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Commit 421d87a7 authored by Neha Hunka's avatar Neha Hunka
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Vector - DISPLAY Vectorizing IPCC classes

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country_summaries/IPCC_classes_DPS/Vector/DISPLAY/.ipynb_checkpoints/DIS_Vector_IPCC_classes-checkpoint.R 0 → 100644
+ 56
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View file @ 421d87a7
#####################################################################################################
#####################################################################################################
packages <- c("raster", "rgdal", "terra", "sf", "sp")
package.check <- lapply(packages, FUN = function(x) {
if (!require(x, character.only = TRUE)) {
library(x, character.only = TRUE, quietly=TRUE)
library(geojsonio)
}
})
#####################################################################################################
#####################################################################################################
options(show.error.locations = TRUE)
options(error = traceback)
args <- commandArgs(trailingOnly = TRUE)
TILE <- args[1]
#####################################################################################################
######################### CONVERT FILE TO 1 KM RESOLUTION USING MODE
INPUT <- args[5]
OUTPUT <- args[2]
if (file.exists(INPUT)) {
gdal_utils(util = "warp", source = INPUT, destination="input/NN.tif", options=c("-co","c(COMPRESS=DEFLATE,PREDICTOR=2,ZLEVEL=9)", "-ts",120,120,"-r","near","-dstnodata",0))
gdal_utils(util = "warp", source = INPUT, destination="input/MM.tif", options=c("-co","c(COMPRESS=DEFLATE,PREDICTOR=2,ZLEVEL=9)", "-ts",120,120,"-r","mode","-dstnodata",0))
}
NN <- rast("input/NN.tif")
MM <- rast("input/MM.tif")
MM[is.na(NN)] <- NA
writeRaster(MM, args[2], wopt= list(gdal=c("COMPRESS=DEFLATE","PREDICTOR=2","ZLEVEL=9")), overwrite=TRUE)
#####################################################################################################
######################## VECTORIZE THE 1 KM AND 30 M RASTERS ########################################
INVALIDS = c(100,200,300,1022,1025,1023,1016,1014,1013,1012,1011,1021,4042,4041,4043,4032,4035,4033,4022,4021,4025,4023,4012,4014,4016,4013,4011,5013,5014,5011,5023,5021,5035,5022,5031,7041,7043,7042,7031,7032,7035,7033,7022,7025,2042,2043,2035,2041,2033,2032,2031,2025,2022,2021,2023,2013,2012,2011,2016,2014,8011,8016,8021,8031,8035,3011,3014,3013,3012,3016,3021,3025,3023,3022,3031,3033,3035,1020,1020,1020,2020,2020,2020,2020,2020,2020,4020,4020,4020,1018,1018,1018,2018,2018,2018,2018,2018,2018,4018,4018,4018,1017,1017,1017,2017,2017,2017,2017,2017,2017,4017,4017,4017,1021,1021,1021,2021,2021,2021,2021,2021,2021,5021,5021,5021,6021,6021,6021,1019,1019,1019,2019,2019,2019,2019,2019,2019,4019,4019,4019,1008,1008,1008,2008,2008,2008,2008,2008,2008,4008,4008,4008,8008,8008,8008,1007,1007,1007,2007,2007,2007,2007,2007,2007,5007,5007,5007,6007,6007,6007,7007,7007,7007,1010,1010,1010,2010,2010,2010,2010,2010,2010,5010,5010,5010,6010,6010,6010,1009,1009,1009,2009,2009,2009,2009,2009,2009,4009,4009,4009,7009,7009,7009,4013,4013,4013,7013,7013,7013,2013,2013,2013,2013,2013,2013,8013,8013,8013,4011,4011,4011,7011,7011,7011,2011,2011,2011,4014,4014,4014,7014,7014,7014,8014,8014,8014,2014,2014,2014,2014,2014,2014,2012,2012,2012,4012,4012,4012,7012,7012,7012,2015,2015,2015,2015,2015,2015,4015,4015,4015,7015,7015,7015,2001,2001,2001,4001,4001,4001,7001,7001,7001,2003,2003,2003,4003,4003,4003,7003,7003,7003,2002,2002,2002,4002,4002,4002,7002,7002,7002,2006,2006,2006,4006,4006,4006,1016,1016,1016,2016,2016,2016,4016,4016,4016,1014,1014,1014,2014,2014,2014,2014,2014,2014,1018,1018,1018,2018,2018,2018,2005,2005,2005,3005,3005,3005,4005,4005,4005,7005,7005,7005,1004,1004,1004,2004,2004,2004,2004,2004,2004,3004,3004,3004,4004,4004,4004,7004,7004,7004,8004,8004,8004,1022,1022,1022,2022,2022,2022,4022,4022,4022,7022,7022,7022)
