WIP/OLD/LB_Phenorice_Aggregate_SEN.R
In lbusett/phenoriceR: Routines for analysis of PhenoRice outputs
# TODO: Add comment
#
# Author: LB
###############################################################################
library(ggplot2)
library(reshape)
library(data.table)
library(rgdal)
library(SDMTools)
library(plyr)
library(gdalUtils)
library(raster)
library(foreign)
library(tools)
memory.limit(16000)
# Define inputs and outputs
main_folder = '//10.0.1.252/nr_working/shared/PhenoRice/Processing/Senegal/Outputs/50_30_30_120_dec_ok/newquarts/masked'
country_code = c('SEN')
years = seq(2003,2014,1)
for (year in years) {
# main_folder = '//10.0.1.252/nr_working/shared/PhenoRice/Processing/IT/Outputs/2013/'
# country_code = c('ITA')
gadm_level = 3
phrice_outfolder = file.path(main_folder,year,'raster')
outputs_folder = "D:/Temp/PhenoRice/Processing/SEN/Outputs/newquarts/masked/" # Folder where to put results of this processing
year_out_folder = paste0(outputs_folder,year)
out_mod_grid_df_file = file.path(year_out_folder,paste0('out_df_modgrid_',year,'.RData'))
# refmap_file= 'D:/Temp/PhenoRice/Processing/PHL/Outputs/2013/Validate/Reference/PHL_DS_2013_Reference.tif'
#- ------------------------------------------------------------------------------- -#
# Initialize: setup input/output files and folders
#- ------------------------------------------------------------------------------- -#
in_phrice_file = list.files(phrice_outfolder, glob2rx('*Full_Out*dat'),full.names = TRUE)
grid_folder = file.path(outputs_folder,'GRIDs') #save the grid here
grid_resolutions = c(231.656358,2084.907, 5096.432, 10192.864,20385.73 ) # Resolution of output grids
grid_shapes <- c('Grid_MODIS_250','Grid_2Km','Grid_5Km','Grid_10Km','Grid_20Km') #this is the grid name
#
dir.create(outputs_folder, recursive = T)
dir.create(year_out_folder, recursive = T)
# out_repro_raster= file.path(outputs_folder,'Reference','Reproj','Reference_Map_SIN.tif')
# dir.create(dirname(out_repro_raster), recursive = T)
in_phrice_file_small = in_phrice_file
# in_phrice_file_small = file.path(outputs_folder,'Input','Clipped','Phenorice_Clipped.tif')
# in_phrice_file_small_vrt= file.path(outputs_folder,'Input','Clipped','Phenorice_Clipped.vrt')
# dir.create(dirname(in_phrice_file_small),recursive = T)
out_grid_rasters = file.path(outputs_folder,'Temporary',paste(grid_shapes,'_raster_HR.tiff',sep = ''))
grid_fullnames = paste(grid_folder,'/',grid_shapes,'.shp',sep = '')
out_grid_df_files = file.path(outputs_folder,paste('out_df_',grid_shapes,'_',year,'.RData', sep = ''))
out_grid_shp_files = file.path(outputs_folder,paste('out_shp_',grid_shapes,'.shp', sep = ''))
#- ------------------------------------------------------------------------------- -#
# Load Phenorice map and retrieve projection and extent
#- ------------------------------------------------------------------------------- -#
phrice_map = raster(in_phrice_file)
in_proj = proj4string(phrice_map)
ext_phrice_map = extent(phrice_map)
#- ------------------------------------------------------------------------------- -#
# Load reference map and define the extent
#- ------------------------------------------------------------------------------- -#
# refmap = raster(refmap_file)
#- ------------------------------------------------------------------------------- -#
# Reproject the reference raster map to MODIS projection
#- ------------------------------------------------------------------------------- -#
# {{
# in_ref = raster(refmap_file)
# in_ref_proj = proj4string(in_ref)
# if(file.exists(out_repro_raster) == FALSE) {
# ref_reproj = gdalwarp(refmap_file,out_repro_raster, s_srs = in_ref_proj, t_srs = in_proj,
# r = "near",of = 'GTiff', overwrite = T, srcnodata = 255, dstnodata = 255,ot = 'Byte', output_Raster = TRUE)
# ext_ref_repr = extent(ref_reproj)
# res_ref_reproj = res(ref_reproj)
# } else {
# ref_reproj = raster(out_repro_raster)
# ext_ref_repr = extent(ref_reproj)
# res_ref_reproj = res(ref_reproj)
#
# }}
#- ---------------------- --- --------------------------------------------------- -#
# Clip phenorice output on extent of reference map, using tap to avoid moving the corner
#- ------------------------------------------------------------------------------- -#
#
# gdalbuildvrt(in_phrice_file, in_phrice_file_small_vrt, tr = c(231.656358,231.656358), te = c(bbox(ext_ref_repr)), tap = TRUE)
# GdalTranslate = gdal_translate(in_phrice_file_small_vrt, in_phrice_file_small, overwrite = TRUE)
in_phrice_clipped = raster(in_phrice_file_small)
# gdalbuildvrt(in_phrice_file, in_phrice_file_small_vrt, tr = c(231.656358,231.656358), te = c(bbox(ext_ref_repr)), tap = TRUE)
# GdalTranslate = gdal_translate(in_phrice_file_small_vrt, in_phrice_file_small, overwrite = TRUE)
# in_phrice_clipped = raster(in_phrice_file)
# in_phrice_file_small = in_phrice_file
grid_extent = extent(in_phrice_clipped)
#- ------------------------------------------------------------------------------- -#
# Create the regular grids (MODIS + 2,5,10,20 K) if needed
#- ------------------------------------------------------------------------------- -#
for (gr_res in seq(along = grid_fullnames)) {
LB_Create_pol_grid = function(in_raster_file, out_res, out_folder, out_name_shp,grid_extent){
library(rgdal)
library(raster)
rast<- raster(in_raster_file)
# bb <- bbox(rast) # Define Bounding box
cs <- c(out_res,out_res) # cell size. To be set by hand!
