added news; cran-comments; allowed plot_slices to be additive

dipterix · Feb 6, 2024 · fe5f2c8 · fe5f2c8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
 Title: 3D Brain Visualization
-Version: 1.0.1.9108
+Version: 1.0.1.9109
 Authors@R: c(
     person("Zhengjia", "Wang", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("John", "Magnotti", email = "[email protected]", role = c("aut", "res")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,46 @@
+threeBrain 1.0.2
+=======
+
+* Removed a `shader` loop that accidentally used dynamic variable for looping, which may crash on `Windows` in certain situations
+* Updated `README.md`
+* Composer effects are removed
+* Added default color to electrodes (JavaScript) to fix the localization electrode color not set correctly issues
+* Added `z-index` base to the side canvas layer (`div`)
+* Removed additional unused parameters from material call
+* Used new material type to make brain more realistic
+* New background color is implemented
+* `Trackball` uses width instead of height of the viewer as the `Arcball` radius; mouse positions is calculated whenever mouse-down event is triggered (allowing more accurate track-ball calculation in `Shiny` applications)
+* Made `col2hexstr` internal function
+* Added a new electrode visibility mode, allowing to show contacts with no values but passing the threshold
+* Added `brain$electrodes$fix_electrode_color` to fix the electrode colors under given data names (to display `DBS` electrodes, for example)
+* Made `controller.load` more robust against errors
+* Fixed the depth issue in `TextSprite`
+* Some default controller values have changed to make more sense
+* Outline render effect is removed; electrode outlines are implemented directly in the `shader`
+* Updated `three.js` to `v160` with light model improved
+* Added `rave_slices.nii` to allowed `MRI` prefix in `FreeSurfer` folder with highest priority, such that this image will be treated as default volume to load in side canvas (default is still `brain.finalsurfs.mgz`)
+* Allow `MRI` to change brightness dynamically in viewer
+* Ensure that `voxels` index from zeros
+* Added `brain$get_atlas_labels` to guess the atlas labels from given masks or atlas files
+* Allowed to spatially transform electrodes to desired coordinate system
+* Updated citation
+* The standalone viewer does not require static server anymore: everything is self-contained (require `pandoc`, which comes with `RStudio`)
+* Changed mechanism on animation color map generator (so the color is more accurate for discrete variables)
+* Added `png` to dependence
+* Added support for `AC-PC` alignment, available in `RAVE` - `YAEL` module
+* Allow `brain` to plot with additional customized geometries
+* Added `plot_slides` to plot `MRI` centered at each electrode contact for slide-to-slide visualization
+* Added Line-of-Sight view mode for side canvas; can be enabled using shortcut `m` (previous shortcut to change the material type is changed to `shift+M`)
+* Fixed `CT` in `JavaScript` when the `sform` and `qform` are different (have different code)
+* Allowed to specify the spacing for interpolation and extrapolation for unequally spaced electrodes
+* Added electrode outlines
+* `YAEL` paper is finally out
+* Fixed incorrect sub-cortical labels
+* Deprecated old format (no cache is needed anymore)
+* Made electrodes opaque on main but transparent in side canvas
+* Let controllers check if the variable is valid before set to avoid invalid viewer state during initialization
+* Added `get_ijk2ras` to get `Norig` and `Torig` matrix
+
 threeBrain 1.0.1
 =======
 

diff --git a/R/class_brain.R b/R/class_brain.R
@@ -893,7 +893,8 @@ Brain2 <- R6::R6Class(
     plot_electrodes_on_slices = function(
       electrodes_to_plot = "all", volume = NULL, elec_table = NULL,
       zoom = 1, adjust_brightness = NA,
-      electrode_color = "green", electrode_size = 2, ...,
+      electrode_color = "green", electrode_size = 2,
+      verbose = TRUE, ...,
       decoration = function(i, j) {
         graphics::points(0, 0, pch = 20, col = electrode_color,
                          cex = electrode_size)
@@ -981,7 +982,7 @@ Brain2 <- R6::R6Class(
       }
       progress <- dipsaus::progress2("Plotting slices",
                                      max = length(plot_idx) + 1,
-                                     shiny_auto_close = TRUE)
+                                     shiny_auto_close = TRUE, quiet = !verbose)
       for(ii in plot_idx) {
         progress$inc(detail = sprintf("Generating graphs for electrode %s", dipsaus::deparse_svec(ii)))
         plot_slices(

