Plotting electrodes on slices now takes numerical adjust_brightness…

… interpreted as quantile
dipterix · Aug 22, 2024 · 3854835 · 3854835
1 parent 47a8db0
commit 3854835
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,7 @@
 ## Changes since last CRAN release
-* `498f62db (HEAD -> master)` [_`dipterix`_]: Changed default color palette for discrete values, removed colors that are too dark or gray
-* `c345aa3a (origin/master, origin/HEAD)` [_`dipterix`_]: Change `CT` threshold back to positive (3000) when switching from `DBS` leads back to `sEEG` leads.
+* `7086b17c (HEAD -> master)` [_`dipterix`_]: Plotting electrodes on slices now takes numerical `adjust_brightness` interpreted as quantile
+* `47a8db0a (origin/master, origin/HEAD)` [_`dipterix`_]: Changed default color palette for discrete values, removed colors that are too dark or gray
+* `c345aa3a` [_`dipterix`_]: Change `CT` threshold back to positive (3000) when switching from `DBS` leads back to `sEEG` leads.
 * `69a3853c` [_`dipterix`_]: Support drag and drop annot files
 * `ac572325` [_`dipterix`_]: Changed electrode material to display front-side only instead of double side to avoid overlapping contacts visually when spacing is small
 * `189fc172` [_`dipterix`_]: Added `Abbott` segmented electrodes 6170-6173, with segmented electrodes clockwise viewing from proximal end

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
 Title: Your Advanced 3D Brain Visualization
-Version: 1.1.1.9011
+Version: 1.1.1.9012
 Authors@R: c(
     person("Zhengjia", "Wang", email = "dipterix.wang@gmail.com", role = c("aut", "cre", "cph")),
     person("John", "Magnotti", email = "John.Magnotti@Pennmedicine.upenn.edu", role = c("ctb", "res")),

diff --git a/R/class_brain.R b/R/class_brain.R
@@ -975,8 +975,11 @@ Brain2 <- R6::R6Class(
       if(is.na(adjust_brightness)) {
         adjust_brightness <- TRUE
       }
-      if( adjust_brightness ) {
-        qt <- quantile(volume$data, c(0, 0.95), na.rm = TRUE)
+      if( isTRUE(adjust_brightness) || isTRUE(adjust_brightness > 0 && adjust_brightness < 1) ) {
+        if(isTRUE(adjust_brightness)) {
+          adjust_brightness <- 0.95
+        }
+        qt <- quantile(volume$data, c(0, adjust_brightness), na.rm = TRUE)
         volume$data[] <- (volume$data - qt[[1]]) / (qt[[2]] - qt[[1]]) * 255
         volume$data[volume$data > 255] <- 255
       }