Merge branch 'main' of https://github.com/mzarowka/HSItools

# Conflicts:
#	R/app.R

DESCRIPTION

@@ -16,19 +16,18 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Suggests: 
     testthat (>= 3.0.0),
-    arrow,
     patchwork,
-    sf,
     knitr,
-    rmarkdown
+    rmarkdown,
+    scales,
+    prospectr
 Config/testthat/edition: 3
 URL: https://github.com/mzarowka/HSItools
 BugReports: https://github.com/mzarowka/HSItools/issues
 Imports: 
     dplyr,
     DT,
     ggplot2,
-    prospectr,
     shiny,
     shinycssloaders,
     shinyFiles,
@@ -41,11 +40,10 @@ Imports:
     rlang,
     data.table,
     shinyalert,
-    stringr,
     tibble,
     readr,
     fs,
-    scales
+    sf
 Depends: 
     R (>= 4.1.0)
 LazyData: true

NAMESPACE

@@ -28,6 +28,10 @@ export(run_core)
 export(spectra_position)
 export(spectra_sub)
 export(stretch_raster_full)
+import(DT)
+import(shiny)
+import(shinyFiles)
 importFrom(ggplot2,theme)
 importFrom(rlang,.data)
+importFrom(shinyalert,shinyalert)
 importFrom(stats,median)

R/app.R

@@ -868,17 +868,32 @@ run_core <- function(autoSave = TRUE){
 
     zoomedPlot <- reactive({
       if (!is.null(input$plotBrush)){
+<<<<<<< HEAD
         a1 <- terra::crop(x=coreRGB(),y=terra::ext(c(x_range(input$plotBrush)[1], x_range(input$plotBrush)[2], y_range(input$plotBrush)[1], y_range(input$plotBrush)[2])))
         suppressWarnings(terra::plotRGB(x = a1, stretch = "hist"))
+=======
+        print("cropping zoomedPlot...")
+        a1 <- terra::crop(x=coreImage(),y=terra::ext(c(x_range(input$plotBrush)[1], x_range(input$plotBrush)[2], y_range(input$plotBrush)[1], y_range(input$plotBrush)[2])))
+        print("plotting zoomedPlot...")
+        suppressWarnings(terra::plotRGB(x = a1, r = RGBlayers()[1], g = RGBlayers()[2], b = RGBlayers()[3], stretch = "hist"))
+>>>>>>> 9c0e37951104438c1a6ebd0c33bfcdb9c4bec40f
       } else {
         terra::plotRGB(x = coreRGB(), stretch = "hist")
       }
     })
 
     output$cropped_plot <- renderPlot({
 
+<<<<<<< HEAD
       a1 <- terra::crop(x=coreRGB(),y=terra::ext(allParams$cropImage))
       suppressWarnings(terra::plotRGB(x = a1, stretch = "hist"))
+=======
+      print("cropping cropped_plot...")
+
+      a1 <- terra::crop(x=coreImage(),y=terra::ext(allParams$cropImage))
+      print("plotting cropped_plot...")
+      suppressWarnings(terra::plotRGB(x = a1, r = RGBlayers()[1], g = RGBlayers()[2], b = RGBlayers()[3], stretch = "hist"))
+>>>>>>> 9c0e37951104438c1a6ebd0c33bfcdb9c4bec40f
 
       if (sum(complete.cases(analysisRegions$DT))>0){
         for (i in 1:nrow(analysisRegions$DT)){

R/extractors.R

@@ -63,7 +63,7 @@ extract_spectral_series <- function(raster, index = NULL, calibration = NULL, ex
   } else if (filename == TRUE) {
     # Check source
     if (terra::sources(raster) == "") {
-      rlang::warn(message = "In memory object. Using working directory instead.")
+      rlang::warn(message = "In memory object. Using working directory.")
 
       filename <- paste0(getwd(), "/spectral_profile.csv")
 

R/normalization.R

@@ -179,6 +179,69 @@ raster_crop <- function(raster, type, dir = NULL, roi) {
   return(raster)
 }
 
