inst/extdata/examples/MT_calculus/lucC_MT_SecondaryVegetation.R
In ammaciel/sits.LUC.Calculus: Land Use Change Calculus2
# RasterBrick Images
#----------------------------------------------------------
# Divide image in blocks, then merge again
#----------------------------------------------------------
library(lucCalculus)
options(digits = 12)
# start time
start.time <- Sys.time()
# without secondary vegetation
file <- c("~/TESTE/raster_mt_by_year_2004.tif")
# create timeline with classified data from SVM method
timeline <- lubridate::as_date(c("2001-09-01", "2002-09-01", "2003-09-01", "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"))
file_name <- basename(tools::file_path_sans_ext(file))
#library(sits)
# create a RasterBrick metadata file based on the information about the files
raster.tb <- sits::sits_coverage(service = "RASTER", files = file, name = file_name, timeline = timeline, bands = "ndvi")
message(paste0("\nLoad RasterBrick! Name: ", raster.tb$name, " ...\n", sep = ""))
# new variable
rb_sits <- raster.tb$r_objs[[1]][[1]]
#label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton", "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_area", "Water"))
label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy", "Soy", "Soy", "Soy", "Soy", "Sugarcane", "Urban_area", "Water"))
lucC_create_blocks(rb_sits, number_blocks_xy = 2, save_images = TRUE) # 4 blocks will be created
#--------------------------------------------
# new set of raster with secondary vegetation
#--------------------------------------------
# all files in folder
all.the.files <- list.files("~/TESTE/MT/MT_SecVeg", full=TRUE, pattern = ".tif")
all.the.files
# merge blocks into a single image
# lucC_merge_rasters(path_open_GeoTIFFs = "~/TESTE/MT/MT_SecVeg", number_raster = 4, pattern_name = "New_Raster_Splitted_", is.rasterBrick = TRUE)
# save each layer of brick as images
# lucC_save_rasterBrick_layers(path_name_GeoTIFF_Brick = "~/TESTE/MT/MT_SecVeg/Mosaic_New_Raster_Splitted_.tif")
# end time
print(Sys.time() - start.time)
#----------------------------------------------------------
# Discover Secondary Vegetation
#----------------------------------------------------------
library(lucCalculus)
options(digits = 12)
# all files in folder
# all.the.files <- list.files("~/Desktop/INPE_2018/Classi_MT_SVM/raster_1splitted", full=TRUE, pattern = ".tif")
all.the.files <- list.files("~/TESTE/MT", full=TRUE, pattern = ".tif")
all.the.files
#-------------
#Carrega os pacotes necessários para realizar o paralelismo
#library(foreach)
# #Checa quantos núcleos existem
# ncl <- parallel::detectCores()-2
# ncl
# #Registra os clusters a serem utilizados
# cl <- parallel::makeCluster(ncl) #ncl
# doParallel::registerDoParallel(6)
# foreach::getDoParWorkers()
# #-------------
# start time
start.time <- Sys.time()
result.list <- list()
sec_veg.tb <- NULL
for (i in 1:length(all.the.files)) {
#sec_veg.tb <- foreach(i = 1:length(all.the.files), .combine=rbind, .packages= c("lucCalculus")) %dopar% {
# file
file <- all.the.files[i]
#file <- list_MT[i]
# create timeline with classified data from SVM method
timeline <- lubridate::as_date(c("2001-09-01", "2002-09-01", "2003-09-01", "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"))
file_name <- basename(tools::file_path_sans_ext(file))
#library(sits)
# create a RasterBrick metadata file based on the information about the files
raster.tb <- sits::sits_coverage(service = "RASTER", files = file, name = file_name, timeline = timeline, bands = "ndvi")
message(paste0("\nLoad RasterBrick! Name: ", raster.tb$name, " ...\n", sep = ""))
# new variable
rb_sits <- raster.tb$r_objs[[1]][[1]]
# ------------- define variables to plot raster -------------
# original label - see QML file, same order
#label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton", "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_area", "Water"))
label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy", "Soy", "Soy", "Soy", "Soy", "Sugarcane", "Urban_area", "Water"))
# colors
colors_1 <- c("#b3cc33", "#8ddbec", "#228b22", "#afe3c8", "#b6a896", "#e1cdb6", "#e5c6a0", "#b69872", "#b68549", "#dec000", "#cc18b4", "#0000f1")
