tmf-implementation/scripts/tmfpython.sh at main · varya-collab/tmf-implementation · GitHub

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#!/bin/bash

#run with command: scripts/tmfpython.sh -i 'maps/aew85/projects' -o '/maps/aew85/tmf_pipe_out' -p 1113 -t 2010 ...

#i: input dir - directory containing project shapefiles

#o: output dir - directory containing pipeline outputs

#p: project name/ID - must match name of shapefile

#t: year of project start (t0)

#e: evaluation year (default: 2022)

#v: verbose - whether to run an ex-post evaluation and knit the results in an R notebook (true/false, default: false).

#NB running evaluations requires the evaluations code

# Check which branch is currently checked out

#current_branch=$(git rev-parse --abbrev-ref HEAD)

set -e

############ DEFAULTS ###############

input_dir=""

output_dir=""

eval_year=2022

verbose=false

#####################################

function display_help() {

echo "Usage: $0 [options]"

echo

echo "Options:"

echo " -i <input_dir> Input directory"

echo " -o <output_dir> Output directory"

echo " -p <proj> Project name"

echo " -t <t0> Start year"

echo " -e <year> Evaluation year"

echo " -v <verbose> Knit ex post evaluation as .Rmd? (true/false)"

echo " -h Display this help message"

echo "Example:"

echo " $0 -i '/maps/aew85/projects' -o '/maps/aew85/tmf_pipe_out -p 1201 -t 2012"

}

# Parse arguments

while getopts "i:o:p:t:e:v:h" flag

case "${flag}" in

i) input_dir=${OPTARG};;

o) output_dir=${OPTARG};;

p) proj=${OPTARG};;

t) t0=${OPTARG};;

e) eval_year=${OPTARG};;

r) verbose=${OPTARG};;

a) ex_ante=${OPTARG};;

h) display_help; exit 0;;

*) echo "Invalid option: -${OPTARG}" >&2; display_help; exit 1;;

esac

done

echo "Input directory: $input_dir"

echo "Output directory: $output_dir"

echo "Project: $proj"

echo "t0: $t0"

echo "Evaluation year: $eval_year"

echo "Ex-post evaluation: $verbose"

if [ $# -eq 0 ]; then

display_help

exit 1

# Make project output folder

mkdir -p "${output_dir}/${proj}"

echo "--Folder created.--"

#Make buffer

tmfpython3 -m methods.inputs.generate_boundary --project "${input_dir}/${proj}.geojson" --output "${output_dir}/${proj}/buffer.geojson"

echo "--Buffer created.--"

#Make leakage area

tmfpython3 -m methods.inputs.generate_leakage --project "${input_dir}/${proj}.geojson" --output "${output_dir}/${proj}/leakage.geojson"

echo "--Leakage created.--"

# Get GEDI data

tmfpython3 -m methods.inputs.locate_gedi_data --granules /maps/4C/gedi/granule/info/ \

--buffer "${output_dir}/${proj}/buffer.geojson" \

--output "${output_dir}/${proj}/gedi_names.csv"

tmfpython3 -m methods.inputs.download_gedi_data /maps/4C/gedi/granule/info/* /maps/4C/gedi/granule/

tmfpython3 -m methods.inputs.filter_gedi_data --granules /maps/4C/gedi/granule/ \

--buffer "${output_dir}/${proj}/buffer.geojson" \

--csv "${output_dir}/${proj}/gedi_names.csv" \

--output "${output_dir}/${proj}/gedi.geojson"

tmfpython3 -m methods.inputs.generate_carbon_density --jrc /maps/forecol/data/JRC/v1_2022/AnnualChange/tifs \

--gedi "${output_dir}/${proj}/gedi.geojson" \

--output "${output_dir}/${proj}/carbon-density.csv"

echo "--GEDI data obtained.--"

#Generate list of overlapping countries

tmfpython3 -m methods.inputs.generate_country_list \

--leakage "${output_dir}/${proj}/leakage.geojson" \

--countries /maps/4C/osm_boundaries.geojson \

--output "${output_dir}/${proj}/country-list.json"

echo "--Country list created.--"

#Generate matching area

tmfpython3 -m methods.inputs.generate_matching_area --project "${input_dir}/${proj}.geojson" \

--countrycodes "${output_dir}/${proj}/country-list.json" \

--countries /maps/4C/osm_boundaries.geojson \

--ecoregions /maps/4C/ecoregions/ecoregions.geojson \

--projects /maps/mwd24/tmf-data/projects \

--output "${output_dir}/${proj}/matching-area.geojson"

echo "--Matching area created.--"

#Download SRTM data

tmfpython3 -m methods.inputs.download_srtm_data --project "${input_dir}/${proj}.geojson" \

--matching "${output_dir}/${proj}/matching-area.geojson" \

--zips "${output_dir}/srtm/zip" \

--tifs "${output_dir}/srtm/tif"

echo "--SRTM downloaded.--"