if (file.exists(args[2])) {
r <- rast(args[2])
p <- as.polygons(r)
names(p)[1] = "IPCC_classes_1km"
for (invalid in INVALIDS){
p <- subset(p, p$"IPCC_classes_1km" != invalid)
}
writeVector(p, args[4])
}
# if (file.exists(args[5])) {
# r <- rast(args[5])
# m <- as.polygons(r)
# names(m)[1] = "IPCC_classes_1km"
# for (invalid in INVALIDS){
# m <- subset(m, m$"IPCC_classes_1km" != invalid)
# }
# writeVector(m, args[3])
# }
#####################################################################################################
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/.ipynb_checkpoints/DIS_Vector_IPCC_classes_ADE-checkpoint.yml 0 → 100644
+ 33
− 0
View file @ 421d87a7
algorithm_description: Runs post processing steps to vectorize IPCC raster classes
algorithm_name: run_DIS_Vector_IPCC_classes_ADE
algorithm_version: DIS_Vector_IPCC_classes_ADE
build_command: biomass_harmonization/country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_build_command_main_ADE.sh
disk_space: 50GB
docker_container_url: mas.maap-project.org/root/maap-workspaces/base_images/r:v3.1.0
inputs:
config: []
file:
- default: 'none1'
description: IPCC_raster
name: IPCC_raster
required: true
positional:
- default: 'none'
description: TILE
name: TILE
required: true
- default: 'none'
description: IPCC_raster_1000m
name: IPCC_raster_1000m
required: true
- default: 'none4'
description: IPCC_vector_30m
name: IPCC_vector_30m
required: true
- default: 'none5'
description: IPCC_vector_1000m
name: IPCC_vector_1000m
required: true
queue: maap-dps-worker-32gb
repository_url: https://repo.maap-project.org/lduncanson/biomass_harmonization.git
run_command: biomass_harmonization/country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_run_IPCC_classes_ADE.sh
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/.ipynb_checkpoints/DIS_Vector_build_command_main_ADE-checkpoint.sh 0 → 100644
+ 17
− 0
View file @ 421d87a7
#!/bin/bash
set -x
basedir=$( cd "$(dirname "$0")" ; pwd -P )
# mamba env update -n r-with-gdal --file "${basedir}/env_main.yaml"
#install requirements packages
mamba env update -f ${basedir}/boreal_env_main_ADE.yaml
pushd ${HOME}
# Do not remove this (PMM Dec 2022)
source activate icesat2_boreal
pip install git+https://github.com/MAAP-Project/maap-py.git#egg=maappy
source activate base
pip3 install pyOpenSSL --upgrade
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/.ipynb_checkpoints/DIS_Vector_env_main_ADE-checkpoint.yaml 0 → 100644
+ 24
− 0
View file @ 421d87a7
name: Packages_for_IPCC_vectorization
channels:
- conda-forge
- defaults
dependencies:
- r-devtools
- r-raster
- r-rgeos
- r-rgdal
- r-geosphere
- r-RColorBrewer
- r-gdalUtils
- r-snow
- r-plyr
- r-scales
- r-maptools
- r-sf
- r-sp
- r-foreign
- r-geojsonio
- r-aws.s3
- r-terra
- r-RCurl
- r-aws.ec2metadata
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/.ipynb_checkpoints/DIS_Vector_run_IPCC_classes_ADE-checkpoint.sh 0 → 100644
+ 16
− 0
View file @ 421d87a7
#!/bin/bash
# source activate r-with-gdal
basedir=$( cd "$(dirname "$0")" ; pwd -P )
mkdir -p output
TILE=${1}
IPCC_raster_1000m="${TILE}_IPCC_classes_10km.tif"
IPCC_vector_30m="${TILE}_IPCC_classes_30m.gpkg"
IPCC_vector_1000m="${TILE}_IPCC_classes_10km.gpkg"
IPCC_raster="input/${TILE}_IPCC_classes.tif"
