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Commit c46b4bd9 authored by Neha Hunka's avatar Neha Hunka
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moving to ecoregions and CCI 2018

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country_summaries/dps/.ipynb_checkpoints/Country_summaries_DPS-checkpoint.R
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− 10
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......@@ -8,15 +8,16 @@
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R GHA /projects/my-public-bucket/Data/Country_boundaries/GEDI_countries_Dubayah_individual/ne_10m_a_1_GHA.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9228 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9228.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9228 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9228.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_clipped/9228_CCI_AOImasked.tif /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
################################# DESCRIPTION OF ARGUMENTS ############################################
# args[1] = Country eco3 code
# args[2] = Source of the shapefile for eco3
# args[3] = maps to be compared (e.g. CCI,JPL,GEDI,NCEO)
# args[4] = GEDI folder # "https://maap-ops-workspace.s3.amazonaws.com/shared/minord/data/GEDI_L4B"
# args[5] = NCEO folder
# args[6] = CCI folder
# args[4] = GEDI file # "https://maap-ops-workspace.s3.amazonaws.com/shared/minord/data/GEDI_L4B"
# args[5] = NCEO file
# args[6] = CCI file
# args[7] = GEDI SE file
####################################### INSTALL AND LOAD PACKAGES USING CONDA ###########################
# args <- commandArgs(trailingOnly = TRUE)
......@@ -28,10 +29,10 @@
# options(repos = r)
# }
# system2(command='bash',args='/projects/biomass_harmonization/country_summaries/dps/Package_list.sh')
# r = getOption("repos")
# r["CRAN"] = "http://cran.us.r-project.org"
# options(repos = r)
system2(command='bash',args='/projects/biomass_harmonization/country_summaries/dps/Package_list.sh')
r = getOption("repos")
r["CRAN"] = "http://cran.us.r-project.org"
options(repos = r)
library(raster)
library(rgdal)
library(rgeos)
......@@ -715,7 +716,7 @@ if (conti=="Seven seas (open ocean)" & (eco3=="MDV" | eco3=='MUS' | eco3=='SYC')
if (conti=="Asia" & (eco3=="TLS" | eco3=='MUS' | eco3=='SYC')){conti = "Oceania"}
aoi <- Cont[Cont$DPS_run == eco3,]
AOI_file = file.path(Out_folder,paste0(eco3,'_aoi.gpkg'))
writeOGR(obj=aoi, dsn=Out_folder, layer=paste0(eco3,'_aoi'), driver="ESRI Shapefile")
# writeOGR(obj=aoi, dsn=Out_folder, layer=paste0(eco3,'_aoi'), driver="ESRI Shapefile")
if (!identical(crs(aoi), crs(Grid_tiles))){aoi <- spTransform(aoi, crs(Grid_tiles))}
intersecting <- as.logical(gIntersects(Grid_tiles, gConvexHull(aoi), byid=TRUE) & !gTouches(Grid_tiles, gConvexHull(aoi), byid=TRUE))
if (sum(intersecting) == 0) {
......@@ -782,7 +783,7 @@ dev.off()
#######################################################################
coarsest_res <- coarsest_resolution(maps_AOImasked=maps_AOImasked)
if (coarsest_res[1] == 'GEDI'){
if (maps[coarsest_res[1]] == 'GEDI'){
print(paste0('Product ',maps[coarsest_res[1]],' was found to have the largest pixel size'))
print('All other products will be resampled to this resolution')
CI_map <- readAGBmap(AOI_file=AOI_file,aoi=aoi,continent=conti,map=paste0(maps[coarsest_res[1]],'_SE'),In_folder=gedi_SE_folder,In_year = eval(parse(text=paste0(maps[coarsest_res[1]],'_year'))),Out_folder=Out_folder)
......
country_summaries/dps/.ipynb_checkpoints/Create_CCI_clips-checkpoint.sh
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......@@ -10,4 +10,4 @@ conda install -c conda-forge r-plyr --yes
conda install -c conda-forge r-geosphere --yes
conda activate r-with-gdal
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R COUNTRYISO3 /projects/my-public-bucket/Data/WWF_NE_Boundaries/DPS_run_COUNTRYISO3.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
\ No newline at end of file
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R COUNTRYISO3 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_COUNTRYISO3.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
country_summaries/dps/.ipynb_checkpoints/Create_CCI_clips_GLOBAL-checkpoint.sh 0 → 100644
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source activate r-with-gdal
conda install -c conda-forge r-raster --yes
conda install -c conda-forge r-rgdal --yes
conda install -c conda-forge r-rColorBrewer --yes
conda install -c conda-forge r-gdalUtils --yes
conda install -c conda-forge r-jpeg --yes
conda install -c conda-forge r-rgeos --yes
conda install -c conda-forge r-sf --yes
conda install -c conda-forge r-plyr --yes
conda install -c conda-forge r-geosphere --yes
conda activate r-with-gdal
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R COUNTRYISO3 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_COUNTRYISO3.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9104 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9104.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9099 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9099.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9082 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9082.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 7452 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_7452.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9344 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9344.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9342 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9342.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9032 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9032.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
country_summaries/dps/.ipynb_checkpoints/algorithm_config-checkpoint.yaml
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algo_name: run_country_summaries
version: AGB_maps
environment: ubuntu
repository_url: https://repo.ops.maap-project.org/lduncanson/biomass_harmonization.git #note username and token is not needed
repository_url: https://repo.ops.maap-project.org/lduncanson/biomass_harmonization.git
docker_url: mas.maap-project.org:5000/root/ade-base-images/r:latest
queue: maap-dps-worker-32gb
description: Test algo for biomass harmonization
......
