## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=FALSE--------------------------------------------------------------- # library(scimesh) # # sphere <- generate_sphere(c(0, 0, 0), radius = 1.2, # segments = 32, color = c(0.9, 0.3, 0.2, 1.0)) # cam <- camera_auto(sphere, direction = c(1.2, 0.8, 1)) # # # Flat-shaded sphere # img <- render_mesh(sphere$vertices, sphere$triangles, # colors = sphere$colors, camera = cam, # options = render_options( # lights = list( # list(position = c(0.5, 1.0, 0.8), intensity = 1.5), # list(position = c(-0.5, 0.2, 0.6), intensity = 0.5)))) # # tmp_file <- tempfile(fileext = ".png") # write_png(img, tmp_file) # printf("Rendered sphere written to: %s\n", tmp_file) ## ----eval=FALSE--------------------------------------------------------------- # library(scimesh) # # white <- freesurferformats::read.fs.surface("sub-01/surf/lh.white") # pial <- freesurferformats::read.fs.surface("sub-01/surf/lh.pial") # # nv <- nrow(white$vertices) # # white_mesh <- list( # vertices = white$vertices, # triangles = white$faces, # colors = matrix(c(0.7, 0.7, 0.7, 1.0), nv, 4, byrow = TRUE)) # # pial_mesh <- list( # vertices = pial$vertices, # triangles = pial$faces, # colors = matrix(c(0.9, 0.3, 0.2, 0.35), nv, 4, byrow = TRUE)) # # cam <- camera_auto(pial_mesh, direction = c(-1, 0, 0.2)) # img <- render_scene(list(white_mesh, pial_mesh), cam, # render_options(width = 1200, height = 900, # backface_culling = FALSE, # specular_color = c(0.4, 0.4, 0.4, 1), # shininess = 64)) # temp_file <- tempfile(fileext = ".png") # write_png(img, temp_file) # printf("Transparent render written to: %s\n", temp_file) ## ----eval=FALSE--------------------------------------------------------------- # surface <- freesurferformats::read.fs.surface("sub-01/surf/lh.white") # sulc <- freesurferformats::read.fs.morph("sub-01/surf/lh.sulc") # cortex <- freesurferformats::read.fs.label("sub-01/label/lh.cortex.label") # # nv <- nrow(surface$vertices) # medial_wall <- !(seq_len(nv) %in% cortex) # sulc[medial_wall] <- NA # no data on the medial wall # # colors <- apply_colormap(sulc, colormap = viridis_colormap(256L), # nan_color = c(1, 1, 1, 1), winsor_percentiles = c(2, 98)) # if (ncol(colors) == 3) colors <- cbind(colors, 1) # colors[medial_wall, 4] <- 0.5 # 50 % transparent # # brain <- list(vertices = surface$vertices, triangles = surface$faces, # colors = colors) # img <- render_scene(list(brain), camera_auto(brain, direction = c(1, 0, 0)), # render_options(background_color = c(1, 1, 1, 1))) ## ----eval=FALSE--------------------------------------------------------------- # quads <- generate_plane(color = c(0.8, 0.2, 0.2, 1)) # quads$colors[, 4] <- rep(c(0, 1), each = nrow(quads$colors) / 2) ## ----eval=FALSE--------------------------------------------------------------- # surf <- generate_sphere(c(0, 0, 0), radius = 1) # cam <- camera_auto(list(surf), direction = c(0, 0, 1)) # opts <- render_options(width = 500, height = 400, # background_color = c(1, 1, 1, 1)) # # sc <- scene(list(surf), camera = cam, options = opts, # texts = list( # # world space: anchored above the sphere, follows the camera # text_layer(matrix(c(0, 1.3, 0), ncol = 3), "superior", # size = 20, adj = c(0.5, 0)), # # a direction label that must stay readable: no depth test # text_layer(matrix(c(1.4, 0, 0), ncol = 3), "anterior", # size = 18, adj = c(0, 0.5), # colors = c(0.75, 0.15, 0.15, 1), depth_test = FALSE), # # screen space: a panel tag in the top-left corner # text_layer(c(12, 10), "A", space = "screen", adj = c(0, 1), # size = 28, halo_color = c(1, 1, 1, 0.9)), # # screen space: a vertical axis label (rotation in degrees, # # counter-clockwise, about the anchor) # text_layer(c(16, 210), "sulcal depth", space = "screen", # adj = c(0, 0.5), size = 16, rotation = 90))) # img <- render_scene(sc) ## ----eval=FALSE--------------------------------------------------------------- # surface <- freesurferformats::read.fs.surface("sub-01/surf/lh.white") # sulc <- freesurferformats::read.fs.morph("sub-01/surf/lh.sulc") # colors <- apply_colormap(sulc, colormap = viridis_colormap(256L), # winsor_percentiles = c(2, 98)) # if (ncol(colors) == 3) colors <- cbind(colors, 1) # # brain <- list(vertices = surface$vertices, triangles = surface$faces, # colors = colors) # cam <- camera_auto(brain, direction = c(1, 0, 0)) # lateral view # # # The free surface is roughly 100 mm wide, so the labels sit at x = +-55 mm. # sc <- scene(list(brain), camera = cam, # options = render_options(width = 600, height = 500, # background_color = c(1, 1, 1, 1)), # texts = list( # text_layer(matrix(c(-55, 0, 0), ncol = 3), "posterior", # size = 22, adj = c(1, 0.5), depth_test = FALSE), # text_layer(matrix(c(55, 0, 0), ncol = 3), "anterior", # size = 22, adj = c(0, 0.5), depth_test = FALSE))) # img <- render_scene(sc) ## ----eval=FALSE--------------------------------------------------------------- # # Read a Wavefront OBJ file (with optional UVs and normals) # mesh <- read_obj("model.obj") # # # Read a Stanford PLY file (with optional vertex colors) # mesh <- read_ply("model.ply") # # # Read an STL file (binary or ASCII) # mesh <- read_stl("model.stl") # # # Write a mesh to STL # tmp_file1 <- tempfile(fileext = ".stl") # tmp_file2 <- tempfile(fileext = ".stl") # # write_stl(mesh, tmp_file1) # binary (default) # write_stl(mesh, tmp_file2, format = "ascii")