x": 1113.046875,
+        "y": 196
+      },
+      "data": {
+        "descriptionFile": "BII>BIIChange.yml"
+      }
+    },
+    {
+      "id": "20",
+      "type": "output",
+      "position": {
+        "x": 1698.046875,
+        "y": 201
+      },
+      "data": {
+        "label": "Output"
+      }
     }
   ],
   "edges": [
@@ -91,6 +113,20 @@
       "target": "18",
       "targetHandle": null,
       "id": "reactflow__edge-15rasters-18"
+    },
+    {
+      "source": "15",
+      "sourceHandle": "rasters",
+      "target": "19",
+      "targetHandle": "rasters",
+      "id": "reactflow__edge-15rasters-19rasters"
+    },
+    {
+      "source": "19",
+      "sourceHandle": "bii_change",
+      "target": "20",
+      "targetHandle": null,
+      "id": "reactflow__edge-19bii_change-20"
     }
   ],
   "inputs": {
@@ -134,7 +170,8 @@
       "weight": 4,
       "example": null
     },
-    "BII>BIIZonalStats.yml@15|start_year": {
+    "BII>BIIChange.yml@19|start_year": {
+      "description": "Reference BII year for raster plotting",
       "label": "Start year for BII raster comparison",
       "type": "options",
       "options": [
@@ -146,7 +183,7 @@
       "example": "2000",
       "weight": 5
     },
-    "BII>BIIZonalStats.yml@15|end_year": {
+    "BII>BIIChange.yml@19|end_year": {
       "description": "BII layer to compare to the start year",
       "label": "End year for BII comparison",
       "type": "options",
@@ -156,8 +193,8 @@
         "2015",
         "2020"
       ],
-      "weight": 6,
-      "example": null
+      "example": "2020",
+      "weight": 6
     }
   },
   "outputs": {
@@ -178,6 +215,12 @@
       "label": "Rasters",
       "type": "image/tiff;application=geotiff[]",
       "weight": 2
+    },
+    "BII>BIIChange.yml@19|bii_change": {
+      "description": "Raster plot of change in BII",
+      "label": "Change in BII",
+      "type": "image/tiff;application=geotiff[]",
+      "weight": 3
     }
   }
 }
diff --git a/scripts/BII/BIIChange.R b/scripts/BII/BIIChange.R
@@ -1,7 +1,34 @@
 # This is to look at change in BII over time
+library("rjson")
+library("terra")
+library("dplyr")
+
+source(paste(Sys.getenv("SCRIPT_LOCATION"), "/data/loadFromStacFun.R", sep = "/"))
+
+input <- fromJSON(file=file.path(outputFolder, "input.json"))
+
+output<- tryCatch({
+
+start_yr <- paste0("bii_nhm_10km_", input$start_year)
+end_yr <- paste0("bii_nhm_10km_", input$end_year)
 
 # Load rasters as a raster stack
+rasters <- terra::rast(c(input$rasters))
+print(names(rasters))
 
+first_raster <- rasters[[names(rasters)==start_yr]]
+end_raster <- rasters[[names(rasters)==end_yr]]
+
+print(names(first_raster))
 # Summarise
+bii_change <- first_raster-end_raster
+
+# Output
+bii_change_path <- file.path(outputFolder, "BII_change.tif")
+writeRaster(bii_change, bii_change_path)
+
+output <- list("bii_change"=bii_change_path)
+}, error = function(e) { list(error = conditionMessage(e)) })
 
-# Output
+jsonData <- toJSON(output, indent=2)
+write(jsonData, file.path(outputFolder,"output.json"))
diff --git a/scripts/BII/BIIChange.yml b/scripts/BII/BIIChange.yml
@@ -1,4 +1,10 @@
 
+script: BIIChange.R
+name: Biodiversity Intactness Index Change
+description: "Look at change in the Biodiversity Intactness Index over time."
+author:
+  - name: Jory Griffith
+    identifier: https://orcid.org/0000-0001-6020-6690
 inputs: 
   rasters:
     label: Rasters of BII

diff --git a/scripts/BII/BIIZonalStats.yml b/scripts/BII/BIIZonalStats.yml
@@ -28,26 +28,6 @@ inputs:
     - Median
     - Mode
     example: Mean
-  start_year:
-    label: Start year for BII raster comparison
-    type: options
-    description: Reference BII year for raster plotting
-    options:
-    - "2000"
-    - "2005"
-    - "2010"
-    - "2015"
-    example: "2000"
-  end_year:
-    label: End year for BII comparison
-    description: BII layer to compare to the start year
-    type: options
-    options:
-    - "2005"
-    - "2010"
-    - "2015"
-    - "2020"
-    example: "2020"
 outputs:
   rasters:
      label: Rasters