+#' #' Create reference SpatRaster
+#' #'
+#' #' @param raster terra SpatRaster of the captured reference.
+#' #' @param roi Region Of Interest: extent to match data raster.
+#' #' @param ref_type type of reference, one of "whiteref" or "darkref".
+#' #' @param ... additional arguments.
+#' #'
+#' #' @return a terra SpatRaster of reference matching the data raster extent.
+#' #' @export
+#' #'
+#' #' @description Creating reference SpatRaster covering core extent
+#' #' Create one mean reference row SpatRaster by averaging data every column by aggregation
+#' #' Create reference SpatRaster matching capture SpatRaster extent by disaggregation.
+#' create_reference_raster_disagg <- function(raster, roi, ref_type, ...) {
+#'   # Store additional parameters
+#'   params <- rlang::list2(...)
+#'
+#'   # Check if correct class is supplied.
+#'   if (!inherits(raster, what = "SpatRaster")) {
+#'     rlang::abort(message = "Supplied data is not a terra SpatRaster.")
+#'   }
+#'
+#'   # Check number of rois and prepare ids.
+#'   if (length(roi) == 1) {
+#'     roi_id <- NULL
+#'   } else {
+#'     roi_id <- paste0("ROI_", seq(1:length(roi)))
+#'   }
+#'
+#'   if (ref_type == "whiteref") {
+#'     name <- "WHITEREF"
+#'
+#'   } else {
+#'     name <- "DARKREF"
+#'   }
+#'
+#'   # Aggregate data into one row SpatRaster, divide by number of rows
+#'   cli::cli_alert("Aggregate { name }")
+#'
+#'   raster <- terra::aggregate(
+#'     raster,
+#'     fact = c(terra::nrow(raster), 1),
+#'     fun = "mean",
+#'     overwrite = TRUE,
+#'     steps = terra::ncell(raster) * terra::nlyr(raster))
+#'
+#'   # Set new extent to match extent of capture SpatRaster
+#'   terra::ext(raster) <- roi
+#'
+#'   # Disaggregate data over entire extent to match capture SpatRaster extent, multiply by ymax
+#'   cli::cli_alert("Disaggregate { name }")
+#'
+#'   raster <- terra::disagg(
+#'     raster,
+#'     fact = c(terra::ymax(raster), 1),
+#'     filename = paste0(params$path, "/products/", name, "_", basename(params$path), "_disaggregated.tif"),
+#'     overwrite = TRUE,
+#'     steps = terra::ncell(raster) * terra::nlyr(raster))
+#'
+#'   # Return raster
+#'   return(raster)
+#' }
+
 #' Create reference SpatRaster
 #'
 #' @param raster terra SpatRaster of the captured reference.
@@ -215,28 +278,33 @@ create_reference_raster <- function(raster, roi, ref_type, ...) {
     name <- "DARKREF"
   }
 
+  # Create 1 row template
+  template_row <- terra::rast(terra::ext(c(terra::xmin(roi), terra::xmax(roi), 0, 1)), resolution = c(1, 1))
+
+  # Create full core template
+  template_core <- terra::rast(terra::ext(roi), resolution = c(1, 1), nlyrs = terra::nlyr(raster))
+
   # Aggregate data into one row SpatRaster, divide by number of rows
   cli::cli_alert("Aggregate { name }")
 
   raster <- terra::aggregate(
     raster,
     fact = c(terra::nrow(raster), 1),
-    fun = "mean",
-    overwrite = TRUE,
-    steps = terra::ncell(raster) * terra::nlyr(raster))
+    fun = "mean") |>
+    terra::resample(
+      template_row)
 
   # Set new extent to match extent of capture SpatRaster
   terra::ext(raster) <- roi
 
-  # Disaggregate data over entire extent to match capture SpatRaster extent, multiply by ymax
-  cli::cli_alert("Disaggregate { name }")
+  # Scale and resample data over entire extent to match capture SpatRaster extent, multiply by ymax
+  cli::cli_alert("Scaling and resampling { name }")
 
-  raster <- terra::disagg(
-    raster,
-    fact = c(terra::ymax(raster), 1),
-    filename = paste0(params$path, "/products/", name, "_", basename(params$path), "_disaggregated.tif"),
-    overwrite = TRUE,
-    steps = terra::ncell(raster) * terra::nlyr(raster))
+  raster <- raster |>
+    terra::rescale(fx = 1, fy = terra::nrow(template_core) * 2) |>
+    terra::resample(
+      template_core,
+      filename = paste0(params$path, "/products/", name, "_", basename(params$path), "_disaggregated.tif"))
 
   # Return raster
   return(raster)

R/utils.R

@@ -155,8 +155,10 @@ pixel_to_distance <- function(core, pixel_ratio, ymax, ymin = 0, sample_start, s
 #' @export
 #'
 #' @examples
+#' if (interactive() == TRUE) {
 #' a1 <- readRDS(file.path(system.file(package = "HSItools"),"extdata/HSItools_core.rds"))
 #' change_output_dir(a1)
+#' }
 #'
 change_output_dir = function(run_core_output){
   #currentRoot <- rprojroot::find_root(rprojroot::criteria$is_rstudio_project)