added usptream

.Rbuildignore

@@ -2,4 +2,6 @@
 ^\.travis\.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^standalone
+^appveyor.yml$
+^standalone$
+^revdep$

.gitignore

@@ -2,4 +2,5 @@
 .Rproj.user
 .Rhistory
 .RData
-.Ruserdata
+.Ruserdata
+/revdep

.travis.yml

@@ -3,9 +3,12 @@ sudo: false
 cache: packages
 
 install:
-- Rscript -e 'install.packages(c("Rcpp","testthat","tractor.base","oro.nifti"))'
+- Rscript -e 'install.packages(c("Rcpp","testthat","covr","tractor.base","oro.nifti"))'
 
 script:
 - R CMD build .
 - R CMD check *tar.gz
 - cd standalone && make clean && make CC="$(R CMD config CC)" CXX="$(R CMD config CXX)" && ./nii_info ../inst/extdata/example.nii.gz
+
+after_success:
+  - Rscript -e 'covr::coveralls()'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RNifti
-Version: 0.7.1
-Date: 2017-09-13
+Version: 0.9.0
+Date: 2018-09-06
 Title: Fast R and C++ Access to NIfTI Images
 Authors@R: c(person("Jon","Clayden",role=c("cre","aut"),email="code@clayden.org"),
              person("Bob","Cox",role="aut"),
@@ -10,16 +10,15 @@ Authors@R: c(person("Jon","Clayden",role=c("cre","aut"),email="code@clayden.org"
              person("Kate","Fissell",role="ctb"),
              person("Jean-loup","Gailly",role="cph"),
              person("Mark","Adler",role="cph"))
-Imports:
-    Rcpp (>= 0.11.0)
-Suggests:
-    testthat (>= 0.11.0)
+Imports: Rcpp (>= 0.11.0)
+Suggests: testthat (>= 0.11.0), covr, reportr
 Enhances: oro.nifti, tractor.base
 LinkingTo: Rcpp
-Description: Provides very fast access to images stored in the NIfTI-1 file
-    format <http://www.nitrc.org/docman/view.php/26/64/nifti1.h>, with seamless
-    synchronisation between compiled C and interpreted R code. Not to be
-    confused with 'RNiftyReg', which provides tools for image registration.
+Description: Provides very fast read and write access to images stored in the
+    NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
+    compiled C and interpreted R code. Also provides a C/C++ API that can be
+    used by other packages. Not to be confused with 'RNiftyReg', which performs
+    image registration.
 License: GPL-2
 URL: https://github.com/jonclayden/RNifti
 BugReports: https://github.com/jonclayden/RNifti/issues

NAMESPACE

@@ -1,27 +1,34 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("$",niftiImage)
+S3method("$<-",niftiImage)
 S3method("dim<-",internalImage)
 S3method("pixdim<-",default)
 S3method("pixunits<-",default)
 S3method(as.array,internalImage)
 S3method(dim,internalImage)
 S3method(pixdim,default)
 S3method(pixunits,default)
+S3method(print,analyzeHeader)
 S3method(print,niftiHeader)
 S3method(print,niftiImage)
 export("orientation<-")
 export("pixdim<-")
 export("pixunits<-")
 export("qform<-")
 export("sform<-")
+export(analyzeHeader)
 export(dumpNifti)
 export(ndim)
+export(niftiHeader)
+export(niftiVersion)
 export(orientation)
 export(origin)
 export(pixdim)
 export(pixunits)
 export(readNifti)
 export(retrieveNifti)
+export(rotation)
 export(updateNifti)
 export(voxelToWorld)
 export(worldToVoxel)

NEWS

@@ -2,6 +2,62 @@ Significant changes to the RNifti package are laid out below for each release.
 
 ===============================================================================
 
+VERSION 0.9.0
+
+- When writing an image using an integer datatype, the scale and slope fields
+  will now be set if the original values are outside the representable range of
+  that datatype. This ensures that the voxel values are accurate when read back
+  from the file (although some precision may, necessarily, be lost). This makes
+  the datatype argument to writeNifti() more generally useful for file size
+  reduction.
+- The dumpNifti() function has been soft-deprecated in favour of niftiHeader(),
+  which works the same way. There is also a new analyzeHeader() function, which
+  returns a list giving the header elements when interpreted according to the
+  ANALYZE-7.5 format. Both functions now return a default header when given no
+  argument.
+- The $ operator can now be used on "niftiImage" objects as a shorthand way to
+  get or set individual header fields.
+- The qform and sform replacement functions now work on lists of class
+  "niftiHeader".
+- The new rotation() function extracts just a pure 3x3 rotation matrix from an
+  image xform or general affine.
+- Functions such as origin() and orientation() now also work directly on xform-
+  like numeric matrices.
+- The offset part of an image's xform matrix (the fourth column) is now
+  properly updated when the image is reoriented. Reorientation should also now
+  work correctly for all possible permutations.
+- NA and NaN values are no longer removed from images on reading.
+- The pixdim attribute should now always contain the absolute values of the
+  pixdim for each dimension.
+
+===============================================================================
+
+VERSION 0.8.1
+
+- A C-level namespace clash on certain platforms has been corrected.
+
+===============================================================================
+
+VERSION 0.8.0
+
+- The new niftiVersion() function identifies the NIfTI format variant used by
+  files on disk.
+- The readNifti() function gains an option which allows only certain volumes
+  to be read from disk.
+- The updateNifti() function gains an option to set the internal datatype, for
+  advanced usage only (issue #8).
+- Calling updateNifti() with a list containing only a few fields could
+  previously reset the remaining metadata to the defaults. This has been
+  corrected.
+- It is now possible to change the cal_min and cal_max fields with the
+  updateNifti() function (issue #9). The scl_slope and scl_inter fields cannot
+  be changed, but this is now documented.
+- R packages using the RNifti API must now ensure that the USING_R symbol is
+  defined (which it is by the main R header, R.h). Conversely, standalone use
+  of RNifti as a C++ library no longer requires _NO_R__ to be defined.
+
+===============================================================================
+
 VERSION 0.7.1
 
 - The package is now more careful about handling NaNs when converting to

R/image.R

@@ -188,3 +188,36 @@ pixunits.default <- function (object)
 
     return (object)
 }
+
+#' Access to metadata elements
+#' 
+#' These methods provide shorthand access to metadata elements from the NIfTI
+#' header corresponding to an image. The extraction version returns the
+#' corresponding element from the result of \code{niftiHeader}, while the
+#' replacement version calls \code{updateNifti} to replace it.
+#' 
+#' @param x A \code{"niftiImage"} object, internal or otherwise.
+#' @param name A string naming the field required.
+#' @param value A new value for the field.
+#' 
+#' @examples
+#' im <- readNifti(system.file("extdata", "example.nii.gz", package="RNifti"))
+#' print(im$descrip)
+#' 
+#' @author Jon Clayden <code@@clayden.org>
+#' @seealso \code{\link{niftiHeader}}, \code{\link{updateNifti}}
+#' @rdname indexing
+#' @export
+"$.niftiImage" <- function (x, name)
+{
+    return (niftiHeader(x)[[name]])
+}
+
+#' @rdname indexing
+#' @export
+"$<-.niftiImage" <- function (x, name, value)
+{
+    template <- list()
+    template[[name]] <- value
+    return (updateNifti(x, template))
+}