-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added support for GIfTI and FreeSurfer surfaces
- Loading branch information
Showing
34 changed files
with
2,993,452 additions
and
130 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| Version: 0.0.1 | ||
| Date: 2024-09-09 04:24:18 UTC | ||
| SHA: fe32ae4e4f7c9d5917c8ecd81c2746bf012804b4 | ||
| Date: 2024-09-09 12:54:50 UTC | ||
| SHA: 53fa43a53ee02067f73f9ed64daad9d840dcd394 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
|
|
||
| fs_lut <- local({ | ||
| lut <- NULL | ||
| impl <- function() { | ||
| # /Users/dipterix/Dropbox (Personal)/projects/ieegio/inst/lookup_table | ||
| "inst/lookup_table/FreeSurferColorLUT.json" | ||
| path <- system.file("lookup_table", "FreeSurferColorLUT.json", package = "ieegio") | ||
| lut <- io_read_json(path) | ||
| data.table::rbindlist(lut$`__global_data__.VolumeColorLUT`$map) | ||
| } | ||
| function() { | ||
| if(is.null(lut)) { | ||
| lut <<- impl() | ||
| } | ||
| lut | ||
| } | ||
| }) | ||
|
|
||
| #' @rdname read_surface | ||
| #' @export | ||
| io_read_fs <- function(file, type = c("geometry", "annotations", "measurements"), | ||
| format = "auto", name = basename(file), ...) { | ||
|
|
||
| type <- match.arg(type) | ||
|
|
||
| # DIPSAUS DEBUG START | ||
| # f_geom <- "/Users/dipterix/rave_data/raw_dir/AnonSEEG_old2/rave-imaging/fs/surf/lh.pial" | ||
| # f_annot <- "/Users/dipterix/rave_data/raw_dir/AnonSEEG_old2/rave-imaging/fs/label/lh.aparc.annot" | ||
| # | ||
| # file <- f_geom | ||
| # format <- "auto" | ||
| # name = basename(file) | ||
|
|
||
|
|
||
|
|
||
| re <- switch( | ||
| type, | ||
| "geometry" = { | ||
| surf <- freesurferformats::read.fs.surface(file, format = format) | ||
| header <- structure( | ||
| class = "fs_geometry", | ||
| list(internal = surf$internal, mesh_face_type = surf$mesh_face_type) | ||
| ) | ||
| # try to get c_ras | ||
| transforms <- list( | ||
| Unknown = structure( | ||
| diag(1, 4), | ||
| source_space = "Unknown", | ||
| target_space = "Unknown" | ||
| ) | ||
| ) | ||
|
|
||
| suppressWarnings({ | ||
| tryCatch( | ||
| { | ||
| line1 <- readLines(file, n = 1L, encoding = "ascii") | ||
| n <- c( | ||
| nchar(line1, type = "bytes"), 8, | ||
| length(surf$vertices) * 4, | ||
| length(surf$faces) * 4 | ||
| ) | ||
| extra_bytes <- file.size(file) - sum(n) | ||
| if(length(extra_bytes)) { | ||
| conn <- base::file(file, "rb") | ||
| on.exit({ close(conn) }) | ||
| invisible({ readBin(conn, "raw", n = sum(n)) }) | ||
| extra <- readBin(conn, "raw", n = extra_bytes, endian = "big") | ||
| extra <- intToUtf8(extra) | ||
| extra <- trimws(strsplit(extra, "\n")[[1]]) | ||
| extra <- extra[startsWith(extra, "cras ")] | ||
| cras <- strsplit(extra, "=", fixed = TRUE)[[1]][[2]] | ||
| cras <- strsplit(trimws(cras), " ")[[1]] | ||
| cras <- cras[cras != ""] | ||
| cras <- as.numeric(cras) | ||
| if(length(cras) == 3 && !anyNA(cras)) { | ||
| names(transforms) <- "ScannerAnat" | ||
| transforms$ScannerAnat[1:3, 4] <- cras | ||
| } | ||
| } | ||
| }, | ||
| error = function(...) {} | ||
| ) | ||
| }) | ||
|
|
||
| return(new_surface(header = header, geometry = list( | ||
