README.md
In OtsuSeg: Raster Thresholding Using Otsu´s Algorithm

OtsuSeg

OtsuSeg is an R package designed for the segmentation of burned areas using smoothed histograms and Otsu's thresholding method applied to spectral indices such as the Normalized Burn Ratio (NBR).

Authors: Hammadi Achour, Olga Viedma, Zina Soltani, Imene Habibi, Wahbi Jaouadi

The package provides tools to:

Apply Otsu's method to smoothed histograms of Relative Burn Ratio (RBR) and delta Normalized Burn Ratio (dNBR) images.
Segment fire scars and assess the accuracy of burn area maps.

Large example datasets are hosted externally and are not bundled in the CRAN/GitHub package to comply with size limits.

These files are hosted at: https://github.com/olgaviedma/OtsuSeg/releases/tag/v0.1.0

library(OtsuSeg)

# Download and extract example data
get_external_data()

# 1.Load a specific file as a raster object
NBRpre <- get_external_data("NBRpre.tif", load = TRUE)
NBRpost <- get_external_data("NBRpost.tif", load = TRUE)
shapefile_reference <- get_external_data("shapefile_reference.shp", load = TRUE)

## 2.Fire scars segments
shapefile_path <- file.path("D:/OLGA/binary_segments.shp")
result <- binarize_raster(NBRpre, NBRpost, shapefile_path = shapefile_path)

print(result$area_hectares)

raster<-result$binary_raster_smoothed
polygons<-st_as_sf(result$binary_shapefile)

plot(raster, main = "Binary Raster (Smoothed)")
plot(polygons, main = "Binary Shapefile")

## 3.Accuracy assessmet
binary_shape <-polygons
reference_shape <- st_as_sf(shapefile_reference)

# Apply Quality Control
result2 <- Quality_control(binary_shape, reference_shape)
print(result2)

This documentation includes examples, illustrations, and step-by-step workflows to guide the use of the package.

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To install the latest version of OtsuSeg:

#The CRAN version:
install.packages("OtsuSeg")

# Install the 'remotes' package if not already installed
install.packages("remotes")

# Install 'otsuSeg' from GitHub
remotes::install_github("olgaviedma/OtsuSeg")