# plot raster brick
# band1 <- rb_sits$X0000_0000.1
# lucC_plot_raster(raster_obj = band1,
# timeline = timeline, label = label,
# custom_palette = TRUE, RGB_color = colors_1, plot_ncol = 6)
#----------------------------
# 2- Discover Secondary Vegetation - LUC Calculus
#----------------------------
# 1. RECUR predicate indicates a class that appear again
message("Start RECUR ...\n")
#system.time(
forest_recur <- lucC_pred_recur(raster_obj = rb_sits, raster_class = "Forest",
time_interval1 = c("2001-09-01","2001-09-01"),
time_interval2 = c("2002-09-01","2016-09-01"),
label = label, timeline = timeline)
#)
#head(forest_recur)
message("RECUR ok! ...\n")
# 2. EVOLVE to verify Forest class that occurs after a different class in 2001
forest_evolve <- NULL
# classes without Forest based on original label
classes <- as.character(c("Cerrado", "Fallow_Cotton", "Pasture", "Soy", "Sugarcane", "Urban_area", "Water"))
message("Start EVOLVE ...\n")
#system.time(
# percor all classes
for(i in seq_along(classes)){
print(classes[i])
temp <- lucC_pred_evolve(raster_obj = rb_sits, raster_class1 = classes[i],
time_interval1 = c("2001-09-01","2001-09-01"), relation_interval1 = "equals",
raster_class2 = "Forest",
time_interval2 = c("2002-09-01","2016-09-01"), relation_interval2 = "contains",
label = label, timeline = timeline)
forest_evolve <- lucC_merge(forest_evolve, temp)
}
#)
message("EVOLVE ok! ...\n")
# 3. Merge both forest_recur and forest_evolve datas
forest_secondary <- lucC_merge(forest_recur, forest_evolve)
# # plot
# lucC_plot_bar_events(forest_secondary, custom_palette = FALSE, pixel_resolution = 232, legend_text = "Legend:")
# 4. Remove column 2001 because it' is not used to replace pixels's only support column
forest_sec <- lucC_remove_columns(data_mtx = forest_secondary, name_columns = c("2001-09-01"))
#head(forest_sec)
rm(forest_recur, forest_evolve, forest_secondary)
gc()
## plot
# lucC_plot_bar_events(forest_sec, custom_palette = FALSE, pixel_resolution = 232, legend_text = "Legend:")
# # 5. Plot secondary vegetation over raster without column 2001 because it' is not used to replace pixels's only support column
# lucC_plot_raster_result(raster_obj = rb_sits,
# data_mtx = forest_sec,
# timeline = timeline,
# label = label, custom_palette = TRUE,
# RGB_color = colors_1, relabel = FALSE) #, shape_point = ".")
#----------------------------
# 3 - Update original raster to add new pixel value
#----------------------------
message("Start update pixel in RasterBrick ...\n")
number_label <- length(label) + 1
# 1. update original RasterBrick with new class
rb_sits_new <- lucC_raster_update(raster_obj = rb_sits,
data_mtx = forest_sec, # without 2001
timeline = timeline,
class_to_replace = "Forest", # only class Forest
new_pixel_value = number_label) # new pixel value
message("Updated pixel in RasterBrick ok! ...\n")
#head(rb_sits_new)
#lucC_plot_bar_events(data_mtx = rb_sits_new, pixel_resolution = 232, custom_palette = FALSE)
# new name
new_file_name <- paste0(dirname(file),"/", file_name, "_new", sep = "")
result.list[[i]] <- rb_sits_new
# 2. save the update matrix as GeoTIFF RasterBrick
lucC_save_GeoTIFF(raster_obj = rb_sits,
data_mtx = rb_sits_new,
path_raster_folder = new_file_name, as_RasterBrick = FALSE ) # FALSE before
lucC_save_GeoTIFF(raster_obj = rb_sits,
data_mtx = rb_sits_new,
path_raster_folder = new_file_name, as_RasterBrick = TRUE ) # FALSE before
message("--------------------------------------------------\n")
# clear environment, except these elements
rm(list=ls()[!(ls() %in% c('all.the.files', "start.time", "end.time", "result.list"))])
gc()
}
#Stop clusters
#parallel::stopCluster(cl)
# end time
print(Sys.time() - start.time)
#----------------------------------------------------
# Merge all blocks and then generate image exit for each band
#----------------------------------------------------
library(lucCalculus)
options(digits = 12)
# start time
start.time <- Sys.time()
# merge blocks into a single image
lucC_merge_rasters(path_open_GeoTIFFs = "~/TESTE/MT/MT_SecVeg/All_blocks_SecVeg", number_raster = 4, pattern_name = "New_Raster_Splitted_", is.rasterBrick = TRUE)
# save each layer of brick as images
lucC_save_rasterBrick_layers(path_name_GeoTIFF_Brick = "~/TESTE/MT/MT_SecVeg/All_blocks_SecVeg/Mosaic_New_Raster_Splitted_.tif")
# end time
print(Sys.time() - start.time)