cc <- c(grid_extent@xmin,grid_extent@ymin) + (cs/2) # cell offset # move 1/2 pixel if necessary
# compute number of cells per direction
if (cs < 300) { # needed to avoid that larger grids cover only one portion of the area --> so, add a row/coulmn for larger grids
cd <- c(dim(rast)[2],dim(rast)[1])
} else {
cd <- ceiling(c(((grid_extent@xmax-grid_extent@xmin)/cs[1]),((grid_extent@ymax-grid_extent@ymin)/cs[2])))
}
grd <- GridTopology(cellcentre.offset=cc, cellsize=cs, cells.dim=cd) # Define grd characteristics
#transform to spatial grid
sp_grd <- SpatialGridDataFrame(grd,
data=data.frame(id=1:prod(cd)),
proj4string=CRS(proj4string(rast)))
summary(sp_grd)
# browser()
sp_polygons = as(sp_grd, "SpatialPolygonsDataFrame")#create the shape
print('Creating MODIS Grid - Please Wait !')
writeOGR(sp_polygons,dsn = out_folder, layer =out_name_shp,driver="ESRI Shapefile", overwrite_layer = T) #save the shapefile
gc()
}
if(file.exists(grid_fullnames[gr_res]) == FALSE) {
LB_Create_pol_grid(in_phrice_clipped , grid_resolutions[gr_res],grid_folder, grid_shapes[gr_res],grid_extent)
}
} #End Cycle on gr_res
#- --------------------- --------------------------------------------------------- -#
# If not already existing, Rasterize polygons on the extent of the reference map, at a resolution
# equal to that of the reference map. For each pixel, values of this raster correspond to a
# unique identifier of the cell of the ERMES grid to which the pixel belongs
#- ------------------------------------------------------------------------------- -#
for (cycle in seq(along = grid_shapes)) {
if (cycle == 1) {
# if (file.exists(out_grid_rasters[cycle]) == FALSE){
# dir.create(dirname(out_grid_rasters[cycle]) ,recursive = T)
# raster_grid = gdal_rasterize(grid_fullnames[cycle],out_grid_rasters[cycle],a = "id", output_Raster = T,
# te = c(ext_ref_repr@xmin, (ext_ref_repr@ymin+res_ref_reproj[1]),(ext_ref_repr@xmax-res_ref_reproj[1]), (ext_ref_repr@ymax)), ot = 'UInt32',tr = res_ref_reproj, tap = T, of = 'GTiff')
# gc()
# }
#- -------------- ------ --- -- --------------------------------------------- -#
# Compute the percentage area classified as rice for each pixel
#- ------------------------------------------------------------------------------- -#
# Get the values of t "du r r of cells codes
# raster_cells <- new("GDALReadOnlyDataset", out_grid_rasters[cycle])
# data_raster_cells = getRasterData(raster_cells)
# dim(data_raster_cells) = dim(data_raster_cells)[1]*dim(data_raster_cells)[2]
# GDAL.close(raster_cells)
# gc()
#
# # Get the values of the "reference map
# ref_map <- new("GDALReadOnlyDataset",out_repro_raster)
# ref_map_data = getRasterData(ref_map)
# dim(ref_map_data) = dim(ref_map_data)[1]*dim(ref_map_data)[2]
# GDAL.close(ref_map)
# gc()
# Create a Data.table with two columns. First column taken from the cell_codes raster - tells to which cell each pixel correspond
# Second column taken from the reference rice map (0 or 1)
# browser()
# cells_dt = data.table(id=data_raster_cells,value = ref_map_data )
# setkey(cells_dt, id) # Set a indexing key to increase speed of zonal statistics computation
# rm(ref_map_data)
# rm(data_raster_cells)
# gc()
#
# # Compute the aggregated Reference Map values for each cell of the ERMES grid - average, stdev, min, max and n? of pixels in each cell
# aggregate_reference_values = cells_dt[, list(ref_rice_fc = mean(value, na.rm = T),
#
# n_cells = as.numeric(length(which(is.finite(value) == T )))
# ), by = key(cells_dt)]
#
# aggregate_reference_values = aggregate_reference_values[id != 0 ]
# rm(cells_dt)
#- --- -------------- ---- -- --------------------------------------------- -#
# Retrieve necessary data from the enorice output rasters
#- -------------------------------- --------------------------------------------- -#
rice_rast = new("GDALReadOnlyDataset", in_phrice_file_small)
data_rice = getRasterData(rice_rast)
data_nrice = data_rice[,,1] ; dim(data_nrice) = dim(data_nrice)[1]*dim(data_nrice)[2]
mins_q1 = data_rice[,,2] ; dim(mins_q1) = dim(mins_q1)[1]*dim(mins_q1)[2]
