Allow masks to be added to T1; Added D99v2 for monkey brain; Adde…

…d demo code; Export `GLTF` for `datacube2`

CHANGELOG.md

@@ -1,6 +1,7 @@
 ## Changes since last CRAN release
-* `f2170170 (HEAD -> master)` [_`dipterix`_]: Fixed `fix_electrode_color` bug
-* `62567274 (origin/master, origin/HEAD)` [_`dipterix`_]: Supported `ISO` surface generation from voxels
+* `a4f02e0e (HEAD -> master)` [_`dipterix`_]: Allow masks to be added to `T1`; Added `D99v2` for monkey brain; Added demo code; Export `GLTF` for `datacube2`
+* `9268886f (origin/master, origin/HEAD)` [_`dipterix`_]: Fixed `fix_electrode_color` bug
+* `62567274` [_`dipterix`_]: Supported `ISO` surface generation from voxels
 * `a6295c2c` [_`dipterix`_]: Added white-matter segmentation as default atlas if user has this file
 * `cd8e15e8` [_`dipterix`_]: Exporting `GLTF` is wrapped with try-catch
 * `963859ed` [_`dipterix`_]: `fix_electrode_color` is exclusive by default; fixed color fixing issue for naive sphere electrodes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: threeBrain
 Type: Package
 Title: Your Advanced 3D Brain Visualization
-Version: 1.1.0.9020
+Version: 1.1.0.9021
 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("aut", "res")),

R/geom_datacube.R

@@ -120,25 +120,38 @@ VolumeGeom <- R6::R6Class(
     color_format = "RedFormat",
     color_map = NULL,
     initialize = function(
-    name, path, group = GeomGroup$new(name = 'default'), layer = 13,
-    color_format = c("RedFormat", "RGBAFormat"), ...){
+      name, path, mask = NULL,
+      group = GeomGroup$new(name = 'default'), layer = 13,
+      color_format = c("RedFormat", "RGBAFormat"), ...){
 
       color_format <- match.arg(color_format)
       abspath <- normalizePath(path, mustWork = TRUE)
       super$initialize(name, position = c(0, 0, 0), layer = layer, ...)
       self$group <- group
 
-      re <- list(
+      volume_data <- list(
         path = path,
         absolute_path = abspath,
         file_name = filename(abspath),
         is_nifti = TRUE,
         is_new_cache = FALSE,
         is_cache = TRUE
       )
-      group$set_group_data("volume_data", value = re, is_cached = TRUE)
+      group$set_group_data("volume_data", value = volume_data, is_cached = TRUE)
       self$color_format <- color_format
 
+      if(length(mask) == 1 && !is.na(mask) && file.exists(mask)) {
+        volume_mask <- list(
+          path = mask,
+          absolute_path = normalizePath(mask, mustWork = TRUE),
+          file_name = filename(mask),
+          is_nifti = TRUE,
+          is_new_cache = FALSE,
+          is_cache = TRUE
+        )
+        group$set_group_data("volume_mask", value = volume_mask, is_cached = TRUE)
+      }
+
     },
 
     to_list = function(){

R/threeBrain.R

@@ -184,6 +184,9 @@ threeBrain <- function(
     "brain.finalsurfs", "synthSR.norm", "synthSR", "brain",
     "brainmask", "brainmask.auto", "T1"
   )
+  allowed_mri_mask_prefix <- c(
+    "brainmask", "brainmask.auto"
+  )
 
   path_mri <- file.path(fs_path, "mri", as.vector(rbind(
     sprintf("%s.nii.gz", allowed_mri_prefix),
@@ -192,6 +195,7 @@ threeBrain <- function(
   )))
   path_mri <- path_mri[file.exists(path_mri)]
   if(length(path_mri)){ path_mri <- path_mri[[1]] }
+
   path_fsmri <- file.path(fs_path, "mri", as.vector(rbind(
     sprintf("%s.nii.gz", allowed_fsmri_prefix),
     sprintf("%s.nii", allowed_fsmri_prefix),
@@ -200,6 +204,14 @@ threeBrain <- function(
   path_fsmri <- path_fsmri[file.exists(path_fsmri)]
   if(length(path_fsmri)){ path_fsmri <- path_fsmri[[1]] }
 
+  path_mask <- file.path(fs_path, "mri", as.vector(rbind(
+    sprintf("%s.nii.gz", allowed_mri_mask_prefix),
+    sprintf("%s.nii", allowed_mri_mask_prefix),
+    sprintf("%s.mgz", allowed_mri_mask_prefix)
+  )))
+  path_mask <- path_mask[file.exists(path_mask)]
+  if(length(path_mask)){ path_mask <- path_mask[[1]] }
+
   # xfm
   path_xfm <- file.path(fs_path, "mri", "transforms", "talairach.xfm")
 
@@ -309,6 +321,7 @@ threeBrain <- function(
       volume = VolumeGeom$new(
         name = sprintf('T1 (%s)', subject_code),
         path = normalizePath(path_mri, winslash = "/"),
+        mask = normalizePath(path_mask, winslash = "/"),
 
