#################################################################
## ##
## (c) Adeline Marinho <adelsud6@gmail.com> ##
## ##
## Image Processing Division ##
## National Institute for Space Research (INPE), Brazil ##
## ##
## ##
## R script to save raster in GeoTIFF format ##
## ##
## 2018-08-28 ##
## ##
## ##
#################################################################
#' @title Save a RasterBrick reclassified in Folder
#' @name lucC_save_GeoTIFF
#' @aliases lucC_save_GeoTIFF
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Save new_raster reclassified in a diretory defined by user.
#' NOTE: Applied only when update a raster with new values, after had applied the
#' function lucC_raster_update.
#'
#' @usage lucC_save_GeoTIFF(raster_obj = NULL, data_mtx = NULL,
#' path_raster_folder = NULL, as_RasterBrick = FALSE)
#'
#' @param raster_obj Raster. A raster brick with classified images
#' @param data_mtx Matrix. A matrix with pixel replaced, can be obtined using lucC_update_raster()
#' @param path_raster_folder Character. Name a path folder to save raster images data. If doesn't exist, a new directory is created
#' @param as_RasterBrick Boolean. If FALSE, each layer will be saved in separate file. If TRUE, write a RasterBrick in a file. Default is FALSE.
#'
#' @keywords datasets
#' @return Raster in geotiff format to open using SIG
#' @importFrom ensurer ensure_that
#' @importFrom raster rasterFromXYZ writeRaster crs
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' a <- lucC_pred_recur(raster_obj = rb_class, raster_class = "Forest",
#' time_interval1 = c("2001-09-01","2001-09-01"),
#' time_interval2 = c("2002-09-01","2016-09-01"),
#' label = my_label, timeline = my_timeline)
#'
#' # update original RasterBrick with new class
#' num_label <- length(my_label) + 1
#' rb_class_new <- lucC_raster_update(raster_obj = rb_class,
#' data_mtx = a,
#' timeline = my_timeline,
#' class_to_replace = "Forest", # the same class previously
#' new_pixel_value = num_label) # new pixel value
#'
#' lucC_plot_bar_events(data_mtx = rb_class_new, pixel_resolution = 232, custom_palette = FALSE)
#'
#' # save the update matrix as GeoTIFF RasterBrick
#' lucC_save_GeoTIFF(raster_obj = rb_class, data_mtx = rb_class_new,
#' path_raster_folder = paste0(getwd(), "/updatedRasterRECUR", sep = ""),
#' as_RasterBrick = FALSE )
#'
#'}
#'
# plot maps with events
lucC_save_GeoTIFF <- function(raster_obj = NULL, data_mtx = NULL, path_raster_folder = NULL, as_RasterBrick = FALSE){
# Ensure if parameters exists
ensurer::ensure_that(raster_obj, !is.null(raster_obj),
err_desc = "raster_obj data, file must be defined!\nA raster brick with classified images.")
ensurer::ensure_that(data_mtx, !is.null(data_mtx),
err_desc = "data_mtx matrix, file must be defined!\nThis data can be obtained using predicates RECUR, HOLDS, EVOLVE and CONVERT and lucC_update_raster().")
ensurer::ensure_that(path_raster_folder, !is.null(path_raster_folder),
err_desc = "path_raster_folder must be defined! Enter a path to SAVE your GeoTIFF images!")
options(digits = 12)
# Create directory if doesn't exist
output_dir <- file.path(path_raster_folder)
if (!dir.exists(output_dir)){
message("\nCreated new directory because the path provided doesn't exist! ...\n")
dir.create(output_dir)
} else {
path_raster_folder <- path_raster_folder
}
# matrix reclassified to raster format
new_raster <- raster::rasterFromXYZ(data_mtx)
names(new_raster) <- gsub("\\..*","", names(new_raster)) # remove dates after point
# crs from original raster
raster::crs(new_raster) <- raster_obj@crs
rm(raster_obj)
gc()
message("Saving... \n")
if(as_RasterBrick == FALSE){
# write as a geoTIFF file using the raster package by each layer
raster::writeRaster(new_raster,
filename= paste0(path_raster_folder,"/New_", sep = ""),
bylayer=TRUE, suffix = names(new_raster), format="GTiff",
datatype="INT1U", overwrite=TRUE)
} else {
file_name <- basename(path_raster_folder)
# write as a geoTIFF file using the raster package as a RasterBrick file
raster::writeRaster(new_raster,
filename= paste0(path_raster_folder,"/New_", file_name, sep = ""),
bylayer=FALSE, format="GTiff", datatype="INT1U", overwrite=TRUE)
}
cat("\nGeoTIFF images saved successfully in directory: '", path_raster_folder, "'\n")
}
#' @title Update a RasterBrick with result from predicates
#' @name lucC_save_raster_result
#' @aliases lucC_save_raster_result
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Update a RasterBrick with new values of pixel discovered from LUC Calculus formalism to create GeoTIFF files. #' NOTE: Used after had applied some of the functions with predicate.
