Merge pull request #514 from natverse/feature/write-mesh-fixes

Feature/write mesh fixes
natverse · Oct 9, 2023 · f2f35ab · f2f35ab
2 parents 1d161fa + 0660ee9
commit f2f35ab
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Showing 4 changed files with 39 additions and 2 deletions.
diff --git a/R/neuron-io.R b/R/neuron-io.R
@@ -672,6 +672,14 @@ is.swc<-function(f, TrustSuffix=TRUE) {
 #'
 #' # write out "myneuron.am" in Amira hxlineset format
 #' write.neuron(Cell07PNs[[1]], format = 'hxlineset', file='myneuron')
+#' 
+#' # write a mesh in Stanford ply 
+#' write.neuron(MBL.surf, file = 'MBL.surf.ply')
+#' # ... or Wavefront obj format
+#' write.neuron(MBL.surf, file = 'MBL.surf.obj')
+#' # specify the format directly if not evident from file suffix
+#' # not recommended though as will probably just cause trouble when reading
+#' write.neuron(MBL.surf, file = 'MBL.surf', format='obj')
 #' }
 write.neuron<-function(n, file=NULL, dir=NULL, format=NULL, ext=NULL, 
                        Force=FALSE, MakeDir=TRUE, metadata=NULL, ...){
@@ -891,7 +899,14 @@ write.neurons<-function(nl, dir, format=NULL, subdir=NULL,
                         INDICES=names(nl), files=NULL, 
                         include.data.frame=FALSE,
                         metadata=FALSE,
-                        Force=FALSE, cl=NULL, ...){
+                        Force=FALSE, cl=NULL, ...) {
+  if(!inherits(nl, 'neuronlist')) {
+    # check if this looks like some of the other kinds of object we might 
+    # write by accident
+    single_object_classes <- c("mesh3d", "neuron", "dotprops", "hxsurf")
+    if(any(single_object_classes %in% class(nl)))
+      stop("Please use `write.neuron` to write a single neuron/mesh object!")
+  }
   if(grepl("\\.zip", dir)) {
     zip_file=dir
     # check if file exists (and we want to overwrite)

diff --git a/R/neuron-mesh.R b/R/neuron-mesh.R
@@ -43,8 +43,16 @@ write.neuron.mesh <- function(x, file, format=c("ply", "obj"), ...) {
   if(!inherits(x, 'mesh3d')) {
     x=tryCatch(as.mesh3d(x), error=function(e) stop("Unable to convert x to mesh3d object! Only neuron meshes can be written in ",format," format!"))
   }
-  if(format=="ply")
+  if(format=="ply") {
+    if(!isTRUE(tools::file_ext(file)=="ply")) {
+      # ply format must end in .ply 
+      origfile=file
+      file=tempfile(fileext = '.ply')
+      on.exit(file.copy(file, origfile, overwrite = T), add = T)
+      on.exit(unlink(file), add = T)
+    }
     Rvcg::vcgPlyWrite(x, filename=file, writeCol = F, writeNormals = F, ...)
+  }
   else if(format=="obj")
     Rvcg::vcgObjWrite(x, filename=file, writeNormals=F, ...)
   else stop("Unknown format")

diff --git a/man/write.neuron.Rd b/man/write.neuron.Rd
diff --git a/tests/testthat/test-neuron-mesh.R b/tests/testthat/test-neuron-mesh.R
@@ -13,13 +13,19 @@ test_that("read/write works", {
   md5.2=tools::md5sum(ff2)
   expect_equal(md5.1, md5.2)
 
+  # error if we try to write one object with write.neurons
+  expect_error(write.neurons(bl[[1]], dir=td, format='ply'))
+
   expect_is(bl2 <- read.neurons(td, format='ply'), 'neuronlist')
   expect_equal(sbl <- summary(bl), summary(bl2))
 
   expect_is(sbl, 'data.frame')
   expect_known_value(sbl, file = 'testdata/summary_bl.rds')
 
   expect_error(write.neurons(Cell07PNs[1:3], format = 'ply'))
+
+  write.neuron(MBL.surf, file=file.path(td, "MBL.surf.ply"), format = 'ply')
+  expect_equal(read.neuron(file.path(td, "MBL.surf.ply")), as.mesh3d(MBL.surf), tolerance = 1e-6)
 })
 
 skip_if_not_installed('readobj')