diff --git a/R/read_fs_label.R b/R/read_fs_label.R index f21e95a..39a9942 100644 --- a/R/read_fs_label.R +++ b/R/read_fs_label.R @@ -65,7 +65,7 @@ read.fs.label.native <- function(filepath, return_one_based_indices=TRUE, full=F vertices = vertices_df$vertex_index; if(length(vertices) != num_verts) { - stop(sprintf("Expected %d vertex rows in label file '%s' from header, but received %d.\n", num_verts, filepath, length(vertices))); + stop(sprintf("Expected %d vertex rows in label file '%s' from header, but received %d.\n", num_verts, filepath, length(vertices))); # nocov } if(any(vertices < 0L)) { @@ -172,15 +172,15 @@ read.fs.label.gii <- function(filepath, label_value=1L, element_index=1L) { gii = gifti::read_gifti(filepath); intent = gii$data_info$Intent[[element_index]]; if(intent != 'NIFTI_INTENT_LABEL') { - warning(sprintf("The intent of the gifti file is '%s', expected 'NIFTI_INTENT_LABEL'.\n", intent)); + warning(sprintf("The intent of the gifti file is '%s', expected 'NIFTI_INTENT_LABEL'.\n", intent)); # nocov } if(is.null(gii$label)) { - stop(sprintf("The gifti file '%s' does not contain label information.\n", filepath)); + stop(sprintf("The gifti file '%s' does not contain label information.\n", filepath)); # nocov } else { #label_data_num_columns = ncol(gii$data[[element_index]]); # must be 1D for surface labels: 1 column of vertex indices (the data is returned as a matrix). if(gii$data_info$Dimensionality != 1L) { - stop(sprintf("Label data has %d dimensions, expected 1. This does not look like a 1D surface label.\n", gii$data_info$Dimensionality)); + stop(sprintf("Label data has %d dimensions, expected 1. This does not look like a 1D surface label.\n", gii$data_info$Dimensionality)); # nocov } annot_data = as.integer(gii$data[[element_index]]); # note that as.integer() turns the (1 column) matrix into a vector. diff --git a/tests/testthat/test-read_fs_label.R b/tests/testthat/test-read_fs_label.R index 7f10293..e7eec06 100644 --- a/tests/testthat/test-read_fs_label.R +++ b/tests/testthat/test-read_fs_label.R @@ -53,6 +53,9 @@ test_that("Our demo label file can be read with one-based R indices", { test_that("Our demo label file can be read into an fs.label instance", { labelfile = system.file("extdata", "lh.entorhinal_exvivo.label", package = "freesurferformats", mustWork = TRUE); + label_zero_based = read.fs.label(labelfile, full=TRUE, return_one_based_indices = FALSE); + expect_true(is.fs.label(label_zero_based)); + label = read.fs.label(labelfile, full=TRUE); known_vertex_count_label = 1085;