version 0.1.0

DESCRIPTION

@@ -0,0 +1,23 @@
+Package: RNifti
+Version: 0.1.0
+Date: 2016-09-01
+Title: Fast R and C++ Access to NIfTI Images
+Author: Jon Clayden
+Maintainer: Jon Clayden <code@clayden.org>
+Imports: Rcpp (>= 0.11.0)
+Suggests: testthat (>= 0.11.0)
+Enhances: oro.nifti, tractor.base
+LinkingTo: Rcpp
+Description: Provides very fast access to images stored in the NIfTI-1 file
+    format <http://nifti.nimh.nih.gov/nifti-1>, with seamless synchronisation
+    between compiled C and interpreted R code. Not to be confused with RNiftyReg,
+    which provides tools for image registration.
+License: GPL-2
+URL: https://github.com/jonclayden/RNifti
+BugReports: https://github.com/jonclayden/RNifti/issues
+Encoding: UTF-8
+RoxygenNote: 5.0.1
+NeedsCompilation: yes
+Packaged: 2016-09-01 11:49:57 UTC; jon
+Repository: CRAN
+Date/Publication: 2016-09-01 17:29:22

MD5

@@ -0,0 +1,61 @@
+fb6b2eadbba2d5e0ea958d3e0a8e45f1 *DESCRIPTION
+e20469301709fc7383310d95f9e8ab4e *NAMESPACE
+2490b4d109b227186f557977ad659dfa *R/image.R
+dc7142a5856b0b84ffc44662cf871530 *R/nifti.R
+0081869ffb660272f2ca812018d60958 *R/xform.R
+33e5b97691485f83c60e3d5c3f3a2cdc *R/zzz.R
+eb8256cd53aa01205304e37eb6dc8a53 *README.md
+ccc527aa65600337ed5e3f832c0eb443 *cleanup
+e1101581081b97d9032639597016d3d8 *cleanup.win
+30c091d208079613a19efc08f87849de *inst/extdata/example.nii.gz
+55418f98f35198af3318c4282618872c *inst/include/RNifti.h
+00aaa92498f68e61f506224a15ed8a4d *inst/include/RNiftiAPI.h
+e407ffd378be4080bee8c1f8076cd051 *inst/include/lib/NiftiImage.h
+fa8b37f676aab680816c08451fe7b1bd *inst/include/lib/print.h
+a34af6ec4b25ecc1a68459bbb5dc76c9 *inst/include/niftilib/nifti1.h
+f7137f566bbb76b092b1274e4ab599fe *inst/include/niftilib/nifti1_io.h
+5407d4c937d8f925665f71aad35c12fa *inst/include/zlib/zconf.h
+1c128a3b0a0fd84c1224754170ee7756 *inst/include/zlib/zlib.h
+6f799f7df2f427678edd3abcc5897ad6 *inst/include/znzlib/znzlib.h
+2cfd1772edd6b9dd9274a8bda954bb14 *man/dumpNifti.Rd
+2fd178c7fd10f45ef39114cd2000ddef *man/internalImage.Rd
+309e4f9d81ae01b7ec5804b16c3da953 *man/ndim.Rd
+a9eb96edafa817a296cf79e755cec722 *man/pixdim.Rd
+2d86c37391f594e57b951da0d28a841f *man/readNifti.Rd
+5cb66c2de80021acfeb35bce9767ff8b *man/retrieveNifti.Rd
+1f4522b43df68a13b6699029d31ce8d1 *man/updateNifti.Rd
+9825b9a8b44206110f5ae2a1ebcf8ad3 *man/voxelToWorld.Rd
+d919580d8145b971a7c9ee71b3c5ca86 *man/writeNifti.Rd
+bf143f6ef896f3bff808ba60804ea88a *man/xform.Rd
+4339fefce4c27fe7c58ef189cb849ac7 *src/Makevars
+a6f806acc64eb9b6b2b53b543f1f8b25 *src/init.cpp
+fd7273caae3c89c02d9c84ddeeb9ade0 *src/main.cpp
+0914eaaf0fca8668ad668d855c23036c *src/niftilib/nifti1_io.c
+ae3bbb54820e1d49fb90cbba222e973f *src/zlib/adler32.c
+7a734598f9792fee943b70b6da8d932f *src/zlib/compress.c
+1339c92938d2594a6eecfa21c374d1b6 *src/zlib/crc32.c
+f28d16b67efecdfafa0d816a7d982124 *src/zlib/crc32.h
+cd7826278ce9d9d9ed5abdefef50c3e2 *src/zlib/deflate.c
+7ceae74a13201f14c91623116af169c3 *src/zlib/deflate.h
+29d02cff161bde3e4e717b25a2ab7050 *src/zlib/gzclose.c
+715df37bf53af0dee6d018d0f34836ad *src/zlib/gzguts.h
+cb70e50d56c980fb8fd2e2e97bb9cd86 *src/zlib/gzlib.c
+62164548c5f9c89dc5e7d8ea382ffd8e *src/zlib/gzread.c
+cb95538e53e594b0d8a4bf4ecb2b5659 *src/zlib/gzwrite.c
+bdb9cc0c602c951ed5f0557798e15299 *src/zlib/infback.c
+9c14c1d95cee9f62465dedea7524c5fb *src/zlib/inffast.c
+f3669099d3f571dbc0426401ed5f50e3 *src/zlib/inffast.h
+7fa3e91804601b6618c915b76a8dc332 *src/zlib/inffixed.h
+46cb3a81ac3fa57789eba65cfecf754d *src/zlib/inflate.c
+8f1b05cdf36a269882a955071b140162 *src/zlib/inflate.h
+3d0a4fce4b156f064e9be2aef36a7897 *src/zlib/inftrees.c
+ec87be89b9bcca8ced80a70f857e823b *src/zlib/inftrees.h
+bc195d555c24fecff56af6c06bd55b1d *src/zlib/trees.c
+51fdcb3e2ccf60ca13c06920c89296a3 *src/zlib/trees.h
+eabe905cdd27f5b935e6378cd0253418 *src/zlib/uncompr.c
+fff257bc1656eb60fc585a7dc35f963d *src/zlib/zutil.c
+de91a463004fd5b944c3d37eab0c1794 *src/zlib/zutil.h
+db1082070d31f780ebd9c051b74adc17 *src/znzlib/znzlib.c
+d4a2abbb6217055b8900c8d86ac6aa53 *tests/testthat.R
+4b0fe74a7776bec4fa562d998fb06226 *tests/testthat/test-05-nifti.R
+67e97715d9000e8325d9f2e38351db0b *tests/testthat/test-10-xform.R