mins_q2 = data_rice[,,3] ; dim(mins_q2) = dim(mins_q2)[1]*dim(mins_q2)[2]
mins_q3 = data_rice[,,4] ; dim(mins_q3) = dim(mins_q3)[1]*dim(mins_q3)[2]
mins_q4 = data_rice[,,5] ; dim(mins_q4) = dim(mins_q4)[1]*dim(mins_q4)[2]
maxs_q1 = data_rice[,,6] ; dim(maxs_q1) = dim(maxs_q1)[1]*dim(maxs_q1)[2]
maxs_q2 = data_rice[,,7] ; dim(maxs_q2) = dim(maxs_q2)[1]*dim(maxs_q2)[2]
maxs_q3 = data_rice[,,8] ; dim(maxs_q3) = dim(maxs_q3)[1]*dim(maxs_q3)[2]
maxs_q4 = data_rice[,,9] ; dim(maxs_q4) = dim(maxs_q4)[1]*dim(maxs_q4)[2]
soss_q1 = data_rice[,,14] ; dim(soss_q1) = dim(soss_q1)[1]*dim(soss_q1)[2]
soss_q2 = data_rice[,,15] ; dim(soss_q2) = dim(soss_q2)[1]*dim(soss_q2)[2]
soss_q3 = data_rice[,,16] ; dim(soss_q3) = dim(soss_q3)[1]*dim(soss_q3)[2]
soss_q4 = data_rice[,,17] ; dim(soss_q4) = dim(soss_q4)[1]*dim(soss_q4)[2]
flows_q1 = data_rice[,,34] ; dim(flows_q1) = dim(flows_q1)[1]*dim(flows_q1)[2]
flows_q2 = data_rice[,,35] ; dim(flows_q2) = dim(flows_q2)[1]*dim(flows_q2)[2]
flows_q3 = data_rice[,,36] ; dim(flows_q3) = dim(flows_q3)[1]*dim(flows_q3)[2]
flows_q4 = data_rice[,,37] ; dim(flows_q4) = dim(flows_q4)[1]*dim(flows_q4)[2]
GDAL.close(rice_rast)
phrice_res_df = read.dbf(file.path(grid_folder,paste(grid_shapes[cycle],'.dbf', sep = '')))
phrice_res_df = data.frame(id = phrice_res_df$id)
phrice_res_df$n_seasons = as.numeric(data_nrice)
phrice_res_df$min_q1 = as.numeric(mins_q1)
phrice_res_df$min_q2 = as.numeric(mins_q2)
phrice_res_df$min_q3 = as.numeric(mins_q3)
phrice_res_df$min_q4 = as.numeric(mins_q4)
phrice_res_df$max_q1 = as.numeric(maxs_q1)
phrice_res_df$max_q2 = as.numeric(maxs_q2)
phrice_res_df$max_q3 = as.numeric(maxs_q3)
phrice_res_df$max_q4 = as.numeric(maxs_q4)
phrice_res_df$sos_q1 = as.numeric(soss_q1)
phrice_res_df$sos_q2 = as.numeric(soss_q2)
phrice_res_df$sos_q3 = as.numeric(soss_q3)
phrice_res_df$sos_q4 = as.numeric(soss_q4)
phrice_res_df$flow_q1 = as.numeric(flows_q1)
phrice_res_df$flow_q2 = as.numeric(flows_q2)
phrice_res_df$flow_q3 = as.numeric(flows_q3)
phrice_res_df$flow_q4 = as.numeric(flows_q4)
phrice_res_df [phrice_res_df == 0 ] = NA
phrice_res_df$min_q1 [which(phrice_res_df$min_q1 >= 400 )] = NA
phrice_res_df$min_q2 [which(phrice_res_df$min_q2 >= 400 )] = NA
phrice_res_df$min_q3 [which(phrice_res_df$min_q3 >= 400 )] = NA
phrice_res_df$min_q4 [which(phrice_res_df$min_q4 >= 400 )] = NA
phrice_res_df$max_q1 [which(phrice_res_df$max_q1 >= 400 )] = NA
phrice_res_df$max_q2 [which(phrice_res_df$max_q2 >= 400 )] = NA
phrice_res_df$max_q3 [which(phrice_res_df$max_q3 >= 400 )] = NA
phrice_res_df$max_q4 [which(phrice_res_df$max_q4 >= 400 )] = NA
phrice_res_df$sos_q1 [which(phrice_res_df$sos_q1 >= 400 )] = NA
phrice_res_df$sos_q2 [which(phrice_res_df$sos_q2 >= 400 )] = NA
phrice_res_df$sos_q3 [which(phrice_res_df$sos_q3 >= 400 )] = NA
phrice_res_df$sos_q4 [which(phrice_res_df$sos_q4 >= 400 )] = NA
phrice_res_df$flow_q1 [which(phrice_res_df$flow_q1 >= 400 )] = NA
phrice_res_df$flow_q2 [which(phrice_res_df$flow_q2 >= 400 )] = NA
phrice_res_df$flow_q3 [which(phrice_res_df$flow_q3 >= 400 )] = NA
phrice_res_df$flow_q4 [which(phrice_res_df$flow_q4 >= 400 )] = NA
phrice_res_df$length_q1 = (phrice_res_df$max_q1+365)-(phrice_res_df$min_q1+365)
phrice_res_df$length_q2 = (phrice_res_df$max_q2+365)-(phrice_res_df$min_q2+365)
phrice_res_df$length_q3 = (phrice_res_df$max_q3+365)-(phrice_res_df$min_q3+365)
phrice_res_df$length_q4 = (phrice_res_df$max_q4+365)-(phrice_res_df$min_q4+365)
rm(mins_q1,mins_q2,mins_q3,mins_q4)
rm(maxs_q1,maxs_q2,maxs_q3,maxs_q4)
rm(soss_q1,soss_q2,soss_q3,soss_q4)
rm(flows_q1,flows_q2,flows_q3,flows_q4)
gc()
#- ------------------------------------------------------------------------------- -#
# Get all the retrieved datasets and put them in a single data frame and save outputs
#- ------------------------------------------------------------------------------- -#
# out_df_modgrid = data.frame(id = aggregate_reference_values$id, ncells = aggregate_reference_values$n_cells,
# ref_rice_fc = aggregate_reference_values$ref_rice_fc)
#
# out_df_modgrid = join(out_df_modgrid,phrice_res_df, by = 'id', type = 'full' )
#
out_df_modgrid = phrice_res_df