         # JS engine requires a group
         group = group

adhoc/demo_stage.R

@@ -0,0 +1,31 @@
+# script to generate demo stages
+
+# run in console:
+'
+JSON.stringify(app.controllerGUI.controllersRecursive().map(c => {
+  return({name: c._name, value: c.getValue()})
+}))
+'
+
+
+json <- '[{"name":"Background Color","value":"#faf7f4"},{"name":"Camera Position","value":"[free rotate]"},{"name":"Display Coordinates","value":false},{"name":"Record","value":false},{"name":"Screenshot"},{"name":"Download GLTF"},{"name":"Reset Canvas"},{"name":"Copy Controller State"},{"name":"Paste to Set State","value":""},{"name":"QR Code"},{"name":"Show Panels","value":false},{"name":"Slice Brightness","value":0},{"name":"Slice Contrast","value":0},{"name":"Slice Mode","value":"canonical"},{"name":"Crosshair Gap","value":0},{"name":"Reset Slice Canvas"},{"name":"Coronal (P - A)","value":0},{"name":"Axial (I - S)","value":0},{"name":"Sagittal (L - R)","value":0},{"name":"Intersect MNI305","value":"-1.4, -18.5, 17.7"},{"name":"Overlay Coronal","value":true},{"name":"Overlay Axial","value":true},{"name":"Overlay Sagittal","value":true},{"name":"Frustum Near","value":5},{"name":"Frustum Far","value":10},{"name":"Voxel Type","value":"none"},{"name":"Voxel Display","value":"anat. slices"},{"name":"Voxel Opacity","value":1},{"name":"Voxel Min","value":-100000},{"name":"Voxel Max","value":100000},{"name":"Voxel Label","value":"1035,3035,1034,3034,1001,1030,3030,2015,2009"},{"name":"ISO Surface","value":false},{"name":"Update ISO Surface"},{"name":"Surface Material","value":"MeshPhysicalMaterial"},{"name":"Surface Type","value":"pial"},{"name":"Clipping Plane","value":"disabled"},{"name":"Left Hemisphere","value":"mesh clipping x 0.3"},{"name":"Right Hemisphere","value":"mesh clipping x 0.3"},{"name":"Left Opacity","value":0.39999999999999997},{"name":"Right Opacity","value":0.39999999999999997},{"name":"Left Mesh Clipping","value":0.20000000000000004},{"name":"Right Mesh Clipping","value":0.20000000000000004},{"name":"Surface Color","value":"none"},{"name":"Blend Factor","value":1},{"name":"Sigma","value":1},{"name":"Decay","value":0.6},{"name":"Range Limit","value":5},{"name":"Subject","value":"cvs_avg35_inMNI152"},{"name":"Map Electrodes","value":true},{"name":"Surface Mapping","value":"sphere.reg"},{"name":"Volume Mapping","value":"mni305"},{"name":"Visibility","value":"all visible"},{"name":"Electrode Shape","value":"prototype+sphere"},{"name":"Outlines","value":"auto"},{"name":"Translucent","value":"contact+outline"},{"name":"Text Scale","value":1.5},{"name":"Text Visibility","value":false},{"name":"Dragdrop Uploader"},{"name":"Clear Uploaded Surfaces"},{"name":"Visibility (all surfaces)","value":"visible"},{"name":"Opacity (all surfaces)","value":1},{"name":"Clear Uploaded Volumes"},{"name":"Visibility (all volumes)","value":"visible"},{"name":"Opacity (all volumes)","value":1},{"name":"Display Data","value":"LabelPrefix"},{"name":"Display Range","value":""},{"name":"Threshold Data","value":"[None]"},{"name":"Threshold Range","value":""},{"name":"Threshold Method","value":"|v| >= T1"},{"name":"Additional Data","value":"[None]"},{"name":"Inactive Color","value":"#c2c2c2"},{"name":"Play/Pause","value":false},{"name":"Speed","value":0.5},{"name":"Time","value":0},{"name":"Video Mode","value":"muted"},{"name":"Show Legend","value":false},{"name":"Show Time","value":false},{"name":"Highlight Box","value":false},{"name":"Info Text","value":false}]'
+
+ignore_names <- c("Time", "Play/Pause", "Speed", "Subject", "Surface Mapping",
+                  "Volume Mapping", "Surface Material", "Intersect MNI305",
+                  "Camera Position", "Record", "Paste to Set State", "Background Color",
+                  "Map Electrodes", "Video Mode")
+on_completion_names <- c(
+  # "Overlay Coronal", "Overlay Axial", "Overlay Sagittal"
+)
+data <- jsonlite::fromJSON(txt = json, flatten = FALSE, simplifyDataFrame = FALSE)
+data <- data[ vapply(data, function(item) { length(item$value) && !is.na(item$value) && !item$name %in% ignore_names }, FALSE) ]
+is_transition <- sapply(data, function(item) { is.numeric(item$value) || startsWith(as.character(item$value), "#")})
+is_post_completion <- sapply(data, function(item) { item$name %in% on_completion_names })
+
+s <- jsonlite::toJSON(list(
+  immediate = data[!is_transition & !is_post_completion],
+  transition = data[is_transition & !is_post_completion],
+  onCompletion = data[is_post_completion]
+), auto_unbox = TRUE, pretty = FALSE)
+
+clipr::write_clip(s)