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| #------------------ Librairies ------------------ | |
| library(rjson) | |
| #------------------ Ontology handling ------------------ | |
| get.id.from.acronym <- function(acronym){ | |
| rec.func <- function(acronym, json){ | |
| if(is.null(json)) | |
| return() | |
| if(acronym == json$acronym) | |
| return(json$id) | |
| return(unlist(lapply(json$children, function(x){return(rec.func(acronym, x))}))) | |
| } | |
| #Loading json data | |
| json_data <- fromJSON(file= paste(path.matrices,'ontology.json',sep='/')) | |
| json <- json_data$msg[[1]] | |
| return(rec.func(acronym, json)) | |
| } | |
| #------------------ 3D handling ------------------ | |
| mesh3d.allen.annot.from.id <- function(id, max.nrows = 349696, bregma = c(5200, 650, 5700)/1000, no.normals = F){ #5400, 650, 5700 In mm, AP/DV/ML | |
| fpath <- sprintf('%s/%d.obj', allen.annot.path, id) | |
| vert.start <- 0 | |
| vert.end <- 0 | |
| norm.start <- 0 | |
| norm.end <- 0 | |
| face.start <- 0 | |
| face.end <- 0 | |
| i <- 0 | |
| con <- file(fpath, 'r') | |
| while(TRUE){ | |
| i <- i + 1 | |
| line = readLines(con, n = 1) | |
| if (length(line) == 0) | |
| break | |
| if(startsWith(line, 'v ') & vert.start == 0) | |
| vert.start <- i | |
| if(vert.start != 0 & vert.end == 0 & !startsWith(line, 'v ')) | |
| vert.end <- i | |
| if(startsWith(line, 'vn') & norm.start == 0) | |
| norm.start <- i | |
| if(norm.start !=0 & norm.end == 0 & !startsWith(line, 'vn')) | |
| norm.end <- i | |
| if(startsWith(line, 'f') & face.start == 0) | |
| face.start <- i | |
| if(face.start !=0 & face.end == 0 & !startsWith(line, 'f')) | |
| face.end <- i | |
| } | |
| if(face.end == 0) | |
| face.end <- i - 1 | |
| close(con) | |
| con <- file(fpath, 'r') | |
| line = readLines(con, n = (vert.start - 1)) | |
| line = readLines(con, n = vert.end - vert.start) | |
| vertices <- strsplit(line, ' ') | |
| vertices.ul <- unlist(vertices) | |
| df.vertices <- data.frame(x = as.numeric(vertices.ul[seq(from = 2, to = 4*length(vertices), by = 4)]), | |
| y = as.numeric(vertices.ul[seq(from = 3, to = 4*length(vertices), by = 4)]), | |
| z = as.numeric(vertices.ul[seq(from = 4, to = 4*length(vertices), by = 4)])) | |
| close(con) | |
| con <- file(fpath, 'r') | |
| line = readLines(con, n = (norm.start - 1)) | |
| line = readLines(con, n = norm.end - norm.start) | |
| norm <- strsplit(line, ' ') | |
| norm.ul <- unlist(vertices) | |
| df.norm <- data.frame( x = as.numeric(norm.ul[seq(from = 2, to = 4*length(norm), by = 4)]), | |
| y = as.numeric(norm.ul[seq(from = 3, to = 4*length(norm), by = 4)]), | |
| z = as.numeric(norm.ul[seq(from = 4, to = 4*length(norm), by = 4)])) | |
| close(con) | |
| con <- file(fpath, 'r') | |
| line = readLines(con, n = (face.start - 1)) | |
| line = readLines(con, n = face.end - face.start) | |
| face <- strsplit(line, ' ') | |
| face <- lapply(face, function(x){return(unlist(strsplit(x, '//')))}) | |
| face.ul <- unlist(face) | |
| df.face <- data.frame( x = as.numeric(face.ul[seq(from = 2, to = 7*length(face), by = 7)]), | |
| y = as.numeric(face.ul[seq(from = 4, to = 7*length(face), by = 7)]), | |
| z = as.numeric(face.ul[seq(from = 6, to = 7*length(face), by = 7)])) | |
| close(con) | |
| if(!no.normals){ | |
| mesh <- tmesh3d(vertices = rbind(t(df.vertices),1), | |
| indices = t(df.face), | |
| normals = t(df.norm)[c(3,2,1),]) | |
| }else{ | |
| mesh <- tmesh3d(vertices = rbind(t(df.vertices),1), | |
| indices = t(df.face)) | |
| } | |
| mesh$vb[1:3,] <- mesh$vb[1:3,] / 1000 | |
| mesh$vb[1,] <- -mesh$vb[1,] + bregma[1] | |
| mesh$vb[2,] <- -mesh$vb[2,] + 0.05 #Maybe not the +0.05 | |
| mesh$vb[3,] <- -mesh$vb[3,] + bregma[3] | |
| tmp <- mesh$vb[1,] | |
| mesh$vb[1,] <- mesh$vb[3,] | |
| mesh$vb[3,] <- tmp | |
| return(mesh) | |
| } | |
| mesh3d.show.outline <- function(col = 'lightgray', alpha = 0.1){ | |
| shade3d(mesh3d.allen.annot.from.id(get.id.from.acronym('root')), col = col, alpha = alpha) | |
| } | |
| mesh3d.new.window <- function(show.outline = TRUE){ | |
| rgl.open() | |
| rgl.bg(color = 'white') | |
| par3d(windowRect = c(0, 0, 1920, 1080)) | |
| if(show.outline) | |
| mesh3d.show.outline() | |
| } | |