is.na(out_df_modgrid) <- do.call(cbind,lapply(out_df_modgrid, is.infinite)) # Convert Infinite to NA
is.na(out_df_modgrid) <- do.call(cbind,lapply(out_df_modgrid, is.nan))
# Compute the ricearea form the percentage of rice area+ncells+resolution of reference map + compute
# total non-nodata area of the pixel
# out_df_modgrid$ref_ricearea = out_df_modgrid$ref_rice_fc*out_df_modgrid$ncells*(res(ref_reproj)[1]^2)
# out_df_modgrid$tot_cellarea = out_df_modgrid$ncells*(res(ref_reproj)[1]^2)
# Download, load and reproject GADM boundaries
# (gadm shapefiles have been used instead of RData since gdal_rasterize needs them)
cat('Download and reproject GADM boundaries...\n')
gadm_shp_url <- paste0('http://biogeo.ucdavis.edu/data/gadm2/shp/',country_code,'_adm.zip')
gadm_shape_dir <- file.path(outputs_folder,'gadm',basename(file_path_sans_ext(gadm_shp_url)))
dir.create(gadm_shape_dir, recursive=TRUE, showWarnings=FALSE)
if (!file.exists(paste0(gadm_shape_dir,'.zip'))) {download.file(gadm_shp_url,paste0(gadm_shape_dir,'.zip'))}
gadm_shape_name = paste0(country_code,'_adm',gadm_level,'_sinu.shp')
if (!file.exists(gadm_shape_name)) {unzip(paste0(gadm_shape_dir,'.zip'), exdir=gadm_shape_dir)}
if (!file.exists(file.path(gadm_shape_dir,gadm_shape_name))) {
ogr2ogr(file.path(gadm_shape_dir,gsub('_sinu','',gadm_shape_name)), file.path(gadm_shape_dir,gadm_shape_name),
f='ESRI Shapefile', s_srs='EPSG:4326', t_srs=in_proj)
}
in_shape_admin_reproj <- readOGR(gadm_shape_dir,file_path_sans_ext(gadm_shape_name))
centroids = getSpPPolygonsLabptSlots(readOGR(grid_folder,grid_shapes[cycle])) # get coordinates of centroids of each 250m cell
centroids = SpatialPoints(centroids,proj4string = CRS(in_proj)) # convert to spatialpoints
admin_cells = over(centroids,in_shape_admin_reproj)
admin_cells = admin_cells [,c("ISO",paste0("ID_", gadm_level),paste0("NAME_", gadm_level))]
admin_cells$id = phrice_res_df$id
out_df_modgrid = join(out_df_modgrid,admin_cells, by = 'id', type = 'left' ) # join to total df the info on Region and Province
# SAve the outputs
save(out_df_modgrid, file = out_mod_grid_df_file) # Save the RData table
# out_shp_dbf = data.frame(id = phrice_res_df$id) # Retrieve cell ids from the "empty grid
# out_shp_dbf = join(out_shp_dbf,out_df_modgrid, by = 'id', type = 'left' ) # join the info using id as base
## write.dbf(out_shp_dbf, file.path(grid_folder,paste(grid_shapes[cycle],'.dbf', sep = ''))) # overwrite the dbf table of the MOD 250m grid shapefile
gc()
} else { # end of 1st cycle
#- ------------------------------------------------------------------------------- -#
# Cycle on the other grids --> For each resolution grid, create a data frame in which
# the information relative to the id of the "coarse" resolution cell to which each MODIS
# pixel belongs is added to the data frame of "outputs" created befor (out_df_modgrid)
#- ------------------------------------------------------------------------------- -#
big_grid = readOGR(grid_folder,grid_shapes[cycle]) # read the shapefile of the grid
# Do an intersect between the centroids of the 250 grid and the big grid--> Identidy the id of the big
# grid for each cell of the 250 m one
cells_on_big_grid = over(centroids,big_grid)
names(cells_on_big_grid)[1] = 'id_big'
cells_on_big_grid$id = phrice_res_df$id # add the id of the 250 m grid
cells_on_big_grid = cells_on_big_grid[which(is.finite(cells_on_big_grid$id_big) == TRUE),] # remove useless cells
cells_on_big_grid = data.table(cells_on_big_grid) # create a data table to be used for tabulate areas
setkey(cells_on_big_grid, 'id_big') # set the key--> id of the coarse resolution
comp_dt = join(cells_on_big_grid,out_df_modgrid, by = 'id', type = 'left') # join the data taken from the mod_grid_data frame
setkey(comp_dt, 'id_big')
save(comp_dt, file = out_grid_df_files[cycle])
# Compute aggregated values on the big grid cells
} #End else on cycle = 1
} #En
}
# }
lbusett/phenoriceR documentation built on May 18, 2019, 9:17 p.m.