diff --git a/R/plot_volume-slices.R b/R/plot_volume-slices.R
@@ -18,14 +18,17 @@
 #' @param zlim image plot value range, default is identical to \code{normalize}
 #' @param main image titles
 #' @param title_position title position; choices are \code{"left"} or \code{"top"}
+#' @param which which plane to plot; default is \code{NULL}, which will trigger
+#' new plots and add titles; set to \code{1} for 'Axial' plane, \code{2} for
+#' 'Sagittal', and \code{3} for 'Coronal'.
 #' @param ... additional arguments passing into \code{\link[graphics]{image}}
 #' @returns Nothing
 #' @export
 plot_slices <- function(
     volume, transform = NULL, positions = NULL, zoom = 1, pixel_width = 0.5,
     col = c("black", "white"), normalize = NULL, zclip = NULL,
     zlim = normalize, main = "", title_position = c("left", "top"),
-    fun = NULL, nc = NA, ...) {
+    fun = NULL, nc = NA, which = NULL, ...) {
   # DIPSAUS DEBUG START
   # volume <- "~/rave_data/raw_dir/YAB/rave-imaging/fs/mri/brain.finalsurfs.mgz"
   # list2env(list(transform = NULL, positions = NULL, zoom = 1, pixel_width = 0.5,
@@ -112,7 +115,7 @@ plot_slices <- function(
   more_args$main <- ''
   more_args$x <- x
   more_args$y <- x
-  more_args$add <- FALSE
+  # more_args$add <- FALSE
 
   oldpar <- graphics::par(no.readonly = TRUE)
 
@@ -123,39 +126,42 @@ plot_slices <- function(
   }
   nc <- min(max(round(nc), 1), npts)
   nr <- ceiling(npts / nc)
-  if( title_position == "left") {
-    lmat <- matrix(seq_len(nr * nc), ncol = nc, byrow = FALSE)
-    lmat <- t(apply(lmat, 1, function(l) {
-      l <- (l - 1) * 4
-      as.vector(rbind(l + 1, l + 2, l + 3, l + 4))
-    }))
-    dim(lmat) <- c(nr, nc * 4)
-    graphics::layout(
-      lmat,
-      widths = rep(c(graphics::lcm(0.8), 1, 1, 1), times = nc)
-    )
-  } else {
-    lmat <- matrix(seq_len(nr * nc), ncol = nc, byrow = TRUE)
-    lmat <- apply(lmat, 2, function(l) {
-      l <- (l - 1) * 4
-      c(rep(l + 1, each = 3), t(outer(l, c(2,3,4), FUN = "+")))
-    })
-    dim(lmat) <- c(nr * 3, nc * 2)
-    lmat <- t(lmat)
-    graphics::layout(
-      lmat,
-      heights = rep(c(graphics::lcm(0.8), 1), times = nc)
+  if(!length(which)) {
+    if( title_position == "left") {
+      lmat <- matrix(seq_len(nr * nc), ncol = nc, byrow = FALSE)
+      lmat <- t(apply(lmat, 1, function(l) {
+        l <- (l - 1) * 4
+        as.vector(rbind(l + 1, l + 2, l + 3, l + 4))
+      }))
+      dim(lmat) <- c(nr, nc * 4)
+      graphics::layout(
+        lmat,
+        widths = rep(c(graphics::lcm(0.8), 1, 1, 1), times = nc)
+      )
+    } else {
+      lmat <- matrix(seq_len(nr * nc), ncol = nc, byrow = TRUE)
+      lmat <- apply(lmat, 2, function(l) {
+        l <- (l - 1) * 4
+        c(rep(l + 1, each = 3), t(outer(l, c(2,3,4), FUN = "+")))
+      })
+      dim(lmat) <- c(nr * 3, nc * 2)
+      lmat <- t(lmat)
+      graphics::layout(
+        lmat,
+        heights = rep(c(graphics::lcm(0.8), 1), times = nc)
+      )
+    }
+
+    graphics::par(
+      bg = pal[[1]],
+      fg = pal[[length(pal)]],
+      col.main = pal[[length(pal)]],
+      col.axis = pal[[1]],
+      mar = c(0,0,0,0)
     )
+    on.exit({ do.call(graphics::par, oldpar) })
   }
 