ammaciel/sits.LUC.Calculus documentation built on May 3, 2019, 9:36 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# RasterBrick Images
#----------------------------------------------------------
# Divide image in blocks, then merge again
#----------------------------------------------------------
library(lucCalculus)
options(digits = 12)
# start time
start.time <- Sys.time()
# without secondary vegetation
file <- c("~/TESTE/raster_mt_by_year_2004.tif")
# create timeline with classified data from SVM method
timeline <- lubridate::as_date(c("2001-09-01", "2002-09-01", "2003-09-01", "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"))
file_name <- basename(tools::file_path_sans_ext(file))
#library(sits)
# create a RasterBrick metadata file based on the information about the files
raster.tb <- sits::sits_coverage(service = "RASTER", files = file, name = file_name, timeline = timeline, bands = "ndvi")
message(paste0("\nLoad RasterBrick! Name: ", raster.tb$name, " ...\n", sep = ""))
# new variable
rb_sits <- raster.tb$r_objs[[1]][[1]]
#label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton", "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_area", "Water"))
label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy", "Soy", "Soy", "Soy", "Soy", "Sugarcane", "Urban_area", "Water"))
lucC_create_blocks(rb_sits, number_blocks_xy = 2, save_images = TRUE) # 4 blocks will be created
#--------------------------------------------
# new set of raster with secondary vegetation
#--------------------------------------------
# all files in folder
all.the.files <- list.files("~/TESTE/MT/MT_SecVeg", full=TRUE, pattern = ".tif")
all.the.files
# merge blocks into a single image
# lucC_merge_rasters(path_open_GeoTIFFs = "~/TESTE/MT/MT_SecVeg", number_raster = 4, pattern_name = "New_Raster_Splitted_", is.rasterBrick = TRUE)
# save each layer of brick as images
# lucC_save_rasterBrick_layers(path_name_GeoTIFF_Brick = "~/TESTE/MT/MT_SecVeg/Mosaic_New_Raster_Splitted_.tif")
# end time
print(Sys.time() - start.time)
#----------------------------------------------------------
# Discover Secondary Vegetation
#----------------------------------------------------------
library(lucCalculus)
options(digits = 12)
# all files in folder
# all.the.files <- list.files("~/Desktop/INPE_2018/Classi_MT_SVM/raster_1splitted", full=TRUE, pattern = ".tif")
all.the.files <- list.files("~/TESTE/MT", full=TRUE, pattern = ".tif")
all.the.files
#-------------
#Carrega os pacotes necessários para realizar o paralelismo
#library(foreach)
# #Checa quantos núcleos existem
# ncl <- parallel::detectCores()-2
# ncl
# #Registra os clusters a serem utilizados
# cl <- parallel::makeCluster(ncl) #ncl
# doParallel::registerDoParallel(6)
# foreach::getDoParWorkers()
# #-------------
# start time
start.time <- Sys.time()
result.list <- list()
sec_veg.tb <- NULL
for (i in 1:length(all.the.files)) {
#sec_veg.tb <- foreach(i = 1:length(all.the.files), .combine=rbind, .packages= c("lucCalculus")) %dopar% {
# file
file <- all.the.files[i]
#file <- list_MT[i]
# create timeline with classified data from SVM method
timeline <- lubridate::as_date(c("2001-09-01", "2002-09-01", "2003-09-01", "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"))
file_name <- basename(tools::file_path_sans_ext(file))
#library(sits)
# create a RasterBrick metadata file based on the information about the files
raster.tb <- sits::sits_coverage(service = "RASTER", files = file, name = file_name, timeline = timeline, bands = "ndvi")
message(paste0("\nLoad RasterBrick! Name: ", raster.tb$name, " ...\n", sep = ""))
# new variable
rb_sits <- raster.tb$r_objs[[1]][[1]]
# ------------- define variables to plot raster -------------
# original label - see QML file, same order
#label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy_Corn", "Soy_Cotton", "Soy_Fallow", "Soy_Millet", "Soy_Sunflower", "Sugarcane", "Urban_area", "Water"))
label <- as.character(c("Cerrado", "Fallow_Cotton", "Forest", "Pasture", "Soy", "Soy", "Soy", "Soy", "Soy", "Sugarcane", "Urban_area", "Water"))
# colors
colors_1 <- c("#b3cc33", "#8ddbec", "#228b22", "#afe3c8", "#b6a896", "#e1cdb6", "#e5c6a0", "#b69872", "#b68549", "#dec000", "#cc18b4", "#0000f1")
# plot raster brick
# band1 <- rb_sits$X0000_0000.1
# lucC_plot_raster(raster_obj = band1,
# timeline = timeline, label = label,
# custom_palette = TRUE, RGB_color = colors_1, plot_ncol = 6)
#----------------------------
