- fix bug when no shade mask provided and no radiometric filtering performed

- fix bug when continuum removal applied on pixels with constant values which were not filtered in previous stages

R/Lib_ContinuumRemoval.R

@@ -66,21 +66,22 @@ ContinuumRemoval <- function(Minit, Spectral_Bands) {
   CR_data$Minit <- c()
   Spectral_Bands <- CR_data$Spectral_Bands
   nbSamples <- CR_data$nbSamples
+  nbSamplesUpDate <- length(CR_data$SamplesToKeep)
   # if samples to be considered
   if (nbSamples > 0) {
     # initialization:
     # spectral band corresponding to each element of the data matrix
-    Lambda <- repmat(matrix(Spectral_Bands, nrow = 1), nbSamples, 1)
+    Lambda <- repmat(matrix(Spectral_Bands, nrow = 1), nbSamplesUpDate, 1)
     # prepare matrices used to check evolution of the CR process
     # - elements still not processed through continuum removal: initialization to 1
-    Still.Need.CR <- matrix(1, nrow = nbSamples, ncol = nbBands)
+    Still.Need.CR <- matrix(1, nrow = nbSamplesUpDate, ncol = nbBands)
     # - value of the convex hull: initially set to 0
-    Convex_Hull <- matrix(0, nrow = nbSamples, ncol = nbBands)
+    Convex_Hull <- matrix(0, nrow = nbSamplesUpDate, ncol = nbBands)
     # - reflectance value for latest interception with convex hull:
     # initialization to value of the first reflectance measurement
     Intercept_Hull <- repmat(matrix(Minit[, 1], ncol = 1), 1, nbBands)
     # - spectral band of latest interception
-    Latest.Intercept <- repmat(matrix(Spectral_Bands[1], ncol = 1), nbSamples, nbBands)
+    Latest.Intercept <- repmat(matrix(Spectral_Bands[1], ncol = 1), nbSamplesUpDate, nbBands)
     # number of spectral bands found as intercept
     nb.Intercept <- 0
     # continues until arbitrary stopping criterion:
@@ -88,7 +89,7 @@ ContinuumRemoval <- function(Minit, Spectral_Bands) {
     while (max(Still.Need.CR[, 1:(nbBands - 2)]) == 1 & (nb.Intercept <= (nbBands / 2))) {
       nb.Intercept <- nb.Intercept + 1
       # Mstep give the position of the values to be updated
-      Update_Data <- matrix(1, nrow = nbSamples, ncol = nbBands)
+      Update_Data <- matrix(1, nrow = nbSamplesUpDate, ncol = nbBands)
       Update_Data[, nbBands] <- 0
       # initial step: first column set to 0; following steps: all bands below
       # max of the convex hull are set to 0
@@ -103,7 +104,7 @@ ContinuumRemoval <- function(Minit, Spectral_Bands) {
         Slope[which(is.na(Slope))] <- -9999
       }
       # get max index for each row and convert into linear index
-      Index.Max.Slope <- RowToLinear(max.col(Slope, ties.method = "last"), nbSamples, nbBands)
+      Index.Max.Slope <- RowToLinear(max.col(Slope, ties.method = "last"), nbSamplesUpDate, nbBands)
       # !!!! OPTIM: replace repmat with column operation
       # update coordinates of latest intercept
       Latest.Intercept <- repmat(matrix(Lambda[Index.Max.Slope], ncol = 1), 1, nbBands)
@@ -163,8 +164,9 @@ filter_prior_CR <- function(Minit, Spectral_Bands) {
   if (length(keep) == 1) {
     Minit <- matrix(Minit, nrow = 1)
   }
+  nbSamplesUpDate <- nrow(Minit)
   # add negative values to the last column and update spectral bands
-  Minit <- cbind(Minit, matrix(-9999, ncol = 1, nrow = nbSamples))
+  Minit <- cbind(Minit, matrix(-9999, ncol = 1, nrow = nbSamplesUpDate))
   nbBands <- ncol(Minit)
   Spectral_Bands[nbBands] <- Spectral_Bands[nbBands - 1] + 10
   my_list <- list("Minit" = Minit, "Spectral_Bands" = Spectral_Bands, "nbSamples" = nbSamples, "SamplesToKeep" = keep)