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# TODO: Add comment
#
# Author: LB
###############################################################################
library(ggplot2)
library(reshape)
library(data.table)
library(rgdal)
library(SDMTools)
library(plyr)
library(gdalUtils)
library(raster)
library(foreign)
library(tools)
memory.limit(16000)
# Define inputs and outputs
main_folder = '//10.0.1.252/nr_working/shared/PhenoRice/Processing/Senegal/Outputs/50_30_30_120_dec_ok/newquarts/masked'
country_code = c('SEN')
years = seq(2003,2014,1)
for (year in years) {
# main_folder = '//10.0.1.252/nr_working/shared/PhenoRice/Processing/IT/Outputs/2013/'
# country_code = c('ITA')
gadm_level = 3
phrice_outfolder = file.path(main_folder,year,'raster')
outputs_folder = "D:/Temp/PhenoRice/Processing/SEN/Outputs/newquarts/masked/" # Folder where to put results of this processing
year_out_folder = paste0(outputs_folder,year)
out_mod_grid_df_file = file.path(year_out_folder,paste0('out_df_modgrid_',year,'.RData'))
# refmap_file= 'D:/Temp/PhenoRice/Processing/PHL/Outputs/2013/Validate/Reference/PHL_DS_2013_Reference.tif'
#- ------------------------------------------------------------------------------- -#
# Initialize: setup input/output files and folders
#- ------------------------------------------------------------------------------- -#
in_phrice_file = list.files(phrice_outfolder, glob2rx('*Full_Out*dat'),full.names = TRUE)
grid_folder = file.path(outputs_folder,'GRIDs') #save the grid here
grid_resolutions = c(231.656358,2084.907, 5096.432, 10192.864,20385.73 ) # Resolution of output grids
grid_shapes <- c('Grid_MODIS_250','Grid_2Km','Grid_5Km','Grid_10Km','Grid_20Km') #this is the grid name
#
dir.create(outputs_folder, recursive = T)
dir.create(year_out_folder, recursive = T)
# out_repro_raster= file.path(outputs_folder,'Reference','Reproj','Reference_Map_SIN.tif')
# dir.create(dirname(out_repro_raster), recursive = T)
in_phrice_file_small = in_phrice_file
# in_phrice_file_small = file.path(outputs_folder,'Input','Clipped','Phenorice_Clipped.tif')
# in_phrice_file_small_vrt= file.path(outputs_folder,'Input','Clipped','Phenorice_Clipped.vrt')
# dir.create(dirname(in_phrice_file_small),recursive = T)
out_grid_rasters = file.path(outputs_folder,'Temporary',paste(grid_shapes,'_raster_HR.tiff',sep = ''))
grid_fullnames = paste(grid_folder,'/',grid_shapes,'.shp',sep = '')
out_grid_df_files = file.path(outputs_folder,paste('out_df_',grid_shapes,'_',year,'.RData', sep = ''))
out_grid_shp_files = file.path(outputs_folder,paste('out_shp_',grid_shapes,'.shp', sep = ''))
#- ------------------------------------------------------------------------------- -#
# Load Phenorice map and retrieve projection and extent
#- ------------------------------------------------------------------------------- -#
phrice_map = raster(in_phrice_file)
in_proj = proj4string(phrice_map)
ext_phrice_map = extent(phrice_map)
#- ------------------------------------------------------------------------------- -#
# Load reference map and define the extent
#- ------------------------------------------------------------------------------- -#
# refmap = raster(refmap_file)
#- ------------------------------------------------------------------------------- -#
# Reproject the reference raster map to MODIS projection
#- ------------------------------------------------------------------------------- -#
# {{
# in_ref = raster(refmap_file)
# in_ref_proj = proj4string(in_ref)
# if(file.exists(out_repro_raster) == FALSE) {
# ref_reproj = gdalwarp(refmap_file,out_repro_raster, s_srs = in_ref_proj, t_srs = in_proj,
# r = "near",of = 'GTiff', overwrite = T, srcnodata = 255, dstnodata = 255,ot = 'Byte', output_Raster = TRUE)
# ext_ref_repr = extent(ref_reproj)
# res_ref_reproj = res(ref_reproj)
# } else {
# ref_reproj = raster(out_repro_raster)
# ext_ref_repr = extent(ref_reproj)
# res_ref_reproj = res(ref_reproj)
#
# }}
#- ---------------------- --- --------------------------------------------------- -#
# Clip phenorice output on extent of reference map, using tap to avoid moving the corner
#- ------------------------------------------------------------------------------- -#
#
# gdalbuildvrt(in_phrice_file, in_phrice_file_small_vrt, tr = c(231.656358,231.656358), te = c(bbox(ext_ref_repr)), tap = TRUE)
# GdalTranslate = gdal_translate(in_phrice_file_small_vrt, in_phrice_file_small, overwrite = TRUE)
in_phrice_clipped = raster(in_phrice_file_small)
# gdalbuildvrt(in_phrice_file, in_phrice_file_small_vrt, tr = c(231.656358,231.656358), te = c(bbox(ext_ref_repr)), tap = TRUE)
# GdalTranslate = gdal_translate(in_phrice_file_small_vrt, in_phrice_file_small, overwrite = TRUE)
# in_phrice_clipped = raster(in_phrice_file)
# in_phrice_file_small = in_phrice_file
grid_extent = extent(in_phrice_clipped)
#- ------------------------------------------------------------------------------- -#
# Create the regular grids (MODIS + 2,5,10,20 K) if needed
#- ------------------------------------------------------------------------------- -#
for (gr_res in seq(along = grid_fullnames)) {
LB_Create_pol_grid = function(in_raster_file, out_res, out_folder, out_name_shp,grid_extent){
library(rgdal)
library(raster)
rast<- raster(in_raster_file)
# bb <- bbox(rast) # Define Bounding box
cs <- c(out_res,out_res) # cell size. To be set by hand!
