Commit 99cec653 authored by jbferet's avatar jbferet
Browse files

- added input argument type for main functions

- added documentation to repository
parent c9600350
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doc
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.Rbuildignore
.Rhistory
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......@@ -13,7 +13,7 @@
#' converts a raster into BIL format as expected by DivMapping codes
#'
#' @param Raster_Path character. Full path for the raster to be converted
#' @param Sensor character. Name of the sensor
#' @param Sensor character. Name of the sensor. a .hdr template for the sensor should be provided in extdata/HDR
#' @param Convert_Integer boolean. Should data be converted into integer ?
#' @param Multiplying_Factor numeric. Multiplying factor (eg convert real reflectance values between 0 and 1 into integer between 0 and 10000).
#' @param Output_Dir character. Path to output directory.
......@@ -154,9 +154,10 @@ raster2BIL <- function(Raster_Path, Sensor = "unknown", Output_Dir = FALSE, Conv
#' Checks if the data to be processed has the format type expected
#'
#' @param Raster_Path full path for the raster to be converted
#' @param Mask is the raster a mask?
#' @param Raster_Path character. full path for the raster to be converted
#' @param Mask boolean. Set true if the raster is a mask
#'
#' @return
#' @export
check_data <- function(Raster_Path, Mask = FALSE) {
HDR_Path <- get_HDR_name(Raster_Path)
......
......@@ -11,16 +11,16 @@
#' Performs radiometric filtering based on three criteria: NDVI, NIR reflectance, Blue reflectance
#'
#' @param Image_Path Path of the image to be processed
#' @param Mask_Path Path of the mask corresponding to the image
#' @param Output_Dir output directory
#' @param TypePCA Type of PCA: "PCA" or "SPCA"
#' @param NDVI_Thresh NDVI threshold applied to produce a mask (select pixels with NDVI>NDVI_Thresh)
#' @param Blue_Thresh Blue threshold applied to produce a mask (select pixels with Blue refl < Blue_Thresh --> filter clouds) refl expected between 0 and 10000
#' @param NIR_Thresh NIR threshold applied to produce a mask (select pixels with NIR refl < NIR_Thresh) refl expected between 0 and 10000
#' @param Blue central wavelength corresponding to the blue spectral band (in nanometers)
#' @param Red central wavelength corresponding to the red spectral band (in nanometers)
#' @param NIR central wavelength corresponding to the NIR spectral band (in nanometers)
#' @param Image_Path character. Path of the image to be processed
#' @param Mask_Path character. Path of the mask corresponding to the image
#' @param Output_Dir character. Path for output directory
#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
#' @param NDVI_Thresh numeric. NDVI threshold applied to produce a mask (select pixels with NDVI>NDVI_Thresh)
#' @param Blue_Thresh numeric. Blue threshold applied to produce a mask (select pixels with Blue refl < Blue_Thresh --> filter clouds) refl expected between 0 and 10000
#' @param NIR_Thresh numeric. NIR threshold applied to produce a mask (select pixels with NIR refl < NIR_Thresh) refl expected between 0 and 10000
#' @param Blue numeric. central wavelength corresponding to the blue spectral band (in nanometers)
#' @param Red numeric. central wavelength corresponding to the red spectral band (in nanometers)
#' @param NIR numeric. central wavelength corresponding to the NIR spectral band (in nanometers)
#'
#' @return ImPathShade = updated shademask file
#' @export
......
......@@ -13,11 +13,11 @@
#' maps spectral species based on PCA file computed previously
#'
#' @param Input_Image_File Path and name of the image to be processed
#' @param Output_Dir output directory
#' @param TypePCA Type of PCA: "PCA" or "SPCA"
#' @param PCA_Files path for PCA file
#' @param ImPathShade path for shade file (= mask)
#' @param Input_Image_File character. Path of the image to be processed
#' @param Output_Dir character. Path for output directory
#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
#' @param PCA_Files character. Path of the PCA image
#' @param ImPathShade character. Path of the mask corresponding to the image
#' @param Pix_Per_Partition number of pixels for each partition
#' @param nb_partitions number of partition
#' @param nbCPU numeric. Number of CPUs to use in parallel.
......
......@@ -11,13 +11,13 @@
#' Performs PCA for all images and create PCA file with either all or a selection of PCs
#'
#' @param ImPath Path and name of the image to be processed
#' @param ImPathShade correponding shade mask
#' @param Output_Dir output directory
#' @param Continuum_Removal boolean: should continuum removal be applied?
#' @param TypePCA Type of PCA: "PCA" or "SPCA"
#' @param FilterPCA boolean. If TRUE 2nd filtering based on PCA
#' @param Excluded_WL boolean. Water Vapor Absorption domains (in nanometers). Can also be used to exclude spectific domains
#' @param ImPath character. Path of the image to be processed
#' @param ImPathShade character. Path of the mask corresponding to the image
#' @param Output_Dir character. Path for output directory
#' @param Continuum_Removal boolean. Set to TRUE if continuum removal should be applied
#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
#' @param FilterPCA boolean. Set to TRUE if 2nd filtering based on PCA is required
#' @param Excluded_WL numeric. Water Vapor Absorption domains (in nanometers, min and max WL). Can also be used to exclude spectific domains. dims = N x 2 (N = number of domains to be eliminated)
#' @param nb_partitions numeric. Number of repetitions to estimate diversity from the raster (averaging repetitions).
#' @param nbCPU numeric. Number fo CPUs in use.
#' @param MaxRAM numeric. Maximum size of chunk in GB to limit RAM allocation when reading image file.
......@@ -482,11 +482,11 @@ define_pixels_per_iter <- function(ImNames, nb_partitions = nb_partitions) {
#' Check if principal components are properly selected as expected by the method
#'
#' @param Output_Dir output directory
#' @param Input_Image_File path for image to be processed
#' @param PCA_Files path of PCA files
#' @param TypePCA Type of PCA: "PCA" or "SPCA"
#' @param File_Open Boolean. automatically opens file if TRUE
#' @param Input_Image_File character. Path of the image to be processed
#' @param Output_Dir character. Path for output directory
#' @param PCA_Files character. Path of the PCA image
#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
#' @param File_Open Boolean. Set to TRUE for file to open automatically
#'
#' @return nothing
#' @importFrom utils file.edit
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