Added neuropil meshes

R/data.R

@@ -13,10 +13,27 @@
 #' }
 "banc.surf"
 
-# How it was obtained:
+#' @export
+#' @rdname banc.surf
+"banc_neuropil.surf"
+
+#' @export
+#' @rdname banc.surf
+"banc_brain_neuropil.surf"
+
+#' @export
+#' @rdname banc.surf
+"banc_vnc_neuropil.surf"
+
+#' @export
+#' @rdname banc.surf
+"banc_neck_connective.surf"
+
+## How it was obtained:
 # res <- httr::GET("https://www.googleapis.com/storage/v1/b/zetta_lee_fly_cns_001_kisuk/o/final%2Fv2%2Fvolume_meshes%2Fmeshes%2F1%3A0.drc?alt=media&neuroglancer=610000b05b6497edcf20b78f29516970")
 # httr::stop_for_status(res)
 # bytes <- httr::content(res, as = "raw")
-# banc.mesh <- decode_neuroglancer_mesh(bytes)
+# banc.mesh <- malevnc:::decode_neuroglancer_mesh(bytes)
 # banc.surf <- as.hxsurf(banc.mesh)
+# banc.surf$Vertices[,"Z"] <- banc.surf$Vertices[,"Z"]*0.9462 # scaling Jasper worked out
 # save(banc.surf, file="data/BANC.surf.rda")

R/meshes.R

@@ -72,7 +72,7 @@ banc_decapitate <- function(x, invert = FALSE, reference = "BANC"){
     v3 <- nat.templatebrains::xform_brain(v3, sample = "BANC", reference = reference)
     y.cut <- v1[,2]
   }
-  ismesh <- any(class(x[[1]]), class(x)) %in% "mesh3d"
+  ismesh <- any( c(class(x[[1]]), class(x)) %in% "mesh3d")
   if(!ismesh & any(class(x)%in%c("neuron","neuronlist","mesh3d"))){
     if (invert){
       z <- subset(x,x$y<y.cut)

R/synapses.R

@@ -8,7 +8,7 @@
 #' @param overwrite Logical, whether or not to overwrite an extant \code{banc_data.sqlite} file.
 #' @param n_max Numeric, the maximum number of rows ot read from \code{path} if you just want to see
 #' a taster of the file.
-#' @param Logical Whether or not to read all data columns in the target synapse \code{.csv}. Defaults to
+#' @param details Logical Whether or not to read all data columns in the target synapse \code{.csv}. Defaults to
 #' \code{FALSE} in order to read only the essential presynapse position data.
 #'
 #' @return a data.frame
@@ -20,10 +20,13 @@
 #' \dontrun{
 #' syns <- banc_all_synapses()
 #' }
+#' Helpful scene: https://spelunker.cave-explorer.org/#!middleauth+https://global.daf-apis.com/nglstate/api/v1/4753860997414912
 banc_all_synapses <- function(path = "gs://zetta_lee_fly_cns_001_synapse/240623_run/assignment/final_edgelist.df",
                               overwrite = FALSE,
                               n_max = 2000,
-                              details = FALSE){
+                              details = FALSE,
+                              min_size = 10,
+                              rawcoords = FALSE){
 
   # Correct path to de-authenticate it, use https
   path <- gsub("^gs\\:\\/","https://storage.googleapis.com",path)
@@ -63,8 +66,8 @@ banc_all_synapses <- function(path = "gs://zetta_lee_fly_cns_001_synapse/240623_
     postsyn_y = readr::col_integer(),
     postsyn_z = readr::col_integer(),
     clefthash = readr::col_number(),
-    partnerhash= readr::col_integer(),
-    size = readr::col_integer()
+    partnerhash = readr::col_integer(),
+    size = readr::col_number()
   )
 
   # Are we just sampling or going for the full thing?
@@ -73,7 +76,7 @@ banc_all_synapses <- function(path = "gs://zetta_lee_fly_cns_001_synapse/240623_
       syns <- readr::read_csv(file=path, col_types = col.types, lazy = TRUE, n_max = n_max)
     }else{
       syns <- readr::read_csv(file=path, col_types = col.types, lazy = TRUE, n_max = n_max,
-                              select = c(presyn_segid, presyn_x, presyn_y, presyn_z, size))
+                              col_select = c(presyn_segid, presyn_x, presyn_y, presyn_z, size))
     }
     return(syns)
   }else if (!table_exists|overwrite){
@@ -82,23 +85,30 @@ banc_all_synapses <- function(path = "gs://zetta_lee_fly_cns_001_synapse/240623_
       syns <- readr::read_csv(file=path, col_types = col.types, lazy = TRUE)
     }else{
       syns <- readr::read_csv(file=path, col_types = col.types, lazy = TRUE,
-                              select = c(presyn_segid, presyn_x, presyn_y, presyn_z, size))
+                              col_select = c(presyn_segid, presyn_x, presyn_y, presyn_z, size))
     }
 
-    # Process
+    # # Process
+    # if(!is.null(min_size)){
+    #   syns <- syns %>%
+    #     dplyr::filter(size>=min_size)
+    # }
+    # if(!rawcoords){
+    #   syns[,c("presyn_x", "presyn_y", "presyn_z")] <- bancr::banc_raw2nm(syns[,c("presyn_x", "presyn_y", "presyn_z")])
+    # }
 
     # Connect to the SQLite database
     con <- DBI::dbConnect(RSQLite::SQLite(), file_path)
 
     # Write the data frame to the 'synapses' table
     # If the table already exists, it will be overwritten
-    DBI::dbWriteTable(con, "synapses", df, overwrite = TRUE)
+    DBI::dbWriteTable(con, "synapses", syns, overwrite = TRUE)
     DBI::dbDisconnect(con)
     message("Added tab synapses, no. rows: ", nrow(syns))
   }
 