cc <- c(grid_extent@xmin,grid_extent@ymin) + (cs/2) # cell offset # move 1/2 pixel if necessary
# compute number of cells per direction
if (cs < 300) { # needed to avoid that larger grids cover only one portion of the area --> so, add a row/coulmn for larger grids
cd <- c(dim(rast)[2],dim(rast)[1])
} else {
cd <- ceiling(c(((grid_extent@xmax-grid_extent@xmin)/cs[1]),((grid_extent@ymax-grid_extent@ymin)/cs[2])))
}
grd <- GridTopology(cellcentre.offset=cc, cellsize=cs, cells.dim=cd) # Define grd characteristics
#transform to spatial grid
sp_grd <- SpatialGridDataFrame(grd,
data=data.frame(id=1:prod(cd)),
proj4string=CRS(proj4string(rast)))
summary(sp_grd)
# browser()
sp_polygons = as(sp_grd, "SpatialPolygonsDataFrame")#create the shape
print('Creating MODIS Grid - Please Wait !')
writeOGR(sp_polygons,dsn = out_folder, layer =out_name_shp,driver="ESRI Shapefile", overwrite_layer = T) #save the shapefile
gc()
}
if(file.exists(grid_fullnames[gr_res]) == FALSE) {
LB_Create_pol_grid(in_phrice_clipped , grid_resolutions[gr_res],grid_folder, grid_shapes[gr_res],grid_extent)
}
} #End Cycle on gr_res
#- --------------------- --------------------------------------------------------- -#
# If not already existing, Rasterize polygons on the extent of the reference map, at a resolution
# equal to that of the reference map. For each pixel, values of this raster correspond to a
# unique identifier of the cell of the ERMES grid to which the pixel belongs
#- ------------------------------------------------------------------------------- -#
for (cycle in seq(along = grid_shapes)) {
if (cycle == 1) {
# if (file.exists(out_grid_rasters[cycle]) == FALSE){
# dir.create(dirname(out_grid_rasters[cycle]) ,recursive = T)
# raster_grid = gdal_rasterize(grid_fullnames[cycle],out_grid_rasters[cycle],a = "id", output_Raster = T,
# te = c(ext_ref_repr@xmin, (ext_ref_repr@ymin+res_ref_reproj[1]),(ext_ref_repr@xmax-res_ref_reproj[1]), (ext_ref_repr@ymax)), ot = 'UInt32',tr = res_ref_reproj, tap = T, of = 'GTiff')
# gc()
# }
#- -------------- ------ --- -- --------------------------------------------- -#
# Compute the percentage area classified as rice for each pixel
#- ------------------------------------------------------------------------------- -#
# Get the values of t "du r r of cells codes
# raster_cells <- new("GDALReadOnlyDataset", out_grid_rasters[cycle])
# data_raster_cells = getRasterData(raster_cells)
# dim(data_raster_cells) = dim(data_raster_cells)[1]*dim(data_raster_cells)[2]
# GDAL.close(raster_cells)
# gc()
#
# # Get the values of the "reference map
# ref_map <- new("GDALReadOnlyDataset",out_repro_raster)
# ref_map_data = getRasterData(ref_map)
# dim(ref_map_data) = dim(ref_map_data)[1]*dim(ref_map_data)[2]
# GDAL.close(ref_map)
# gc()
# Create a Data.table with two columns. First column taken from the cell_codes raster - tells to which cell each pixel correspond
# Second column taken from the reference rice map (0 or 1)
# browser()
# cells_dt = data.table(id=data_raster_cells,value = ref_map_data )
# setkey(cells_dt, id) # Set a indexing key to increase speed of zonal statistics computation
# rm(ref_map_data)
# rm(data_raster_cells)
# gc()
#
# # Compute the aggregated Reference Map values for each cell of the ERMES grid - average, stdev, min, max and n? of pixels in each cell
# aggregate_reference_values = cells_dt[, list(ref_rice_fc = mean(value, na.rm = T),
#
# n_cells = as.numeric(length(which(is.finite(value) == T )))
# ), by = key(cells_dt)]
#
# aggregate_reference_values = aggregate_reference_values[id != 0 ]
# rm(cells_dt)
#- --- -------------- ---- -- --------------------------------------------- -#
# Retrieve necessary data from the enorice output rasters
#- -------------------------------- --------------------------------------------- -#
rice_rast = new("GDALReadOnlyDataset", in_phrice_file_small)
data_rice = getRasterData(rice_rast)
data_nrice = data_rice[,,1] ; dim(data_nrice) = dim(data_nrice)[1]*dim(data_nrice)[2]
mins_q1 = data_rice[,,2] ; dim(mins_q1) = dim(mins_q1)[1]*dim(mins_q1)[2]