#'
#' @usage lucC_save_raster_result(raster_obj = NULL, data_mtx = NULL,
#' timeline = NULL, label = NULL, path_raster_folder = NULL, as_RasterBrick = FALSE)
#'
#' @param raster_obj Raster. A raster brick with classified images
#' @param data_mtx Matrix. A matrix with values obtained from predicates RECUR, EVOLVE, CONVERT or HOLDS
#' @param timeline Character. A list of all dates of classified raster, timeline
#' @param label Character Vector. All labels of each value of pixel from classified raster
#' @param path_raster_folder Character. Name a path folder to save raster images data. If doesn't exist, a new directory is created
#' @param as_RasterBrick Boolean. If FALSE, each layer will be saved in separate file. If TRUE, write a RasterBrick in a file. Default is FALSE.
#'
#' @keywords datasets
#' @return Matrix with raster and pixels to create a RasterBrick with result
#' @importFrom ensurer ensure_that
#' @importFrom lubridate year
#' @importFrom raster rasterToPoints
#' @importFrom dplyr mutate select everything
#' @importFrom tidyr gather spread
#' @importFrom reshape2 dcast
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterSample.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#' my_label <- c("Degradation", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton",
#' "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_Area", "Water")
#' my_timeline <- c("2001-09-01", "2002-09-01", "2003-09-01", "2004-09-01", "2005-09-01",
#' "2006-09-01", "2007-09-01", "2008-09-01", "2009-09-01", "2010-09-01",
#' "2011-09-01", "2012-09-01", "2013-09-01", "2014-09-01", "2015-09-01",
#' "2016-09-01")
#'
#' a <- lucC_pred_recur(raster_obj = rb_class, raster_class = "Forest",
#' time_interval1 = c("2001-09-01","2001-09-01"),
#' time_interval2 = c("2002-09-01","2016-09-01"),
#' label = my_label, timeline = my_timeline)
#'
#' lucC_plot_raster_result(raster_obj = rb_class, data_mtx = a, timeline = my_timeline,
#' label = my_label, custom_palette = FALSE)
#' # save in file
#' lucC_save_raster_result(raster_obj = rb_class, data_mtx = a,
#' timeline = my_timeline, label = my_label,
#' path_raster_folder = paste0(getwd(), "/onlyRECUR", sep = ""),
#' as_RasterBrick = FALSE)
#'
#'}
#'
# plot maps for input data
lucC_save_raster_result <- function(raster_obj = NULL, data_mtx = NULL, timeline = NULL, label = NULL, path_raster_folder = NULL, as_RasterBrick = FALSE) {
# Ensure if parameters exists
ensurer::ensure_that(raster_obj, !is.null(raster_obj),
err_desc = "raster_obj data, file must be defined!\nA raster brick with classified images.")
ensurer::ensure_that(data_mtx, !is.null(data_mtx),
err_desc = "data_mtx matrix, file must be defined!\nThis data can be obtained using predicates RECUR, HOLDS, EVOLVE and CONVERT.")
ensurer::ensure_that(timeline, !is.null(timeline),
err_desc = "timeline must be defined!")
ensurer::ensure_that(path_raster_folder, !is.null(path_raster_folder),
err_desc = "path_raster_folder must be defined! Enter a path to SAVE your GeoTIFF images!")