#Generate slopes

tmfpython3 -m methods.inputs.generate_slope --input "${output_dir}/srtm/tif" --output "${output_dir}/slopes"

echo "--Slope created.--"

#Rescale to JRC tiles

tmfpython3 -m methods.inputs.rescale_tiles_to_jrc --jrc /maps/forecol/data/JRC/v1_2022/AnnualChange/tifs \

--tiles "${output_dir}/srtm/tif" \

--output "${output_dir}/rescaled-elevation"

tmfpython3 -m methods.inputs.rescale_tiles_to_jrc \

--jrc /maps/forecol/data/JRC/v1_2022/AnnualChange/tifs \

--tiles "${output_dir}/slopes" \

--output "${output_dir}/rescaled-slopes"

echo "--JRC rescaled.--"

#Create country raster

tmfpython3 -m methods.inputs.generate_country_raster --jrc /maps/forecol/data/JRC/v1_2022/AnnualChange/tifs \

--matching "${output_dir}/${proj}/matching-area.geojson" \

--countries /maps/4C/osm_boundaries.geojson \

--output "${output_dir}/${proj}/countries.tif"

echo "--Country raster created.--"

#Matching: calculate set K

tmfpython3 -m methods.matching.calculate_k \

--project "${input_dir}/${proj}.geojson" \

--start_year "$t0" \

--evaluation_year "$eval_year" \

--jrc /maps/forecol/data/JRC/v1_2022/AnnualChange/tifs \

--cpc /maps/rhm31/fine_circular_coverage/forecol_complete/ \

--ecoregions /maps/4C/ecoregions/ \

--elevation "${output_dir}/rescaled-elevation" \

--slope "${output_dir}/rescaled-slopes" \

--access /maps/4C/access \

--countries-raster "${output_dir}/${proj}/countries.tif" \

--output "${output_dir}/${proj}/k.parquet"

echo "--Set K created.--"

#Matching: calculate set M

tmfpython3 -m methods.matching.find_potential_matches \

--k "${output_dir}/${proj}/k.parquet" \

--matching "${output_dir}/${proj}/matching-area.geojson" \

--start_year "$t0" \

--evaluation_year "$eval_year" \

--jrc /maps/forecol/data/JRC/v1_2022/AnnualChange/tifs \

--cpc /maps/rhm31/fine_circular_coverage/forecol_complete/ \

--ecoregions /maps/4C/ecoregions/ \

--elevation "${output_dir}/rescaled-elevation" \

--slope "${output_dir}/rescaled-slopes" \

--access /maps/4C/access \

--countries-raster "${output_dir}/${proj}/countries.tif" \

--output "${output_dir}/${proj}/matches"

tmfpython3 -m methods.matching.build_m_raster \

--rasters_directory "${output_dir}/${proj}/matches" \

--output "${output_dir}/${proj}/matches.tif" \

-j 20

tmfpython3 -m methods.matching.build_m_table \

--raster "${output_dir}/${proj}/matches.tif" \

--matching "${output_dir}/${proj}/matching-area.geojson" \

--start_year "$t0" \

--evaluation_year "$eval_year" \

--jrc /maps/forecol/data/JRC/v1_2022/AnnualChange/tifs \

--cpc /maps/rhm31/fine_circular_coverage/forecol_complete/ \

--ecoregions /maps/4C/ecoregions/ \

--elevation "${output_dir}/rescaled-elevation" \

--slope "${output_dir}/rescaled-slopes" \

--access /maps/4C/access \

--countries-raster "${output_dir}/${proj}/countries.tif" \

--output "${output_dir}/${proj}/matches.parquet"

echo "--Set M created.--"

#Matching: find pairs

tmfpython3 -m methods.matching.find_pairs \

--k "${output_dir}/${proj}/k.parquet" \

--m "${output_dir}/${proj}/matches.parquet" \

--start_year "$t0" \

--output "${output_dir}/${proj}/pairs" \

--seed 42 \

-j 1

echo "--Pairs matched.--"

#Calculate additionality

tmfpython3 -m methods.outputs.calculate_additionality \

--project "${input_dir}/${proj}.geojson" \

--project_start "$t0" \

--evaluation_year "$eval_year" \

--density "${output_dir}/${proj}/carbon-density.csv" \

--matches "${output_dir}/${proj}/pairs" \

--output "${output_dir}/${proj}/additionality.csv"

echo "--Additionality calculated.--"

# Run ex post evaluation

if [ "$verbose" == "true" ]; then

evaluations_dir="~/evaluations"

ep_output_file="${evaluations_dir}/${proj}_ex_post_evaluation.html"

Rscript -e "rmarkdown::render(input='~/evaluations/R/ex_post_evaluation_template.Rmd',output_file='${ep_output_file}',params=list(proj='${proj}',t0='${t0}',eval_year='${eval_year}',input_dir='${input_dir}',output_dir='${output_dir}'))"

tmf-implementation/scripts/tmfpython.sh at main · varya-collab/tmf-implementation · GitHub

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