mins_q2 = data_rice[,,3] ; dim(mins_q2) = dim(mins_q2)[1]*dim(mins_q2)[2]
mins_q3 = data_rice[,,4] ; dim(mins_q3) = dim(mins_q3)[1]*dim(mins_q3)[2]
mins_q4 = data_rice[,,5] ; dim(mins_q4) = dim(mins_q4)[1]*dim(mins_q4)[2]
maxs_q1 = data_rice[,,6] ; dim(maxs_q1) = dim(maxs_q1)[1]*dim(maxs_q1)[2]
maxs_q2 = data_rice[,,7] ; dim(maxs_q2) = dim(maxs_q2)[1]*dim(maxs_q2)[2]
maxs_q3 = data_rice[,,8] ; dim(maxs_q3) = dim(maxs_q3)[1]*dim(maxs_q3)[2]
maxs_q4 = data_rice[,,9] ; dim(maxs_q4) = dim(maxs_q4)[1]*dim(maxs_q4)[2]
soss_q1 = data_rice[,,14] ; dim(soss_q1) = dim(soss_q1)[1]*dim(soss_q1)[2]
soss_q2 = data_rice[,,15] ; dim(soss_q2) = dim(soss_q2)[1]*dim(soss_q2)[2]
soss_q3 = data_rice[,,16] ; dim(soss_q3) = dim(soss_q3)[1]*dim(soss_q3)[2]
soss_q4 = data_rice[,,17] ; dim(soss_q4) = dim(soss_q4)[1]*dim(soss_q4)[2]
flows_q1 = data_rice[,,34] ; dim(flows_q1) = dim(flows_q1)[1]*dim(flows_q1)[2]
flows_q2 = data_rice[,,35] ; dim(flows_q2) = dim(flows_q2)[1]*dim(flows_q2)[2]
flows_q3 = data_rice[,,36] ; dim(flows_q3) = dim(flows_q3)[1]*dim(flows_q3)[2]
flows_q4 = data_rice[,,37] ; dim(flows_q4) = dim(flows_q4)[1]*dim(flows_q4)[2]
GDAL.close(rice_rast)
phrice_res_df = read.dbf(file.path(grid_folder,paste(grid_shapes[cycle],'.dbf', sep = '')))
phrice_res_df = data.frame(id = phrice_res_df$id)
phrice_res_df$n_seasons = as.numeric(data_nrice)
phrice_res_df$min_q1 = as.numeric(mins_q1)
phrice_res_df$min_q2 = as.numeric(mins_q2)
phrice_res_df$min_q3 = as.numeric(mins_q3)
phrice_res_df$min_q4 = as.numeric(mins_q4)
phrice_res_df$max_q1 = as.numeric(maxs_q1)
phrice_res_df$max_q2 = as.numeric(maxs_q2)
phrice_res_df$max_q3 = as.numeric(maxs_q3)
phrice_res_df$max_q4 = as.numeric(maxs_q4)
phrice_res_df$sos_q1 = as.numeric(soss_q1)
phrice_res_df$sos_q2 = as.numeric(soss_q2)
phrice_res_df$sos_q3 = as.numeric(soss_q3)
phrice_res_df$sos_q4 = as.numeric(soss_q4)
phrice_res_df$flow_q1 = as.numeric(flows_q1)
phrice_res_df$flow_q2 = as.numeric(flows_q2)
phrice_res_df$flow_q3 = as.numeric(flows_q3)
phrice_res_df$flow_q4 = as.numeric(flows_q4)
phrice_res_df [phrice_res_df == 0 ] = NA
phrice_res_df$min_q1 [which(phrice_res_df$min_q1 >= 400 )] = NA
phrice_res_df$min_q2 [which(phrice_res_df$min_q2 >= 400 )] = NA
phrice_res_df$min_q3 [which(phrice_res_df$min_q3 >= 400 )] = NA
phrice_res_df$min_q4 [which(phrice_res_df$min_q4 >= 400 )] = NA
phrice_res_df$max_q1 [which(phrice_res_df$max_q1 >= 400 )] = NA
phrice_res_df$max_q2 [which(phrice_res_df$max_q2 >= 400 )] = NA
phrice_res_df$max_q3 [which(phrice_res_df$max_q3 >= 400 )] = NA
phrice_res_df$max_q4 [which(phrice_res_df$max_q4 >= 400 )] = NA
phrice_res_df$sos_q1 [which(phrice_res_df$sos_q1 >= 400 )] = NA
phrice_res_df$sos_q2 [which(phrice_res_df$sos_q2 >= 400 )] = NA
phrice_res_df$sos_q3 [which(phrice_res_df$sos_q3 >= 400 )] = NA
phrice_res_df$sos_q4 [which(phrice_res_df$sos_q4 >= 400 )] = NA
phrice_res_df$flow_q1 [which(phrice_res_df$flow_q1 >= 400 )] = NA
phrice_res_df$flow_q2 [which(phrice_res_df$flow_q2 >= 400 )] = NA
phrice_res_df$flow_q3 [which(phrice_res_df$flow_q3 >= 400 )] = NA
phrice_res_df$flow_q4 [which(phrice_res_df$flow_q4 >= 400 )] = NA
phrice_res_df$length_q1 = (phrice_res_df$max_q1+365)-(phrice_res_df$min_q1+365)
phrice_res_df$length_q2 = (phrice_res_df$max_q2+365)-(phrice_res_df$min_q2+365)
phrice_res_df$length_q3 = (phrice_res_df$max_q3+365)-(phrice_res_df$min_q3+365)
phrice_res_df$length_q4 = (phrice_res_df$max_q4+365)-(phrice_res_df$min_q4+365)
rm(mins_q1,mins_q2,mins_q3,mins_q4)
rm(maxs_q1,maxs_q2,maxs_q3,maxs_q4)
rm(soss_q1,soss_q2,soss_q3,soss_q4)
rm(flows_q1,flows_q2,flows_q3,flows_q4)
gc()
#- ------------------------------------------------------------------------------- -#
# Get all the retrieved datasets and put them in a single data frame and save outputs
#- ------------------------------------------------------------------------------- -#
# out_df_modgrid = data.frame(id = aggregate_reference_values$id, ncells = aggregate_reference_values$n_cells,
# ref_rice_fc = aggregate_reference_values$ref_rice_fc)
#
# out_df_modgrid = join(out_df_modgrid,phrice_res_df, by = 'id', type = 'full' )
#
out_df_modgrid = phrice_res_df