NAMESPACE

@@ -0,0 +1,29 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method("dim<-",internalImage)
+S3method("pixdim<-",default)
+S3method("pixunits<-",default)
+S3method(as.array,internalImage)
+S3method(dim,internalImage)
+S3method(pixdim,default)
+S3method(pixunits,default)
+S3method(print,niftiHeader)
+S3method(print,niftiImage)
+export("pixdim<-")
+export("pixunits<-")
+export("qform<-")
+export("sform<-")
+export(dumpNifti)
+export(ndim)
+export(pixdim)
+export(pixunits)
+export(readNifti)
+export(retrieveNifti)
+export(updateNifti)
+export(voxelToWorld)
+export(worldToVoxel)
+export(writeNifti)
+export(xform)
+importFrom(Rcpp,evalCpp)
+importFrom(utils,object.size)
+useDynLib(RNifti)

R/image.R

@@ -0,0 +1,182 @@
+#' Internal images
+#' 
+#' An internal image is a simple R object with a few attributes including a
+#' pointer to an internal C structure, which contains the full image data. They
+#' are used in the package for efficiency, but can be converted to a normal
+#' R array using the \code{as.array} method. Attributes of these objects should
+#' not be changed.
+#' 
+#' @param x An \code{"internalImage"} object.
+#' @param value Not used. Changing the dimensions of an internal image is
+#'   invalid, and will produce an error.
+#' @param ... Additional parameters to methods. Currently unused.
+#' 
+#' @author Jon Clayden <code@@clayden.org>
+#' @aliases internalImage
+#' @rdname internalImage
+#' @export
+dim.internalImage <- function (x)
+{
+    return (attr(x, "imagedim"))
+}
+
+#' @rdname internalImage
+#' @export
+"dim<-.internalImage" <- function (x, value)
+{
+    stop("Dimensions of an internal image cannot be changed")
+}
+
+#' @rdname internalImage
+#' @export
+as.array.internalImage <- function (x, ...)
+{
+    return (.Call("pointerToArray", x, PACKAGE="RNifti"))
+}
+
+#' @export
+print.niftiImage <- function (x, ...)
+{
+    dim <- dim(x)
+    ndim <- length(dim)
+    pixdim <- attr(x, "pixdim")
+    pixunits <- attr(x, "pixunits")
+
+    if ("internalImage" %in% class(x))
+        cat(paste0("Internal image: \"", x, "\"\n"))
+    else
+        cat(paste0("Image array of mode \"", storage.mode(x), "\" (", format(object.size(x),"auto"), ")\n"))
+
+    cat(paste("-", paste(dim,collapse=" x "), ifelse(ndim>2,"voxels\n","pixels\n")))
+
+    if (!is.null(pixdim))
+    {
+        spaceUnit <- grep("m$", pixunits, perl=TRUE, value=TRUE)
+        cat(paste("-", paste(signif(pixdim[1:min(3,ndim)],4),collapse=" x ")))
+        if (length(spaceUnit) > 0)
+            cat(paste0(" ", spaceUnit[1]))
+
+        if (ndim > 3)
+        {
+            timeUnit <- grep("s$", pixunits, perl=TRUE, value=TRUE)
+            cat(paste(" x", signif(pixdim[4],4)))
+            if (length(timeUnit) > 0)
+                cat(paste0(" ", timeUnit[1]))
+        }
+        if (ndim > 4)
+            cat(paste(" x", paste(signif(pixdim[5:ndim],4),collapse=" x ")))
+