   # Read
-  DBI::dbReadTable(con, "synapses")
+  dplyr::tbl(src = con, from = "synapses")
 
 }
 

R/xform.R

@@ -1,33 +1,77 @@
-
-# for nm
+#' Set Default View for BANC EM Dataset
+#'
+#' @description
+#' This function sets a default view for visualizing the 'BANC' Electron Microscopy (EM) dataset
+#' using the rgl package. It adjusts the viewpoint to a specific orientation and zoom level
+#' that is optimal for viewing this particular dataset.
+#'
+#' @details
+#' The function uses `rgl::rgl.viewpoint()` to set a predefined user matrix and zoom level.
+#' This matrix defines the rotation and translation of the view, while the zoom parameter
+#' adjusts the scale of the visualization.
+#'
+#' @return
+#' This function is called for its side effect of changing the rgl viewpoint.
+#' It does not return a value.
+#'
+#' @examples
+#' \dontrun{
+#' # Assuming you have already plotted your BANC EM data
+#' banc_view()
+#' }
+#'
+#' @note
+#' This function assumes that an rgl device is already open and that the BANC EM dataset
+#' has been plotted. It will not create a new plot or open a new rgl device.
+#'
+#' @seealso
+#' \code{\link[rgl]{rgl.viewpoint}} for more details on setting viewpoints in rgl.
+#'
+#' @export
 banc_view <- function(){
-  rgl::rgl.viewpoint(userMatrix = structure(c(0.961547076702118, 0.037275392562151,
-                                0.27209860086441, 0, 0.0369537360966206, -0.999296963214874,
-                                0.00630810856819153, 0, 0.272142440080643, 0.00398948788642883,
-                                -0.962248742580414, 0, 0, 0, 0, 1), dim = c(4L, 4L)), zoom = 0.822702646255493)
+  rgl::rgl.viewpoint(userMatrix  = banc_rotation_matrices[["main"]], zoom = 0.82)
 }
 
 # for nm
+#' @export
+#' @rdname banc_view
 banc_side_view <- function(){
-  rgl::rgl.viewpoint(userMatrix = structure(c(0.188666880130768, 0.137750864028931,
-                                -0.972331881523132, 0, 0.130992725491524, -0.98479551076889,
-                                -0.114099271595478, 0, -0.97326534986496, -0.105841755867004,
-                                -0.203842639923096, 0, 0, 0, 0, 1), dim = c(4L, 4L)), zoom = 0.783526360988617)
+  rgl::rgl.viewpoint(userMatrix = banc_rotation_matrices[["side"]], zoom = 0.29)
 }
 
 # for nm
+#' @export
+#' @rdname banc_view
 banc_front_view <- function(){
-  rgl::rgl.viewpoint(userMatrix = structure(c(0.99931389093399, 0.0139970388263464,
-                                -0.0342894680798054, 0, -0.0321401171386242, -0.132316529750824,
-                                -0.990686297416687, 0, -0.0184037387371063, 0.991108655929565,
-                                -0.131775915622711, 0, 0, 0, 0, 1), dim = c(4L, 4L)), zoom = 0.613913536071777)
+  rgl::rgl.viewpoint(userMatrix = banc_rotation_matrices[["front"]], zoom = 0.62)
 }
 
 # for nm
+#' @export
+#' @rdname banc_view
 banc_vnc_view <- function(){
-  rgl::rgl.viewpoint(userMatrix = structure(c(0.992902159690857, 0.113465532660484,
-                                0.0356490463018417, 0, 0.103959240019321, -0.973584711551666,
-                                0.203286483883858, 0, 0.0577733889222145, -0.198137611150742,
-                                -0.978470027446747, 0, 33598.359375, 191755.796875, -6508.533203125,
-                                1), dim = c(4L, 4L)), zoom = 0.505068242549896)
+  rgl::rgl.viewpoint(userMatrix = banc_rotation_matrices[["vnc"]], zoom = 0.51)
 }
+
+# hidden
+banc_rotation_matrices <- list(
+  main = structure(c(0.961547076702118, 0.037275392562151,
+                                  0.27209860086441, 0, 0.0369537360966206, -0.999296963214874,
+                                  0.00630810856819153, 0, 0.272142440080643, 0.00398948788642883,
+                                  -0.962248742580414, 0, 0, 0, 0, 1), dim = c(4L, 4L)),
+  side = structure(c(0.188666880130768, 0.137750864028931,
+                     -0.972331881523132, 0, 0.130992725491524, -0.98479551076889,
+                     -0.114099271595478, 0, -0.97326534986496, -0.105841755867004,
+                     -0.203842639923096, 0, 0, 0, 0, 1), dim = c(4L, 4L)),
+  front = structure(c(0.99931389093399, 0.0139970388263464,
+                      -0.0342894680798054, 0, -0.0321401171386242, -0.132316529750824,
+                      -0.990686297416687, 0, -0.0184037387371063, 0.991108655929565,
+                      -0.131775915622711, 0, 0, 0, 0, 1), dim = c(4L, 4L)),
+  vnc = structure(c(0.159858450293541, -0.951453745365143,
+                                 0.263022243976593, 0, -0.95634800195694, -0.0832427442073822,
+                                 0.280123054981232, 0, -0.244629606604576, -0.296320915222168,
+                                 -0.923228204250336, 0, 169877.109375, 8134.845703125, -597.831604003906,
+                                 1), dim = c(4L, 4L)))
+
+
+