is.na(out_df_modgrid) <- do.call(cbind,lapply(out_df_modgrid, is.infinite)) # Convert Infinite to NA
is.na(out_df_modgrid) <- do.call(cbind,lapply(out_df_modgrid, is.nan))
# Compute the ricearea form the percentage of rice area+ncells+resolution of reference map + compute
# total non-nodata area of the pixel
# out_df_modgrid$ref_ricearea = out_df_modgrid$ref_rice_fc*out_df_modgrid$ncells*(res(ref_reproj)[1]^2)
# out_df_modgrid$tot_cellarea = out_df_modgrid$ncells*(res(ref_reproj)[1]^2)
# Download, load and reproject GADM boundaries
# (gadm shapefiles have been used instead of RData since gdal_rasterize needs them)
cat('Download and reproject GADM boundaries...\n')
gadm_shp_url <- paste0('http://biogeo.ucdavis.edu/data/gadm2/shp/',country_code,'_adm.zip')
gadm_shape_dir <- file.path(outputs_folder,'gadm',basename(file_path_sans_ext(gadm_shp_url)))
dir.create(gadm_shape_dir, recursive=TRUE, showWarnings=FALSE)
if (!file.exists(paste0(gadm_shape_dir,'.zip'))) {download.file(gadm_shp_url,paste0(gadm_shape_dir,'.zip'))}
gadm_shape_name = paste0(country_code,'_adm',gadm_level,'_sinu.shp')
if (!file.exists(gadm_shape_name)) {unzip(paste0(gadm_shape_dir,'.zip'), exdir=gadm_shape_dir)}
if (!file.exists(file.path(gadm_shape_dir,gadm_shape_name))) {
ogr2ogr(file.path(gadm_shape_dir,gsub('_sinu','',gadm_shape_name)), file.path(gadm_shape_dir,gadm_shape_name),
f='ESRI Shapefile', s_srs='EPSG:4326', t_srs=in_proj)
}
in_shape_admin_reproj <- readOGR(gadm_shape_dir,file_path_sans_ext(gadm_shape_name))
centroids = getSpPPolygonsLabptSlots(readOGR(grid_folder,grid_shapes[cycle])) # get coordinates of centroids of each 250m cell
centroids = SpatialPoints(centroids,proj4string = CRS(in_proj)) # convert to spatialpoints
admin_cells = over(centroids,in_shape_admin_reproj)
admin_cells = admin_cells [,c("ISO",paste0("ID_", gadm_level),paste0("NAME_", gadm_level))]
admin_cells$id = phrice_res_df$id
out_df_modgrid = join(out_df_modgrid,admin_cells, by = 'id', type = 'left' ) # join to total df the info on Region and Province
# SAve the outputs
save(out_df_modgrid, file = out_mod_grid_df_file) # Save the RData table
# out_shp_dbf = data.frame(id = phrice_res_df$id) # Retrieve cell ids from the "empty grid
# out_shp_dbf = join(out_shp_dbf,out_df_modgrid, by = 'id', type = 'left' ) # join the info using id as base
## write.dbf(out_shp_dbf, file.path(grid_folder,paste(grid_shapes[cycle],'.dbf', sep = ''))) # overwrite the dbf table of the MOD 250m grid shapefile
gc()
} else { # end of 1st cycle
#- ------------------------------------------------------------------------------- -#
# Cycle on the other grids --> For each resolution grid, create a data frame in which
# the information relative to the id of the "coarse" resolution cell to which each MODIS
# pixel belongs is added to the data frame of "outputs" created befor (out_df_modgrid)
#- ------------------------------------------------------------------------------- -#
big_grid = readOGR(grid_folder,grid_shapes[cycle]) # read the shapefile of the grid
# Do an intersect between the centroids of the 250 grid and the big grid--> Identidy the id of the big
# grid for each cell of the 250 m one
cells_on_big_grid = over(centroids,big_grid)
names(cells_on_big_grid)[1] = 'id_big'
cells_on_big_grid$id = phrice_res_df$id # add the id of the 250 m grid
cells_on_big_grid = cells_on_big_grid[which(is.finite(cells_on_big_grid$id_big) == TRUE),] # remove useless cells
cells_on_big_grid = data.table(cells_on_big_grid) # create a data table to be used for tabulate areas
setkey(cells_on_big_grid, 'id_big') # set the key--> id of the coarse resolution
comp_dt = join(cells_on_big_grid,out_df_modgrid, by = 'id', type = 'left') # join the data taken from the mod_grid_data frame
setkey(comp_dt, 'id_big')
save(comp_dt, file = out_grid_df_files[cycle])
# Compute aggregated values on the big grid cells
} #End else on cycle = 1
} #En
}
# }
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