| vertices = t(cbind(surf$vertices[, c(1, 2, 3)], 1)), | ||
| faces = t(surf$faces), | ||
| face_start = 1L, | ||
| transforms = transforms, | ||
| meta = list(Name = name) | ||
| ))) | ||
| }, | ||
| "annotations" = { | ||
| # list( | ||
| # label_table = parse_label_table(gii$label), | ||
| # data_table = NULL, | ||
| # meta = list() | ||
| # ) | ||
| annot <- freesurferformats::read.fs.annot(file, default_label_name = "Unlabeled") | ||
| # lut <- fs_lut() | ||
|
|
||
| annot_name <- name | ||
|
|
||
| label_table <- data.table::data.table( | ||
| Key = annot$colortable_df$struct_index, | ||
| Label = annot$colortable_df$struct_name, | ||
| Red = annot$colortable_df$r / 255, | ||
| Green = annot$colortable_df$g / 255, | ||
| Blue = annot$colortable_df$b / 255, | ||
| Color = annot$colortable_df$hex_color_string_rgb | ||
| ) | ||
|
|
||
| # annot$vertices | ||
| lut <- structure( | ||
| names = as.character(label_table$Label), | ||
| label_table$Key | ||
| ) | ||
| unames <- as.character(unique(annot$label_names)) | ||
| unames <- unames[!unames %in% label_table$Label] | ||
| if(length(unames)) { | ||
| lut[unames] <- 0 | ||
| } | ||
| data_table <- data.table::data.table(V = unname(lut[annot$label_names])) | ||
|
|
||
| names(data_table) <- annot_name | ||
| annotations <- list( | ||
| label_table = label_table, | ||
| data_table = data_table, | ||
| meta = structure(names = annot_name, list(annot$metadata)) | ||
| ) | ||
| node_index <- annot$vertices | ||
| if(length(node_index)) { | ||
| node_index <- list( | ||
| node_index = as.integer(node_index) + 1L, | ||
| node_index_start = 1L | ||
| ) | ||
| } else { | ||
| node_index <- NULL | ||
| } | ||
| return( | ||
| new_surface( | ||
| header = structure( | ||
| class = "fs_annot", | ||
| list(orig_ctab = annot$colortable_df) | ||
| ), | ||
| annotations = annotations, | ||
| sparse_node_index = node_index | ||
| ) | ||
| ) | ||
| }, | ||
| "measurements" = { | ||
| meas <- freesurferformats::read.fs.curv(file, format = format, with_header = TRUE) | ||
|
|
||
| data_table <- data.table::data.table(V = meas$data) | ||
| names(data_table) <- name | ||
| measurements <- list( | ||
| data_table = data_table, | ||
| meta = list() | ||
| ) | ||
| return( | ||
| new_surface( | ||
| header = structure( | ||
| class = "fs_measurement", | ||
| meas$header | ||
| ), | ||
| measurements = measurements | ||
| ) | ||
| ) | ||
| }, | ||
| "color" = { | ||
|
|
||
| }, | ||
| "time_series" = { | ||
|
|
||
| } | ||
| ) | ||
|
|
||
|
|
||
| # if(FALSE) { | ||
| # f_geom <- "/Users/dipterix/rave_data/raw_dir/AnonSEEG_old2/rave-imaging/fs/surf/lh.pial" | ||
| # f_annot <- "/Users/dipterix/rave_data/raw_dir/AnonSEEG_old2/rave-imaging/fs/label/lh.aparc.annot" | ||
| # f_meas <- "/Users/dipterix/rave_data/raw_dir/AnonSEEG_old2/rave-imaging/fs/surf/lh.curv" | ||
| # | ||
| # file <- f_meas | ||
| # x <- merge( | ||
| # io_read_fs(f_geom, "geometry"), | ||
| # io_read_fs(f_annot, "annot"), | ||
| # io_read_fs(f_meas, "mea") | ||
| # ) | ||
| # plot(x, name = c("measure", "lh.curv"), col = c("black", "white", "black")) | ||
| # } | ||
|
|
||
|
|
||
| re | ||
|
|
||
| } | ||
|
|
Oops, something went wrong.