+        cat(paste(" per", ifelse(ndim>2,"voxel\n","pixel\n")))
+    }
+}
+
+#' Number of dimensions
+#' 
+#' This function is shorthand for \code{length(dim(object))}.
+#' 
+#' @param object An R object.
+#' @return The dimensionality of the object. Objects without a \code{dim}
+#'   attribute will produce zero.
+#' 
+#' @author Jon Clayden <code@@clayden.org>
+#' @export
+ndim <- function (object)
+{
+    length(dim(object))
+}
+
+#' Pixel dimensions and units
+#' 
+#' By default, these generic functions return or replace the \code{"pixdim"}
+#' and \code{"pixunits"} attributes of their arguments. These represent the
+#' physical step size between pixel or voxel centre points, and the spatial and
+#' temporal units that they are given in. The former defaults to 1 in each
+#' dimension, if there is no attribute.
+#' 
+#' @param object An R object, generally an image.
+#' @param value Numeric vector of pixel dimensions along each axis, or
+#'   character vector of abbreviated units. For dimensions, a scalar
+#'   \code{value} will be recycled if necessary.
+#' @return \code{pixdim} returns a numeric vector of pixel dimensions.
+#'   \code{pixunits} returns a character vector of length up to two, giving the
+#'   spatial and temporal unit names.
+#' 
+#' @author Jon Clayden <code@@clayden.org>
+#' @export
+pixdim <- function (object)
+{
+    UseMethod("pixdim")
+}
+
+#' @rdname pixdim
+#' @export
+pixdim.default <- function (object)
+{
+    if (!is.null(attr(object, "pixdim")))
+        return (attr(object, "pixdim"))
+    else if (!is.null(dim(object)))
+        return (rep(1, length(dim(object))))
+    else
+        return (1)
+}
+
+#' @rdname pixdim
+#' @export
+"pixdim<-" <- function (object, value)
+{
+    UseMethod("pixdim<-")
+}
+
+#' @rdname pixdim
+#' @export
+"pixdim<-.default" <- function (object, value)
+{
+    if ("internalImage" %in% class(object))
+        stop("Pixel dimensions of an internal image cannot be changed")
+
+    if (is.numeric(value))
+    {
+        if (length(value) == ndim(object))
+            attr(object, "pixdim") <- value
+        else if (length(value) == 1)
+            attr(object, "pixdim") <- rep(value, ndim(object))
+    }
+    return (object)
+}
+
+#' @rdname pixdim
+#' @export
+pixunits <- function (object)
+{
+    UseMethod("pixunits")
+}
+
+#' @rdname pixdim
+#' @export
+pixunits.default <- function (object)
+{
+    if (!is.null(attr(object, "pixunits")))
+        return (attr(object, "pixunits"))
+    else
+        return ("Unknown")
+}
+
+#' @rdname pixdim
+#' @export
+"pixunits<-" <- function (object, value)
+{
+    UseMethod("pixunits<-")
+}
+
+#' @rdname pixdim
+#' @export
+"pixunits<-.default" <- function (object, value)
+{
+    if ("internalImage" %in% class(object))
+        stop("Pixel units of an internal image cannot be changed")
+
+    if (is.character(value))
+        attr(object, "pixunits") <- value
+
+    return (object)
+}