\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).}
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)}