add unit test for VTK mesh reading and writing, strip names when reading

dfsp-spirit · Apr 9, 2020 · a68df6b · a68df6b
1 parent 9daf5c9
commit a68df6b
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Showing 2 changed files with 19 additions and 4 deletions.
diff --git a/R/read_fs_surface.R b/R/read_fs_surface.R
@@ -19,8 +19,8 @@ read.fs.surface.asc <- function(filepath) {
   faces_df = read.table(filepath, skip=2L + num_verts, col.names = c('vertex1', 'vertex2', 'vertex3', 'value'), colClasses = c("integer", "integer", "integer", "numeric"), nrows=num_faces);
 
   ret_list = list();
-  ret_list$vertices = data.matrix(vertices_df[1:3]);
-  ret_list$faces = data.matrix(faces_df[1:3]) + 1L;  # the +1 is because the surface should use R indices (one-based)
+  ret_list$vertices = unname(data.matrix(vertices_df[1:3]));
+  ret_list$faces = unname(data.matrix(faces_df[1:3])) + 1L;  # the +1 is because the surface should use R indices (one-based)
   class(ret_list) = c("fs.surface", class(ret_list));
 
   if(nrow(ret_list$vertices) != num_verts) {
@@ -92,8 +92,8 @@ read.fs.surface.vtk <- function(filepath) {
 
 
   ret_list = list();
-  ret_list$vertices = data.matrix(vertices_df[1:3]);
-  ret_list$faces = data.matrix(faces_df[2:4]) + 1L;  # the +1 is because the surface should use R indices (one-based)
+  ret_list$vertices = unname(data.matrix(vertices_df[1:3]));
+  ret_list$faces = unname(data.matrix(faces_df[2:4])) + 1L;  # the +1 is because the surface should use R indices (one-based)
   class(ret_list) = c("fs.surface", class(ret_list));
 
   return(ret_list);

diff --git a/tests/testthat/test-write-fs-surface.R b/tests/testthat/test-write-fs-surface.R
@@ -74,3 +74,18 @@ test_that("One can read, write and re-read triangular surface data", {
   expect_equal(surf$vertices, surf_re$vertices);
   expect_equal(surf$faces, surf_re$faces);
 })
+
+
+test_that("Surface files in VTK format can be read and written", {
+
+  surface_file = system.file("extdata", "lh.tinysurface", package = "freesurferformats", mustWork = TRUE);
+  surf = read.fs.surface(surface_file);
+
+  tmp_vtk_file = tempfile(fileext=".vtk");
+  write.fs.surface.vtk(tmp_vtk_file, surf$vertices, surf$faces);
+
+  surf_re = read.fs.surface(tmp_vtk_file);
+  expect_equal(surf$vertices, surf_re$vertices);
+  expect_equal(surf$faces, surf_re$faces);
+})
+