-  graphics::par(
-    bg = pal[[1]],
-    fg = pal[[length(pal)]],
-    col.main = pal[[length(pal)]],
-    col.axis = pal[[1]],
-    mar = c(0,0,0,0)
-  )
-  on.exit({ do.call(graphics::par, oldpar) })
 
   # Calculate plt
   pin <- graphics::par("din")
@@ -188,58 +194,69 @@ plot_slices <- function(
   }
 
   lapply(seq_len(npts), function(ii) {
+
     pos_pt <- c(positions[ii, ], 0)
 
     adjust_plt(reset = TRUE)
-    graphics::plot.new()
-    if(title_position == "top") {
-      graphics::mtext(side = 1, line = -1, text = main[[ii]], las = 0)
-    } else {
-      graphics::mtext(side = 4, line = -1.5, text = main[[ii]], las = 0)
+
+    if(!length(which)) {
+      graphics::plot.new()
+      if(title_position == "top") {
+        graphics::mtext(side = 1, line = -1, text = main[[ii]], las = 0)
+      } else {
+        graphics::mtext(side = 4, line = -1.5, text = main[[ii]], las = 0)
+      }
     }
 
-    # Axial
-    # translate x transform_inv x translate^-1 x Norig
-    IJK <- round(world2ijk[c(1, 2, 3), ] %*% (transform_inv %*% pos + pos_pt)) + 1L
-    sel <- IJK[1,] > shape[[1]] | IJK[2,] > shape[[2]] | IJK[3,] > shape[[3]]
-    IJK[,sel] <- NA
-    IJK[IJK < 1] <- NA
-    idx <- t(IJK - 1) %*% cumshape + 1
-    slice <- nu(volume$data[idx])
-
-    dim(slice) <- c(nx, nx)
-    more_args$z <- slice
-    adjust_plt()
-    do.call(graphics::image, more_args)
-    panel_last( ii, 1 )
-
-    # Sagittal
-    IJK <- round(world2ijk[c(1, 2, 3), ] %*% (pos[c(3,1,2,4), , drop = FALSE] + pos_pt)) + 1L
-    sel <- IJK[1,] > shape[[1]] | IJK[2,] > shape[[2]] | IJK[3,] > shape[[3]]
-    IJK[,sel] <- NA
-    IJK[IJK < 1] <- NA
-    idx <- t(IJK - 1) %*% cumshape + 1
-    slice <- nu(volume$data[idx])
-
-    dim(slice) <- c(nx, nx)
-    more_args$z <- slice
-    adjust_plt()
-    do.call(graphics::image, more_args)
-    panel_last( ii, 2 )
-
-    # Coronal
-    IJK <- round(world2ijk[c(1, 2, 3), ] %*% (pos[c(1,3,2,4), , drop = FALSE] + pos_pt)) + 1L
-    sel <- IJK[1,] > shape[[1]] | IJK[2,] > shape[[2]] | IJK[3,] > shape[[3]]
-    IJK[,sel] <- NA
-    IJK[IJK < 1] <- NA
-    idx <- t(IJK - 1) %*% cumshape + 1
-    slice <- nu(volume$data[idx])
-
-    dim(slice) <- c(nx, nx)
-    more_args$z <- slice
-    adjust_plt()
-    do.call(graphics::image, more_args)
-    panel_last( ii, 3 )
+    if(!length(which) || 1 %in% which) {
+      # Axial
+      # translate x transform_inv x translate^-1 x Norig
+      IJK <- round(world2ijk[c(1, 2, 3), ] %*% (transform_inv %*% pos + pos_pt)) + 1L
+      sel <- IJK[1,] > shape[[1]] | IJK[2,] > shape[[2]] | IJK[3,] > shape[[3]]
+      IJK[,sel] <- NA
+      IJK[IJK < 1] <- NA
+      idx <- t(IJK - 1) %*% cumshape + 1
+      slice <- nu(volume$data[idx])
+
+      dim(slice) <- c(nx, nx)
+      more_args$z <- slice
+      adjust_plt()
+      do.call(graphics::image, more_args)
+      panel_last( ii, 1 )
+    }
+
+
+    if(!length(which) || 2 %in% which) {
+      # Sagittal
+      IJK <- round(world2ijk[c(1, 2, 3), ] %*% (pos[c(3,1,2,4), , drop = FALSE] + pos_pt)) + 1L
+      sel <- IJK[1,] > shape[[1]] | IJK[2,] > shape[[2]] | IJK[3,] > shape[[3]]
+      IJK[,sel] <- NA
+      IJK[IJK < 1] <- NA
+      idx <- t(IJK - 1) %*% cumshape + 1
+      slice <- nu(volume$data[idx])
+
+      dim(slice) <- c(nx, nx)
+      more_args$z <- slice
+      adjust_plt()
+      do.call(graphics::image, more_args)
+      panel_last( ii, 2 )
+    }
+
+    if(!length(which) || 3 %in% which) {
+      # Coronal
+      IJK <- round(world2ijk[c(1, 2, 3), ] %*% (pos[c(1,3,2,4), , drop = FALSE] + pos_pt)) + 1L
+      sel <- IJK[1,] > shape[[1]] | IJK[2,] > shape[[2]] | IJK[3,] > shape[[3]]
+      IJK[,sel] <- NA
+      IJK[IJK < 1] <- NA
+      idx <- t(IJK - 1) %*% cumshape + 1
+      slice <- nu(volume$data[idx])
+
+      dim(slice) <- c(nx, nx)
+      more_args$z <- slice
+      adjust_plt()
+      do.call(graphics::image, more_args)
+      panel_last( ii, 3 )
+    }
 