OUTPUTDIR="${PWD}/output"
Rscript ${basedir}/DIS_Vector_IPCC_classes.R ${TILE} output/${IPCC_raster_1000m} output/${IPCC_vector_30m} output/${IPCC_vector_1000m} ${IPCC_raster}
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_IPCC_classes.R 0 → 100644
+ 56
− 0
View file @ 421d87a7
#####################################################################################################
#####################################################################################################
packages <- c("raster", "rgdal", "terra", "sf", "sp")
package.check <- lapply(packages, FUN = function(x) {
if (!require(x, character.only = TRUE)) {
library(x, character.only = TRUE, quietly=TRUE)
library(geojsonio)
}
})
#####################################################################################################
#####################################################################################################
options(show.error.locations = TRUE)
options(error = traceback)
args <- commandArgs(trailingOnly = TRUE)
TILE <- args[1]
#####################################################################################################
######################### CONVERT FILE TO 1 KM RESOLUTION USING MODE
INPUT <- args[5]
OUTPUT <- args[2]
if (file.exists(INPUT)) {
gdal_utils(util = "warp", source = INPUT, destination="input/NN.tif", options=c("-co","c(COMPRESS=DEFLATE,PREDICTOR=2,ZLEVEL=9)", "-ts",120,120,"-r","near","-dstnodata",0))
gdal_utils(util = "warp", source = INPUT, destination="input/MM.tif", options=c("-co","c(COMPRESS=DEFLATE,PREDICTOR=2,ZLEVEL=9)", "-ts",120,120,"-r","mode","-dstnodata",0))
}
NN <- rast("input/NN.tif")
MM <- rast("input/MM.tif")
MM[is.na(NN)] <- NA
writeRaster(MM, args[2], wopt= list(gdal=c("COMPRESS=DEFLATE","PREDICTOR=2","ZLEVEL=9")), overwrite=TRUE)
#####################################################################################################
######################## VECTORIZE THE 1 KM AND 30 M RASTERS ########################################
INVALIDS = c(100,200,300,1022,1025,1023,1016,1014,1013,1012,1011,1021,4042,4041,4043,4032,4035,4033,4022,4021,4025,4023,4012,4014,4016,4013,4011,5013,5014,5011,5023,5021,5035,5022,5031,7041,7043,7042,7031,7032,7035,7033,7022,7025,2042,2043,2035,2041,2033,2032,2031,2025,2022,2021,2023,2013,2012,2011,2016,2014,8011,8016,8021,8031,8035,3011,3014,3013,3012,3016,3021,3025,3023,3022,3031,3033,3035,1020,1020,1020,2020,2020,2020,2020,2020,2020,4020,4020,4020,1018,1018,1018,2018,2018,2018,2018,2018,2018,4018,4018,4018,1017,1017,1017,2017,2017,2017,2017,2017,2017,4017,4017,4017,1021,1021,1021,2021,2021,2021,2021,2021,2021,5021,5021,5021,6021,6021,6021,1019,1019,1019,2019,2019,2019,2019,2019,2019,4019,4019,4019,1008,1008,1008,2008,2008,2008,2008,2008,2008,4008,4008,4008,8008,8008,8008,1007,1007,1007,2007,2007,2007,2007,2007,2007,5007,5007,5007,6007,6007,6007,7007,7007,7007,1010,1010,1010,2010,2010,2010,2010,2010,2010,5010,5010,5010,6010,6010,6010,1009,1009,1009,2009,2009,2009,2009,2009,2009,4009,4009,4009,7009,7009,7009,4013,4013,4013,7013,7013,7013,2013,2013,2013,2013,2013,2013,8013,8013,8013,4011,4011,4011,7011,7011,7011,2011,2011,2011,4014,4014,4014,7014,7014,7014,8014,8014,8014,2014,2014,2014,2014,2014,2014,2012,2012,2012,4012,4012,4012,7012,7012,7012,2015,2015,2015,2015,2015,2015,4015,4015,4015,7015,7015,7015,2001,2001,2001,4001,4001,4001,7001,7001,7001,2003,2003,2003,4003,4003,4003,7003,7003,7003,2002,2002,2002,4002,4002,4002,7002,7002,7002,2006,2006,2006,4006,4006,4006,1016,1016,1016,2016,2016,2016,4016,4016,4016,1014,1014,1014,2014,2014,2014,2014,2014,2014,1018,1018,1018,2018,2018,2018,2005,2005,2005,3005,3005,3005,4005,4005,4005,7005,7005,7005,1004,1004,1004,2004,2004,2004,2004,2004,2004,3004,3004,3004,4004,4004,4004,7004,7004,7004,8004,8004,8004,1022,1022,1022,2022,2022,2022,4022,4022,4022,7022,7022,7022)