country_summaries/dps/.ipynb_checkpoints/env_main-checkpoint.yaml
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name: r-with-gdal # updating r-with-gdal, building the packages on it.
name: r-with-gdal
channels:
- conda-forge
- defaults
dependencies:
# find out what packages you're using from the R terminal (for replicating in future, use the SAME versions, specify versions...)
- r-raster
- r-rgdal
- r-rColorBrewer
......
country_summaries/dps/.ipynb_checkpoints/run_country_summaries-checkpoint.sh
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#!/bin/bash
# this is intended for running DPS jobs; the input directory is where four files have been pulled because download=TRUE in the algorithm_config.yaml file
# a tar file of biomass models, a data table csv, and two raster stack geotiff files
source activate r-with-gdal
basedir=$( cd "$(dirname "$0")" ; pwd -P )
mkdir output #(has to be called 'output', you can't change this name)
mkdir output
# Note: the numbered args are fed in with the in_param_dict in the Run DPS chunk of run_country_summaries.ipynb
ISO3_code=${1}
Shapefile=${2}
Map_list=${3}
......@@ -16,7 +13,6 @@ NCEO_file=${5}
CCI_file=${6}
GEDI_SE_file=${7}
# This PWD is wherever the job is run (where the .sh is called from)
OUTPUTDIR="${PWD}/output"
Rscript ${basedir}/Country_summaries_DPS.R ${ISO3_code} ${Shapefile} ${Map_list} ${GEDI_file} ${NCEO_file} ${CCI_file} ${GEDI_SE_file}
\ No newline at end of file
country_summaries/dps/Country_summaries_DPS.R
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......@@ -8,16 +8,16 @@
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R GHA /projects/my-public-bucket/Data/Country_boundaries/GEDI_countries_Dubayah_individual/ne_10m_a_1_GHA.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9228 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9228.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9228 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9228.gpkg CCI,GEDI,NCEO /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_clipped/9228_CCI_AOImasked.tif /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
################################# DESCRIPTION OF ARGUMENTS ############################################
# args[1] = Country eco3 code
# args[2] = Source of the shapefile for eco3
# args[3] = maps to be compared (e.g. CCI,JPL,GEDI,NCEO)
# args[4] = GEDI folder # "https://maap-ops-workspace.s3.amazonaws.com/shared/minord/data/GEDI_L4B"
# args[5] = NCEO folder
# args[6] = CCI folder
# args[7] = CCI folder
# args[4] = GEDI file # "https://maap-ops-workspace.s3.amazonaws.com/shared/minord/data/GEDI_L4B"
# args[5] = NCEO file
# args[6] = CCI file
# args[7] = GEDI SE file
####################################### INSTALL AND LOAD PACKAGES USING CONDA ###########################
# args <- commandArgs(trailingOnly = TRUE)
......@@ -29,10 +29,10 @@
# options(repos = r)
# }
# system2(command='bash',args='/projects/biomass_harmonization/country_summaries/dps/Package_list.sh')
# r = getOption("repos")
# r["CRAN"] = "http://cran.us.r-project.org"
# options(repos = r)
system2(command='bash',args='/projects/biomass_harmonization/country_summaries/dps/Package_list.sh')
r = getOption("repos")
r["CRAN"] = "http://cran.us.r-project.org"
options(repos = r)
library(raster)
library(rgdal)
library(rgeos)
......@@ -716,7 +716,7 @@ if (conti=="Seven seas (open ocean)" & (eco3=="MDV" | eco3=='MUS' | eco3=='SYC')
if (conti=="Asia" & (eco3=="TLS" | eco3=='MUS' | eco3=='SYC')){conti = "Oceania"}
aoi <- Cont[Cont$DPS_run == eco3,]
AOI_file = file.path(Out_folder,paste0(eco3,'_aoi.gpkg'))
writeOGR(obj=aoi, dsn=Out_folder, layer=paste0(eco3,'_aoi'), driver="ESRI Shapefile")
# writeOGR(obj=aoi, dsn=Out_folder, layer=paste0(eco3,'_aoi'), driver="ESRI Shapefile")
if (!identical(crs(aoi), crs(Grid_tiles))){aoi <- spTransform(aoi, crs(Grid_tiles))}
intersecting <- as.logical(gIntersects(Grid_tiles, gConvexHull(aoi), byid=TRUE) & !gTouches(Grid_tiles, gConvexHull(aoi), byid=TRUE))
if (sum(intersecting) == 0) {
......@@ -783,7 +783,7 @@ dev.off()
#######################################################################
coarsest_res <- coarsest_resolution(maps_AOImasked=maps_AOImasked)
if (coarsest_res[1] == 'GEDI'){
if (maps[coarsest_res[1]] == 'GEDI'){
print(paste0('Product ',maps[coarsest_res[1]],' was found to have the largest pixel size'))
print('All other products will be resampled to this resolution')
CI_map <- readAGBmap(AOI_file=AOI_file,aoi=aoi,continent=conti,map=paste0(maps[coarsest_res[1]],'_SE'),In_folder=gedi_SE_folder,In_year = eval(parse(text=paste0(maps[coarsest_res[1]],'_year'))),Out_folder=Out_folder)
......