     NULL
   })

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,9 +1,22 @@
 # Update logs (for R-cran only)
 
-## 2023-07-03
-**Version 1.0.1 (current)**
+## 2024-02-06
+**Version 1.0.2 (current)**
+
+Self check: 0 errors | 0 warnings | 1 note
+
+```
+❯ checking installed package size ... NOTE
+    installed size is  5.4Mb
+    sub-directories of 1Mb or more:
+      R              2.0Mb
+      threeBrainJS   1.8Mb
+```
 
-Self check: 0 errors | 0 warnings | 0 notes
+I (tried, but) can't reduce the size anymore from `JavaScript` engine and package functions.
+
+## 2023-07-03
+**Version 1.0.1 (passed)**
 
 ## 2023-06-03
 **Version 1.0.0 (passed)**
@@ -23,13 +36,6 @@ Self check: 0 errors | 0 warnings | 0 notes
 ## 2021-12-02
 **Version 0.2.4 (passed)**
 
-Starting from this version, the package size will be greater than `5Mb`, which will trigger the check note. However, I can't reduce the size since most are from the `JavaScript` engine.
-
-```
-checking installed package size ... NOTE
-  installed size is  5.3Mb
-```
-
 ## 2021-10-13
 **Version 0.2.3 (passed)**
 

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,11 +1,13 @@
 AFNI
 AbstractGeom
+Affine
 BRIK
 CMD
 CRS
 DICOM
 DOI
 ECoG
+Eneuro
 FREESURFER
 FreeSurfer
 GeomGroup
@@ -15,6 +17,7 @@ JS
 JSON
 Localizer
 MNI
+MPL
 NIFTI
 NeuroImage
 Nifti
@@ -28,6 +31,7 @@ Threejs
 UI
 WebGL
 XYZ
+YAEL
 asc
 autorecon
 commissure
@@ -52,6 +56,7 @@ neuroimage
 nibabel
 nii
 npx
+parcellation
 pial
 px
 readgii

diff --git a/man/plot_slices.Rd b/man/plot_slices.Rd