options(digits = 12)
#-------------------- prepare rasterBrick --------------------------------
df <- raster::rasterToPoints(raster_obj) %>%
as.data.frame()
df[,1:2] <- round(df[,1:2], 5) # limit 5 decimal digits after comman
# replace colnames to timeline
colnames(df)[c(3:ncol(df))] <- as.character(lubridate::year(timeline))
#raster_df <- reshape2::melt(as.data.frame(df), id.vars = c("x","y"))
raster_df <- df %>%
tidyr::gather(variable, value, -x, -y)
rm(df)
gc()
# remove factor
raster_df$value <- 0
#-------------------- prepare matrix with events --------------------------------
# x and y as factor
data_mtx$x <- as.numeric(as.character(as.factor(data_mtx$x)))
data_mtx$y <- as.numeric(as.character(as.factor(data_mtx$y)))
data_mtx[,1:2] <- round(data_mtx[,1:2], 5) # limit 5 decimal digits after comman
# replace new clase by new pixel value
class_name <- unique(data_mtx[3:ncol(data_mtx)][!duplicated(as.vector(data_mtx[3:ncol(data_mtx)])) & !is.na(data_mtx[3:ncol(data_mtx)])] )
# return index the first match
class <- match(class_name, label) # which(label %in% class_name)
# replace string by values
temp <- data.frame(A = class_name, B = class)
data_mtx[c(3:ncol(data_mtx))] <- lapply(data_mtx[c(3:ncol(data_mtx))], function(x) temp[match(x, temp$A), "B"])
# data matrix to new raster
colnames(data_mtx)[c(3:ncol(data_mtx))] <- as.character(lubridate::year(colnames(data_mtx)[c(3:ncol(data_mtx))]))
#point_df <- reshape2::melt(new_df, id.vars = c("x","y"), na.rm = TRUE)
point_df <- data_mtx %>%
tidyr::gather(variable, value, -x, -y, na.rm = TRUE)
rm(data_mtx)
gc()
## remove factors
#point_df$x = as.numeric(levels(point_df$x))[point_df$x]
#point_df$y = as.numeric(levels(point_df$y))[point_df$y]
# ------------------ replace point_df in raster_df ---------------------
a <- as.matrix(raster_df)
b <- as.matrix(point_df)
rm(raster_df, point_df)
gc()
# change original by new values - ok
raster_rows_both <- base::merge(a, b, by = c("x","y","variable")) #, all = TRUE)
raster_rows_only <- as.matrix(dplyr::anti_join(as.data.frame(a), as.data.frame(b), by = c("x","y","variable"))) #NEW
raster_rows_both[,] <- lapply(raster_rows_both, function(x) {as.numeric(as.character(x))}) # remove factor
raster_rows_both <- raster_rows_both %>%
dplyr::mutate(value = ifelse(is.na(.$value.y), .$value.x, .$value.y)) %>%
dplyr::select(-value.x, -value.y) %>%
.[order(.$variable),]
rm(a, b)
gc()
# remove duplicates
raster_rows_both <- raster_rows_both[!duplicated(raster_rows_both), ]
raster_output <- rbind(raster_rows_both,raster_rows_only) #NEW
#raster_rows_both <- dplyr::mutate(raster_rows_both, row = 1:nrow(raster_rows_both))
#raster_df_update <- reshape2::dcast(raster_rows_both, x + y ~ variable, value.var= 'value', fun.aggregate = mean)
raster_df_update <- reshape2::dcast(raster_output, x + y ~ variable, value.var= 'value') # raster_rows_both
#raster_df_update <- tidyr::spread(raster_rows_both, variable, value, -x, -y)
