Ready for CRAN

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ieegio
 Title: File IO for Intracranial Electroencephalography
-Version: 0.0.2.9011
+Version: 0.0.3
 Language: en-US
 Encoding: UTF-8
 Authors@R: 

NEWS.md

@@ -1,3 +1,22 @@
+# ieegio 0.0.3
+
+* Cleaned `h5py` loader
+* `mat_to_quaternion` always returns non-negative `w` now
+* Added generics `dim` and `length` to volume object
+* Fixed annotation issues in `EDF` format
+* Time selection is double-sided using greater equal and less equal signs
+* Added more sample data
+* Supports colored (`RGB[A]`) formats
+* Fixed color intensity when `cal_min` and `cal_max` is set
+* Using `r3js` for visualizing surfaces
+* Added `resample_volume` to sample images (currently only nearest neighbor)
+* Added `burn_volume` to burn contacts (positions given in the image native `RAS` coordinate) with any given colors
+* Fixed `io_h5_names` returning wrong names when using with `h5py`
+* Exported internal class `LazyH5` for down-stream packages
+* Added `as_ieegio_volume` and `as_ieegio_surface` to enclose volume or surface data
+* Added a flag to disable using `Python`
+
+
 # ieegio 0.0.2
 
 * Added `h5py` as an alternative back-end support

R/aaa-generics-surface.R

@@ -810,7 +810,8 @@ plot.ieegio_surface <- function(
 #' @param name name of the data; default is the file name
 #' @param ... for \code{read_surface}, the arguments will be passed to
 #' \code{io_read_fs} if the file is a 'FreeSurfer' file.
-#' @returns A surface object container
+#' @returns A surface object container for \code{read_surface}, and
+#' the file path for \code{write_surface}
 #' @examples
 #'
 #'
@@ -888,7 +889,7 @@ write_surface <- function(
 
   if(format == "gifti") {
     re <- io_write_gii(x = x, con = con, ...)
-    return(re)
+    return(invisible(re))
   }
 
   type <- match.arg(type)
@@ -981,6 +982,8 @@ write_surface <- function(
     }
   )
 
+  invisible(con)
+
 }
 
 

R/aaa-generics-volume.R

@@ -221,7 +221,8 @@ names.ieegio_volume <- function(x) {
 #' @param datatype_code,xyzt_units,intent_code additional flags for
 #' 'NIfTI' headers, for advanced users
 #' @param ... passed to other methods
-#' @returns imaging readers return \code{ieegio_volume} objects.
+#' @returns Imaging readers return \code{ieegio_volume} objects. The writers
+#' return the file path to where the file is saved to.
 #'
 #' @examples
 #'
@@ -662,7 +663,7 @@ plot.ieegio_volume <- function(
         main = main
       )
     }
-    vox_data <- t(vox_data)[ncol(vox_data):1L, , drop = FALSE]
+    vox_data <- t(vox_data)[rev(seq_len(ncol(vox_data))), , drop = FALSE]
     if(!is.na(alpha)) {
       alpha_255 <- floor(alpha * 255)
       alpha_255[alpha_255 < 0] <- 0
@@ -845,6 +846,8 @@ length.ieegio_volume <- function(x) {
 #' as array of colors; default is true when \code{x} is a raster matrix (
 #' matrix of color strings) and false when \code{x} is not a character array.
 #'
+#' @returns An \code{ieegio} volume object; see \code{\link{imaging-volume}}
+#'
 #' @examples
 #'
 #'

R/hdf5-class.R

@@ -89,7 +89,9 @@ h5FileValid <- function(filename){
 }
 
 #' @title Lazy 'HDF5' file loader
-#' @description provides hybrid data structure for 'HDF5' file
+#' @description Provides hybrid data structure for 'HDF5' file. The class is
+#' not intended for direct-use. Please see \code{\link{io_read_h5}} and
+#' \code{\link{io_write_h5}}.
 #' @export
 LazyH5 <- R6::R6Class(
   classname = 'LazyH5',

R/math-volume.R

@@ -204,7 +204,7 @@ resample_vox2ras <- function(vox2ras, old_dim, new_dim) {
 #' is an array
 #' @param preview indices (integer) of the position to visualize; default is
 #' \code{NULL} (no preview)
-#' @returns Color image that is burnt
+#' @returns Color image that is burnt; see \code{\link{imaging-volume}}.
 #'
 #' @examples
 #'

inst/WORDLIST

@@ -23,6 +23,7 @@ Neuroimaging
 PyNWB
 RAS
 YAML
+affine
 cloneable
 iEEG
 json