- updated Rd files

- import check_data into perform_radiometric_filtering and perform_PCA

.gitignore

 Meta
+doc
 .Rproj.user
 .Rbuildignore
 .Rhistory

R/Lib_CheckConvertData.R

@@ -208,7 +208,7 @@ check_data <- function(Raster_Path, Mask = FALSE) {
       if ((HDR$`wavelength units` == "nanometers") | (HDR$`wavelength units` == "Nanometers")) {
         message("")
         message("*********************************************************")
-        message("       All information seem OK for image processing      ")
+        message("               Raster format OK for processing           ")
         message("*********************************************************")
         message("")
       }

R/Lib_FilterData.R

@@ -25,6 +25,9 @@
 #' @return ImPathShade = updated shademask file
 #' @export
 perform_radiometric_filtering <- function(Image_Path, Mask_Path, Output_Dir, TypePCA = "SPCA", NDVI_Thresh = 0.5, Blue_Thresh = 500, NIR_Thresh = 1500, Blue = 480, Red = 700, NIR = 835) {
+  # check if format of raster data is as expected
+  check_data(Image_Path)
+  check_data(Mask_Path)
   # define full output directory
   Output_Dir_Full <- define_output_directory(Output_Dir, Image_Path, TypePCA)
   # define dimensions of the image

R/Lib_PerformPCA.R

@@ -25,6 +25,9 @@
 #' @return list of paths corresponding to resulting PCA files
 #' @export
 perform_PCA  <- function(ImPath, ImPathShade, Output_Dir, Continuum_Removal = TRUE, TypePCA = "SPCA", FilterPCA = FALSE, Excluded_WL = FALSE, nb_partitions = 20, nbCPU = 1, MaxRAM = 0.25) {
+  # check if format of raster data is as expected
+  check_data(ImPath)
+  check_data(ImPathShade)
   # define the path corresponding to image, mask and output directory
   ImNames <- list()
   ImNames$Input.Image <- ImPath

man/check_data.Rd

@@ -7,9 +7,9 @@
 check_data(Raster_Path, Mask = FALSE)
 }
 \arguments{
-\item{Raster_Path}{full path for the raster to be converted}
+\item{Raster_Path}{character. full path for the raster to be converted}
 
-\item{Mask}{is the raster a mask?}
+\item{Mask}{boolean. Set true if the raster is a mask}
 }
 \description{
 Checks if the data to be processed has the format type expected

man/map_spectral_species.Rd

@@ -9,19 +9,19 @@ map_spectral_species(Input_Image_File, Output_Dir, PCA_Files, ImPathShade,
   nbCPU = 1, MaxRAM = FALSE)
 }
 \arguments{
-\item{Input_Image_File}{Path and name of the image to be processed}
+\item{Input_Image_File}{character. Path of the image to be processed}
 
-\item{Output_Dir}{output directory}
+\item{Output_Dir}{character. Path for output directory}
 
-\item{PCA_Files}{path for PCA file}
+\item{PCA_Files}{character. Path of the PCA image}
 
-\item{ImPathShade}{path for shade file (= mask)}
+\item{ImPathShade}{character. Path of the mask corresponding to the image}
 
 \item{Pix_Per_Partition}{number of pixels for each partition}
 
 \item{nb_partitions}{number of partition}
 
-\item{TypePCA}{Type of PCA: "PCA" or "SPCA"}
+\item{TypePCA}{character. Type of PCA: choose either "PCA" or "SPCA"}
 
 \item{nbclusters}{number of clusters defined in k-Means}
 

man/perform_PCA.Rd

@@ -9,19 +9,19 @@ perform_PCA(ImPath, ImPathShade, Output_Dir, Continuum_Removal = TRUE,
   nb_partitions = 20, nbCPU = 1, MaxRAM = 0.25)
 }
 \arguments{
-\item{ImPath}{Path and name of the image to be processed}
+\item{ImPath}{character. Path of the image to be processed}
 
-\item{ImPathShade}{correponding shade mask}
+\item{ImPathShade}{character. Path of the mask corresponding to the image}
 
-\item{Output_Dir}{output directory}
+\item{Output_Dir}{character. Path for output directory}
 
-\item{Continuum_Removal}{boolean: should continuum removal be applied?}
+\item{Continuum_Removal}{boolean. Set to TRUE if continuum removal should be applied}
 