country_summaries/dps/Create_CCI_clips.sh
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......@@ -10,4 +10,4 @@ conda install -c conda-forge r-plyr --yes
conda install -c conda-forge r-geosphere --yes
conda activate r-with-gdal
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R COUNTRYISO3 /projects/my-public-bucket/Data/WWF_NE_Boundaries/DPS_run_COUNTRYISO3.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
\ No newline at end of file
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 6847 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_6847.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
country_summaries/dps/Create_CCI_clips_GLOBAL.sh 0 → 100644
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source activate r-with-gdal
conda install -c conda-forge r-raster --yes
conda install -c conda-forge r-rgdal --yes
conda install -c conda-forge r-rColorBrewer --yes
conda install -c conda-forge r-gdalUtils --yes
conda install -c conda-forge r-jpeg --yes
conda install -c conda-forge r-rgeos --yes
conda install -c conda-forge r-sf --yes
conda install -c conda-forge r-plyr --yes
conda install -c conda-forge r-geosphere --yes
conda activate r-with-gdal
# Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R COUNTRYISO3 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_COUNTRYISO3.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9104 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9104.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9099 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9099.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9082 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9082.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 7452 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_7452.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9344 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9344.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9342 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9342.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
Rscript /projects/biomass_harmonization/country_summaries/dps/Country_summaries_DPS.R 9032 /projects/my-public-bucket/Data/WWF_NE_ecoregions/DPS_run_9032.gpkg CCI /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_MU.tif /projects/shared-buckets/minord/data/nceo_africa_biomass/clipped/AGB_map_2017v0m.tif /projects/my-public-bucket/Data/Biomass_maps/CCI_2018/dap.ceda.ac.uk/neodc/esacci/biomass/data/agb/maps/v3.0/geotiff/ /projects/shared-buckets/minord/data/GEDI_L4B/GEDI04_B_MW019MW138_02_002_05_R01000M_SE.tif
country_summaries/dps/algorithm_config.yaml
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algo_name: run_country_summaries
version: AGB_maps
environment: ubuntu
repository_url: https://repo.ops.maap-project.org/lduncanson/biomass_harmonization.git #note username and token is not needed
repository_url: https://repo.ops.maap-project.org/lduncanson/biomass_harmonization.git
docker_url: mas.maap-project.org:5000/root/ade-base-images/r:latest
queue: maap-dps-worker-32gb
description: Test algo for biomass harmonization
......
country_summaries/dps/env_main.yaml
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name: r-with-gdal # updating r-with-gdal, building the packages on it.
name: r-with-gdal
channels:
- conda-forge
- defaults
dependencies:
# find out what packages you're using from the R terminal (for replicating in future, use the SAME versions, specify versions...)
- r-raster
- r-rgdal
- r-rColorBrewer
......
country_summaries/dps/run_country_summaries.ipynb
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country_summaries/dps/run_country_summaries.sh
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#!/bin/bash
# this is intended for running DPS jobs; the input directory is where four files have been pulled because download=TRUE in the algorithm_config.yaml file
# a tar file of biomass models, a data table csv, and two raster stack geotiff files
source activate r-with-gdal
basedir=$( cd "$(dirname "$0")" ; pwd -P )
mkdir output #(has to be called 'output', you can't change this name)
mkdir output
# Note: the numbered args are fed in with the in_param_dict in the Run DPS chunk of run_country_summaries.ipynb
ISO3_code=${1}
Shapefile=${2}
Map_list=${3}
......@@ -16,7 +13,6 @@ NCEO_file=${5}
CCI_file=${6}
GEDI_SE_file=${7}
# This PWD is wherever the job is run (where the .sh is called from)
OUTPUTDIR="${PWD}/output"
Rscript ${basedir}/Country_summaries_DPS.R ${ISO3_code} ${Shapefile} ${Map_list} ${GEDI_file} ${NCEO_file} ${CCI_file} ${GEDI_SE_file}
\ No newline at end of file
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