From 1292331f8a62b0a72c9021dc4fb939a4ad9a3586 Mon Sep 17 00:00:00 2001
From: michael <mdcatchen@gmail.com>
Date: Fri, 6 Oct 2023 11:32:26 -0400
Subject: [PATCH] weightLayers script

---
 scripts/Block3/weightLayers.jl  | 43 +++++++++++++++++++++++++++++++++
 scripts/Block3/weightLayers.yml | 33 +++++++++++++++++++++++++
 2 files changed, 76 insertions(+)
 create mode 100644 scripts/Block3/weightLayers.jl
 create mode 100644 scripts/Block3/weightLayers.yml

diff --git a/scripts/Block3/weightLayers.jl b/scripts/Block3/weightLayers.jl
new file mode 100644
index 00000000..3f01da7e
--- /dev/null
+++ b/scripts/Block3/weightLayers.jl
@@ -0,0 +1,43 @@
+using JSON
+using CSV
+using DataFrames
+using SpeciesDistributionToolkit
+
+function read_inputs_dict(runtime_dir)
+    filepath = joinpath(runtime_dir, "input.json")
+    output_dir = joinpath(runtime_dir, "data/")
+    isdir(output_dir) || mkdir(output_dir)
+    return JSON.parsefile(filepath) 
+end 
+
+function write_outputs(runtime_dir, priority)
+    outpath = joinpath(runtime_dir, "priority.tif")
+    SpeciesDistributionToolkit._write_geotiff(outpath, priority; compress="COG")
+
+    output_json_path = joinpath(runtime_dir, "output.json")
+    open(output_json_path, "w") do f
+        write(f, JSON.json(Dict(:priority_map=>outpath)))
+    end 
+end
+
+function main()
+    runtime_dir = ARGS[1]   
+    inputs = read_inputs_dict(runtime_dir)
+
+    β = inputs["weights"]
+
+    uncert_path = inputs["uncertainty"]
+    uniqueness_path = inputs["climate_uniqueness"]
+    velocity_path = inputs["climate_velocity"]
+    access_path = inputs["accessability"]
+    
+    layer_paths = [uncert_path, uniqueness_path, velocity_path, access_path]
+
+    layers = [rescale(SimpleSDMPredictor(joinpath(runtime_dir, layer_path)), (0,1)) for layer_path in layer_paths]
+
+    priority = sum([β[i] .* layers[i].grid for i in eachindex(β)])
+
+    write_outputs(runtime_dir, priority)    
+end 
+
+main()
\ No newline at end of file
diff --git a/scripts/Block3/weightLayers.yml b/scripts/Block3/weightLayers.yml
new file mode 100644
index 00000000..c6cbad19
--- /dev/null
+++ b/scripts/Block3/weightLayers.yml
@@ -0,0 +1,33 @@
+script: weightLayers.jl
+name: Weight Layers
+description: "This script takes in multiple layers and computes a priority map based on a weighted average of those layers"
+author:
+  - name: Michael D. Catchen 
+    identifier: https://orcid.org/0000-0002-6506-6487
+inputs:
+  uncertainty:
+    label: uncertainty
+    description: uncertainty in the inference of some value across space
+    example: null
+  climate_uniqueness:
+    label: climate uniqueness
+    description: foobar
+    example: null
+  climate_velocity: 
+    label: climate uniqueness
+    description: foobar
+    example: null
+  accessibility:
+    label: accessibility
+    descrpition: foobar
+    example: null
+  weights:
+    label: weights
+    description: weight vector that sums to one. Weights correnspond to layers in this order, [uncertainty, uniqueness, velocity, accessability]
+    example: [0.3, 0.2, 0.4, 0.1]
+outputs:
+  priority_map:
+    label: priority_map
+    description: Sampling priority map.
+    type: image/tiff;application=geotiff
+