-\item{TypePCA}{Type of PCA: "PCA" or "SPCA"}
+\item{TypePCA}{character. Type of PCA: choose either "PCA" or "SPCA"}
 
-\item{FilterPCA}{boolean. If TRUE 2nd filtering based on PCA}
+\item{FilterPCA}{boolean. Set to TRUE if 2nd filtering based on PCA is required}
 
-\item{Excluded_WL}{boolean. Water Vapor Absorption domains (in nanometers). Can also be used to exclude spectific domains}
+\item{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)}
 
 \item{nb_partitions}{numeric. Number of repetitions to estimate diversity from the raster (averaging repetitions).}
 

man/perform_radiometric_filtering.Rd

@@ -9,25 +9,25 @@ perform_radiometric_filtering(Image_Path, Mask_Path, Output_Dir,
   NIR_Thresh = 1500, Blue = 480, Red = 700, NIR = 835)
 }
 \arguments{
-\item{Image_Path}{Path of the image to be processed}
+\item{Image_Path}{character. Path of the image to be processed}
 
-\item{Mask_Path}{Path of the mask corresponding to the image}
+\item{Mask_Path}{character. Path of the mask corresponding to the image}
 
-\item{Output_Dir}{output directory}
+\item{Output_Dir}{character. Path for output directory}
 
-\item{TypePCA}{Type of PCA: "PCA" or "SPCA"}
+\item{TypePCA}{character. Type of PCA: choose either "PCA" or "SPCA"}
 
-\item{NDVI_Thresh}{NDVI threshold applied to produce a mask (select pixels with NDVI>NDVI_Thresh)}
+\item{NDVI_Thresh}{numeric. NDVI threshold applied to produce a mask (select pixels with NDVI>NDVI_Thresh)}
 
-\item{Blue_Thresh}{Blue threshold applied to produce a mask (select pixels with Blue refl < Blue_Thresh --> filter clouds) refl expected between 0 and 10000}
+\item{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}
 
-\item{NIR_Thresh}{NIR threshold applied to produce a mask (select pixels with NIR refl < NIR_Thresh) refl expected between 0 and 10000}
+\item{NIR_Thresh}{numeric. NIR threshold applied to produce a mask (select pixels with NIR refl < NIR_Thresh) refl expected between 0 and 10000}
 
-\item{Blue}{central wavelength corresponding to the blue spectral band (in nanometers)}
+\item{Blue}{numeric. central wavelength corresponding to the blue spectral band (in nanometers)}
 
-\item{Red}{central wavelength corresponding to the red spectral band (in nanometers)}
+\item{Red}{numeric. central wavelength corresponding to the red spectral band (in nanometers)}
 
-\item{NIR}{central wavelength corresponding to the NIR spectral band (in nanometers)}
+\item{NIR}{numeric. central wavelength corresponding to the NIR spectral band (in nanometers)}
 }
 \value{
 ImPathShade = updated shademask file

man/raster2BIL.Rd

@@ -11,7 +11,7 @@ raster2BIL(Raster_Path, Sensor = "unknown", Output_Dir = FALSE,
 \arguments{
 \item{Raster_Path}{character. Full path for the raster to be converted}
 
-\item{Sensor}{character. Name of the sensor}
+\item{Sensor}{character. Name of the sensor. a .hdr template for the sensor should be provided in extdata/HDR}
 
 \item{Output_Dir}{character. Path to output directory.}
 

man/select_PCA_components.Rd

@@ -8,15 +8,15 @@ select_PCA_components(Input_Image_File, Output_Dir, PCA_Files,
   TypePCA = "SPCA", File_Open = FALSE)
 }
 \arguments{
-\item{Input_Image_File}{path for image to be processed}
+\item{Input_Image_File}{character. Path of the image to be processed}
 
-\item{Output_Dir}{output directory}
+\item{Output_Dir}{character. Path for output directory}
 
-\item{PCA_Files}{path of PCA files}
+\item{PCA_Files}{character. Path of the PCA image}
 
-\item{TypePCA}{Type of PCA: "PCA" or "SPCA"}
+\item{TypePCA}{character. Type of PCA: choose either "PCA" or "SPCA"}
 
-\item{File_Open}{Boolean. automatically opens file if TRUE}
+\item{File_Open}{Boolean. Set to TRUE for file to open automatically}
 }
 \value{
 nothing