# raster_df_update <- raster_rows_both %>%
# dplyr::mutate(row = 1:nrow(.)) %>% # because error "Error: Duplicate identifiers for rows..."
# tidyr::spread(variable, value) %>%
# dplyr::select(-row)
# check if the raster result does not have all years of timeline
dates_result <- as.character(colnames(raster_df_update)[c(3:ncol(raster_df_update))])
dates_timeline <- as.character(lubridate::year(timeline))
if(length(dates_timeline[!(dates_timeline %in% dates_result)]) > 0){
years_missing <- as.list(dates_timeline[!(dates_timeline %in% dates_result)])
df <- do.call(cbind.data.frame, years_missing) # pass to dataframe
df[1,] <- NA # set NA as values of rows
raster_df_update <- cbind(raster_df_update,df) # merge columns missing
raster_df_update <- raster_df_update %>% # sort columns and put x and y first
dplyr::select(sort(names(.))) %>%
dplyr::select(., x, y, dplyr::everything())
#
colnames(raster_df_update)[c(3:ncol(raster_df_update))] <- as.character(lubridate::year(timeline))
raster_df_update <- droplevels(raster_df_update)
} else {
raster_df_update <- raster_df_update
}
rm(raster_rows_both, years_missing, df, dates_result, dates_timeline, raster_rows_only)
gc()
# pass to complete date, but we prefer leaver only with years
# colnames(raster_df_update)[c(3:ncol(raster_df_update))] <- as.character(timeline)
lucC_save_GeoTIFF(raster_obj = raster_obj, data_mtx = raster_df_update, path_raster_folder = path_raster_folder, as_RasterBrick = as_RasterBrick)
lucC_remove_TmpFilesRaster()
}
#' @title Save a RasterBrick by layers
#' @name lucC_save_rasterBrick_by_layers
#' @aliases lucC_save_rasterBrick_by_layers
#' @author Adeline M. Maciel
#' @docType data
#'
#' @description Save a RasterBrick into individual layers files GeoTIFFs
#'
#' @usage lucC_save_rasterBrick_by_layers(path_name_GeoTIFF_Brick = NULL)
#'
#' @param path_name_GeoTIFF_Brick Character. Name file and path folder to SPLIT rasterBrick by layers
#'
#' @keywords datasets
#' @return A set of GeoTIFF separate images
#' @importFrom ensurer ensure_that
#' @importFrom raster raster writeRaster brick
#' @importFrom tools file_path_sans_ext
#' @export
#'
#' @examples \dontrun{
#' library(lucCalculus)
#'
#' file <- c(system.file("extdata/raster/rasterItanhanga.tif", package = "lucCalculus"))
#' rb_class <- raster::brick(file)
#'
#' # blocks saved in folder
#' lucC_blocks_raster_create(raster_obj = rb_class, number_blocks_xy = 2, save_images = TRUE)
#'
#' lucC_blocks_raster_merge(path_open_GeoTIFFs = paste0(getwd(), "/Blocks_RasterBrick", sep = ""),
#' number_raster = 4, pattern_name = "Raster_Block_", is.rasterBrick = TRUE)
#'
#' lucC_save_rasterBrick_by_layers(
#' path_name_GeoTIFF_Brick = paste0(getwd(),"/Blocks_RasterBrick/Mosaic_Raster_Block_.tif", sep = ""))
#'
#'
#'
#'}
#'
# plot maps for input data
lucC_save_rasterBrick_by_layers <- function(path_name_GeoTIFF_Brick = NULL) {
# Ensure if parameters exists
ensurer::ensure_that(path_name_GeoTIFF_Brick, !is.null(path_name_GeoTIFF_Brick),
err_desc = "path_name_GeoTIFF_Brick file, must be defined! Enter a path to OPEN your GeoTIFF image RasterBrick.")
message("Verifying if GeoTIFF image exist ...")
# chack file exists
if(file.exists(path_name_GeoTIFF_Brick)){
cat(path_name_GeoTIFF_Brick, sep = "\n")
raster <- raster::brick(path_name_GeoTIFF_Brick)
} else
stop("There is no path or file with this name!\n")
path_save <- basename(tools::file_path_sans_ext(path_name_GeoTIFF_Brick))
# Create directory if doesn't exist
output_dir <- file.path(paste0(dirname(path_name_GeoTIFF_Brick), "/", path_save, sep = ""))
if (!dir.exists(output_dir)){
message("\nCreated new directory because the path provided doesn't exist! ...\n")
dir.create(output_dir)
path_raster_folder <- output_dir
} else {
path_raster_folder <- path_raster_folder
}
message("Saving... \n")
# write as a geoTIFF file using the raster package by layer
raster::writeRaster(raster, filename= paste0(path_raster_folder,"/New_", sep = ""),
bylayer=TRUE, suffix = names(raster), format="GTiff",
datatype="INT1U", overwrite=TRUE)
}
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