R/Lib_PerformPCA.R

@@ -233,7 +233,7 @@ filter_PCA <- function(ImPath, HDR, MaskPath, Shade_Update, Spectral, CR, PCA_mo
     nbLines <- SeqRead_Shade$Lines_Per_Chunk[i]
     lenBin <- SeqRead_Shade$ReadByte_End[i] - SeqRead_Shade$ReadByte_Start[i] + 1
     ImgFormat <- "Shade"
-    if (!MaskPath == "") {
+    if ((!MaskPath == FALSE) & (!MaskPath == "")) {
       Shade_Chunk <- read_image_subset(MaskPath, HDR_Shade, Byte_Start, lenBin, nbLines, Shade_Format, ImgFormat)
     } else {
       Shade_Chunk <- ones(nbLines * HDR$samples, 1)
@@ -306,8 +306,12 @@ filter_PCA <- function(ImPath, HDR, MaskPath, Shade_Update, Spectral, CR, PCA_mo
 write_PCA_raster <- function(ImPath, MaskPath, PCA_Path, PCA_model, Spectral, Nb_PCs, CR, TypePCA, nbCPU = 1, MaxRAM = 0.25) {
   ImPathHDR <- get_HDR_name(ImPath)
   HDR <- read_ENVI_header(ImPathHDR)
-  ShadeHDR <- get_HDR_name(MaskPath)
-  HDR_Shade <- read_ENVI_header(ShadeHDR)
+  if ((!MaskPath == FALSE) & (!MaskPath == "")) {
+    ShadeHDR <- get_HDR_name(MaskPath)
+    HDR_Shade <- read_ENVI_header(ShadeHDR)
+  } else {
+    HDR_Shade <- FALSE
+  }
   # 1- create hdr and binary files corresponding to PCA file
   HDR_PCA <- HDR
   HDR_PCA$bands <- Nb_PCs
@@ -337,7 +341,17 @@ write_PCA_raster <- function(ImPath, MaskPath, PCA_Path, PCA_model, Spectral, Nb
   # read image file sequentially
   Image_Format <- ENVI_type2bytes(HDR)
   PCA_Format <- ENVI_type2bytes(HDR_PCA)
-  Shade_Format <- ENVI_type2bytes(HDR_Shade)
+
+  if (typeof(HDR_Shade) == 'list') {
+    Shade_Format <- ENVI_type2bytes(HDR_Shade)
+  } else if (typeof(HDR_Shade) == 'logical'){
+    Shade_Format <- FALSE
+  }
+  # if (!HDR_Shade == FALSE) {
+  #   Shade_Format <- ENVI_type2bytes(HDR_Shade)
+  # } else {
+  #   Shade_Format <- FALSE
+  # }
   # prepare for sequential processing: SeqRead_Image informs about byte location to read
   nbPieces <- split_image(HDR, LimitSizeGb = MaxRAM)
   SeqRead_Image <- where_to_read(HDR, nbPieces)
@@ -357,13 +371,16 @@ write_PCA_raster <- function(ImPath, MaskPath, PCA_Path, PCA_model, Spectral, Nb
     Byte_Start <- SeqRead_Shade$ReadByte_Start[i]
     nbLines <- SeqRead_Shade$Lines_Per_Chunk[i]
     lenBin <- SeqRead_Shade$ReadByte_End[i] - SeqRead_Shade$ReadByte_Start[i] + 1
-    ImgFormat <- "Shade"
-    Shade_Chunk <- read_image_subset(MaskPath, HDR_Shade, Byte_Start, lenBin, nbLines, Shade_Format, ImgFormat)
-
-    elimShade <- which(Shade_Chunk == 0)
-    keepShade <- which(Shade_Chunk == 1)
-    Image_Chunk <- Image_Chunk[keepShade, ]
 
+    if (typeof(HDR_Shade) == 'list') {
+      ImgFormat <- "Shade"
+      Shade_Chunk <- read_image_subset(MaskPath, HDR_Shade, Byte_Start, lenBin, nbLines, Shade_Format, ImgFormat)
+      elimShade <- which(Shade_Chunk == 0)
+      keepShade <- which(Shade_Chunk == 1)
+      Image_Chunk <- Image_Chunk[keepShade, ]
+    } else {
+      keepShade <- matrix(1,ncol = 1,nrow = nrow(Image_Chunk))
+    }
     # apply Continuum removal if needed
     if (CR == TRUE) {
       Image_Chunk <- apply_continuum_removal(Image_Chunk, Spectral, nbCPU = nbCPU)