# 2- Discover Secondary Vegetation - LUC Calculus
#----------------------------
# 1. RECUR predicate indicates a class that appear again
message("Start RECUR ...\n")
#system.time(
forest_recur <- lucC_pred_recur(raster_obj = rb_sits, raster_class = "Forest",
time_interval1 = c("2001-09-01","2001-09-01"),
time_interval2 = c("2002-09-01","2016-09-01"),
label = label, timeline = timeline)
#)
#head(forest_recur)
message("RECUR ok! ...\n")
# 2. EVOLVE to verify Forest class that occurs after a different class in 2001
forest_evolve <- NULL
# classes without Forest based on original label
classes <- as.character(c("Cerrado", "Fallow_Cotton", "Pasture", "Soy", "Sugarcane", "Urban_area", "Water"))
message("Start EVOLVE ...\n")
#system.time(
# percor all classes
for(i in seq_along(classes)){
print(classes[i])
temp <- lucC_pred_evolve(raster_obj = rb_sits, raster_class1 = classes[i],
time_interval1 = c("2001-09-01","2001-09-01"), relation_interval1 = "equals",
raster_class2 = "Forest",
time_interval2 = c("2002-09-01","2016-09-01"), relation_interval2 = "contains",
label = label, timeline = timeline)
forest_evolve <- lucC_merge(forest_evolve, temp)
}
#)
message("EVOLVE ok! ...\n")
# 3. Merge both forest_recur and forest_evolve datas
forest_secondary <- lucC_merge(forest_recur, forest_evolve)
# # plot
# lucC_plot_bar_events(forest_secondary, custom_palette = FALSE, pixel_resolution = 232, legend_text = "Legend:")
# 4. Remove column 2001 because it' is not used to replace pixels's only support column
forest_sec <- lucC_remove_columns(data_mtx = forest_secondary, name_columns = c("2001-09-01"))
#head(forest_sec)
rm(forest_recur, forest_evolve, forest_secondary)
gc()
## plot
# lucC_plot_bar_events(forest_sec, custom_palette = FALSE, pixel_resolution = 232, legend_text = "Legend:")
# # 5. Plot secondary vegetation over raster without column 2001 because it' is not used to replace pixels's only support column
# lucC_plot_raster_result(raster_obj = rb_sits,
# data_mtx = forest_sec,
# timeline = timeline,
# label = label, custom_palette = TRUE,
# RGB_color = colors_1, relabel = FALSE) #, shape_point = ".")
#----------------------------
# 3 - Update original raster to add new pixel value
#----------------------------
message("Start update pixel in RasterBrick ...\n")
number_label <- length(label) + 1
# 1. update original RasterBrick with new class
rb_sits_new <- lucC_raster_update(raster_obj = rb_sits,
data_mtx = forest_sec, # without 2001
timeline = timeline,
class_to_replace = "Forest", # only class Forest
new_pixel_value = number_label) # new pixel value
message("Updated pixel in RasterBrick ok! ...\n")
#head(rb_sits_new)
#lucC_plot_bar_events(data_mtx = rb_sits_new, pixel_resolution = 232, custom_palette = FALSE)
# new name
new_file_name <- paste0(dirname(file),"/", file_name, "_new", sep = "")
result.list[[i]] <- rb_sits_new
# 2. save the update matrix as GeoTIFF RasterBrick
lucC_save_GeoTIFF(raster_obj = rb_sits,
data_mtx = rb_sits_new,
path_raster_folder = new_file_name, as_RasterBrick = FALSE ) # FALSE before
lucC_save_GeoTIFF(raster_obj = rb_sits,
data_mtx = rb_sits_new,
path_raster_folder = new_file_name, as_RasterBrick = TRUE ) # FALSE before
message("--------------------------------------------------\n")
# clear environment, except these elements
rm(list=ls()[!(ls() %in% c('all.the.files', "start.time", "end.time", "result.list"))])
gc()
}
#Stop clusters
#parallel::stopCluster(cl)
# end time
print(Sys.time() - start.time)
#----------------------------------------------------
# Merge all blocks and then generate image exit for each band
#----------------------------------------------------
library(lucCalculus)
options(digits = 12)
# start time
start.time <- Sys.time()
# merge blocks into a single image
lucC_merge_rasters(path_open_GeoTIFFs = "~/TESTE/MT/MT_SecVeg/All_blocks_SecVeg", number_raster = 4, pattern_name = "New_Raster_Splitted_", is.rasterBrick = TRUE)
# save each layer of brick as images
lucC_save_rasterBrick_layers(path_name_GeoTIFF_Brick = "~/TESTE/MT/MT_SecVeg/All_blocks_SecVeg/Mosaic_New_Raster_Splitted_.tif")
# end time
print(Sys.time() - start.time)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.