if (file.exists(args[2])) {
r <- rast(args[2])
p <- as.polygons(r)
names(p)[1] = "IPCC_classes_1km"
for (invalid in INVALIDS){
p <- subset(p, p$"IPCC_classes_1km" != invalid)
}
writeVector(p, args[4])
}
# if (file.exists(args[5])) {
# r <- rast(args[5])
# m <- as.polygons(r)
# names(m)[1] = "IPCC_classes_1km"
# for (invalid in INVALIDS){
# m <- subset(m, m$"IPCC_classes_1km" != invalid)
# }
# writeVector(m, args[3])
# }
#####################################################################################################
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_IPCC_classes_ADE.yml 0 → 100644
+ 33
− 0
View file @ 421d87a7
algorithm_description: Runs post processing steps to vectorize IPCC raster classes
algorithm_name: run_DIS_Vector_IPCC_classes_ADE
algorithm_version: DIS_Vector_IPCC_classes_ADE
build_command: biomass_harmonization/country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_build_command_main_ADE.sh
disk_space: 50GB
docker_container_url: mas.maap-project.org/root/maap-workspaces/base_images/r:v3.1.0
inputs:
config: []
file:
- default: 'none1'
description: IPCC_raster
name: IPCC_raster
required: true
positional:
- default: 'none'
description: TILE
name: TILE
required: true
- default: 'none'
description: IPCC_raster_1000m
name: IPCC_raster_1000m
required: true
- default: 'none4'
description: IPCC_vector_30m
name: IPCC_vector_30m
required: true
- default: 'none5'
description: IPCC_vector_1000m
name: IPCC_vector_1000m
required: true
queue: maap-dps-worker-32gb
repository_url: https://repo.maap-project.org/lduncanson/biomass_harmonization.git
run_command: biomass_harmonization/country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_run_IPCC_classes_ADE.sh
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_build_command_main_ADE.sh 0 → 100644
+ 17
− 0
View file @ 421d87a7
#!/bin/bash
set -x
basedir=$( cd "$(dirname "$0")" ; pwd -P )
# mamba env update -n r-with-gdal --file "${basedir}/env_main.yaml"
#install requirements packages
mamba env update -f ${basedir}/boreal_env_main_ADE.yaml
pushd ${HOME}
# Do not remove this (PMM Dec 2022)
source activate icesat2_boreal
pip install git+https://github.com/MAAP-Project/maap-py.git#egg=maappy
source activate base
pip3 install pyOpenSSL --upgrade
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_env_main_ADE.yaml 0 → 100644
+ 24
− 0
View file @ 421d87a7
name: Packages_for_IPCC_vectorization
channels:
- conda-forge
- defaults
dependencies:
- r-devtools
- r-raster
- r-rgeos
- r-rgdal
- r-geosphere
- r-RColorBrewer
- r-gdalUtils
- r-snow
- r-plyr
- r-scales
- r-maptools
- r-sf
- r-sp
- r-foreign
- r-geojsonio
- r-aws.s3
- r-terra
- r-RCurl
- r-aws.ec2metadata
\ No newline at end of file
country_summaries/IPCC_classes_DPS/Vector/DISPLAY/DIS_Vector_run_IPCC_classes_ADE.sh 0 → 100644
+ 16
− 0
View file @ 421d87a7
#!/bin/bash
# source activate r-with-gdal
basedir=$( cd "$(dirname "$0")" ; pwd -P )
mkdir -p output
TILE=${1}
IPCC_raster_1000m="${TILE}_IPCC_classes_10km.tif"
IPCC_vector_30m="${TILE}_IPCC_classes_30m.gpkg"
IPCC_vector_1000m="${TILE}_IPCC_classes_10km.gpkg"
IPCC_raster="input/${TILE}_IPCC_classes.tif"
OUTPUTDIR="${PWD}/output"
Rscript ${basedir}/DIS_Vector_IPCC_classes.R ${TILE} output/${IPCC_raster_1000m} output/${IPCC_vector_30m} output/${IPCC_vector_1000m} ${IPCC_raster}
\ No newline at end of file
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