Merge branch 'hotfix/mixed-pixel.idx-orders' into dev

Claudius-Appel · Mar 28, 2024 · 5f0a450 · 5f0a450
2 parents e2e9609 + 08811ab
commit 5f0a450
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: duflor
 Title: Plant Image Analysis For Determination of Leaf- and Root-Area 
-Version: 0.0.1.9016
+Version: 0.0.1.9017
 Author: Claudius Appel
 Authors@R: c(
     person("Claudius", "Appel", email =   "claudius.appel@freenet.de" , role = c("aut", "cre"))

diff --git a/R/apply_hsv_color_to_image_subset.R b/R/apply_hsv_color_to_image_subset.R
@@ -9,12 +9,12 @@
 apply_hsv_color_to_image_subset <- function(pixel.array,pixel.idx,target.color.hsv, mask_extreme = FALSE) {
     pa_t <- as.array(pixel.array)
     for (i in 1:nrow(pixel.idx)) {
-        pa_t[pixel.idx[i, 1], pixel.idx[i, 2],1,1] <- target.color.hsv[1]
-        pa_t[pixel.idx[i, 1], pixel.idx[i, 2],1,2] <- target.color.hsv[2]
+        pa_t[pixel.idx[i, "x"], pixel.idx[i, "y"],1,1] <- target.color.hsv[1]
+        pa_t[pixel.idx[i, "x"], pixel.idx[i, "y"],1,2] <- target.color.hsv[2]
     }
     if (isTRUE(as.logical(mask_extreme))) {
         for (i in 1:nrow(pixel.idx)) {
-            pa_t[pixel.idx[i, 1], pixel.idx[i, 2],1,3] <- target.color.hsv[3]
+            pa_t[pixel.idx[i, "x"], pixel.idx[i, "y"],1,3] <- target.color.hsv[3]
         }
     }
     pixel.array <- imager::as.cimg(pa_t)

diff --git a/R/helper.R b/R/helper.R
@@ -158,7 +158,7 @@ diagonal_adjacency <- function(pixel.idx) {
 #'     )
 #' }
 retrieve_adjacency_coords <- function(pixel.idx,cluster_id) {
-    pixel.idx[pixel.idx[,3]==cluster_id,]
+    pixel.idx[pixel.idx[,"clus"]==cluster_id,]
 }
 
 #' wrapper around `object.size()`

diff --git a/R/rectangularRange_HSV.R b/R/rectangularRange_HSV.R
@@ -39,6 +39,7 @@ rectangularRange_HSV <- function(pixel.array, upper_bound, lower_bound) {
                  # & (lower_bound[3] <= pixel.array[, , 1, 3] & pixel.array[, , 1, 3] <= upper_bound[3])
                  ,arr.ind = TRUE
     )
+    dimnames(idx)[[2]] <- c("x","y")
     if (length(idx) == 0) { # no pixels match the requirements.
         return(idx)
     } else {

diff --git a/R/validate_mask_edges.R b/R/validate_mask_edges.R
@@ -37,10 +37,10 @@ validate_mask_edges <- function(mask.idx,mask_name,array_dim,image.path) {
     # get the matched pixels that are as close to the edges as possible
     # array_dim[1]: width of pixel.array
     # array_dim[2]: height of pixel.array
-    y_bottom <- max(mask.idx[,2])
-    y_top <- min(mask.idx[,2])
-    x_right<- max(mask.idx[,1])
-    x_left <- min(mask.idx[,1])
+    y_bottom <- max(mask.idx[,"y"])
+    y_top <- min(mask.idx[,"y"])
+    x_right<- max(mask.idx[,"x"])
+    x_left <- min(mask.idx[,"x"])
     ret <- list(left = FALSE,
                 right = FALSE,
                 top = FALSE,

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/duflor.html b/docs/articles/duflor.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   duflor: duflor.html
-last_built: 2024-03-22T10:58Z
+last_built: 2024-03-28T14:01Z
 urls:
   reference: https://Claudius-Appel.github.io/duflor/reference
   article: https://Claudius-Appel.github.io/duflor/articles

diff --git a/docs/reference/HSVtoRGB.html b/docs/reference/HSVtoRGB.html
diff --git a/docs/reference/RGBtoHSV.html b/docs/reference/RGBtoHSV.html
diff --git a/docs/reference/adjacency.html b/docs/reference/adjacency.html
diff --git a/docs/reference/apply_hsv_color_to_image_subset.html b/docs/reference/apply_hsv_color_to_image_subset.html
diff --git a/docs/reference/change_pixel_color_HSV.html b/docs/reference/change_pixel_color_HSV.html
diff --git a/docs/reference/convert_pixels_to_area.html b/docs/reference/convert_pixels_to_area.html
diff --git a/docs/reference/diagonal_adjacency.html b/docs/reference/diagonal_adjacency.html
diff --git a/docs/reference/dot-main_args.html b/docs/reference/dot-main_args.html
diff --git a/docs/reference/dot-onAttach.html b/docs/reference/dot-onAttach.html
diff --git a/docs/reference/dot-onLoad.html b/docs/reference/dot-onLoad.html
diff --git a/docs/reference/dot-onUnLoad.html b/docs/reference/dot-onUnLoad.html
diff --git a/docs/reference/duflor-package.html b/docs/reference/duflor-package.html
diff --git a/docs/reference/extract_pixels_HSV.html b/docs/reference/extract_pixels_HSV.html
diff --git a/docs/reference/get_indicator_image.html b/docs/reference/get_indicator_image.html
diff --git a/docs/reference/get_javaVM_exceptions.html b/docs/reference/get_javaVM_exceptions.html
diff --git a/docs/reference/get_unique_list_elements.html b/docs/reference/get_unique_list_elements.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/load_image.html b/docs/reference/load_image.html
diff --git a/docs/reference/norm_to_range_01.html b/docs/reference/norm_to_range_01.html
diff --git a/docs/reference/objs.html b/docs/reference/objs.html
diff --git a/docs/reference/plot_array_as_image_sRGB.html b/docs/reference/plot_array_as_image_sRGB.html
diff --git a/docs/reference/plot_indicator_image.html b/docs/reference/plot_indicator_image.html