version 1.6.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RNifti
-Version: 1.5.1
-Date: 2023-11-27
+Version: 1.6.0
+Date: 2024-02-15
 Title: Fast R and C++ Access to NIfTI Images
 Authors@R: c(person("Jon", "Clayden", role=c("cre","aut"),
     email="code@clayden.org", comment=c(ORCID="0000-0002-6608-0619")),
@@ -27,7 +27,7 @@ BugReports: https://github.com/jonclayden/RNifti/issues
 Encoding: UTF-8
 RoxygenNote: 7.2.3
 NeedsCompilation: yes
-Packaged: 2023-11-28 11:18:58 UTC; jon
+Packaged: 2024-02-15 16:27:14 UTC; jon
 Author: Jon Clayden [cre, aut] (<https://orcid.org/0000-0002-6608-0619>),
   Bob Cox [aut],
   Mark Jenkinson [aut],
@@ -38,4 +38,4 @@ Author: Jon Clayden [cre, aut] (<https://orcid.org/0000-0002-6608-0619>),
   Mark Adler [cph]
 Maintainer: Jon Clayden <code@clayden.org>
 Repository: CRAN
-Date/Publication: 2023-11-28 12:10:12 UTC
+Date/Publication: 2024-02-15 17:20:02 UTC

MD5

@@ -1,24 +1,24 @@
-a30c9b714a9dce08fda52433ee5d0324 *DESCRIPTION
+6fc172b39781ad6ec2fb8f0f5197698d *DESCRIPTION
 b94d5d2bf459e2903296147cf718349d *NAMESPACE
-44864e0b14c644955b119fa29afcdb6c *NEWS
+3a3d731e3dd52253df0eb0eb481ee8b0 *NEWS
 48127c25699df64079656e5eb7fcd1d2 *R/extensions.R
 a45b6c1b24ab18fa3818f783bf93a84c *R/image.R
-0f3541bd599edbfd113439d69b5f693b *R/nifti.R
+46e14f10e18c2dee71fa72ff7cdc8f70 *R/nifti.R
 72db1a838f07adbc2f834ec36dd21f32 *R/rgb.R
 81e0d85d15f23b2f3d102d6760a36bc3 *R/viewer.R
 3a52b438782f0fc4f0a005012ee2cba5 *R/xform.R
 0b6222eb8972506a715ac81c6cce2c33 *R/zzz.R
-670e72fe47adc1d9545f4fe4dfc46b21 *README.md
-e3d31206c28f1700a9cf327ed830369b *cleanup
+768dc560b52c4f3a17897d3899ab2457 *README.md
+de3a96bc3b47cf2717cdc84e20eac575 *cleanup
 7c2c1d94dfe6a983036431788e83b6e4 *cleanup.win
-2f8989e7304bad7a66be87c041e8c296 *configure
-ece526a031b3767436ac7381a8ac41e5 *configure.ac
+f63f838e72ef37a38b2fa23c3145b065 *configure
+d7f17ed909040ac92c623f8af8a4dde5 *configure.ac
 fb6ea71c285b8fc5d86bf53c4e104348 *inst/COPYRIGHTS
 bad67894bda1a1b3b135369d6c07df6a *inst/extdata/example.nii.gz
 e8547f4bc7609814adfbab6fe9c1c288 *inst/extdata/example_4d.nii.gz
 c26818fcb45b7b7a9d4154d5487230e1 *inst/extdata/example_rgb.nii.gz
-bdc38ee7810c9f6b00579488566ee382 *inst/include/RNifti.h
-e2c74e0083e3937157cced62c63414e0 *inst/include/RNifti/NiftiImage.h
+27b3377916ff84a549f8ec2cd8f3aef8 *inst/include/RNifti.h
+034a48f9e5b92ed077c271db7ad36fc8 *inst/include/RNifti/NiftiImage.h
 a43b0c2c9871d4edf6185c6c6060073a *inst/include/RNifti/NiftiImage_impl.h
 f80b24dc1fac288092c6758dfe0b36f3 *inst/include/RNifti/NiftiImage_matrix.h
 8a9527a48edffbebde2170c000a321ad *inst/include/RNifti/NiftiImage_print.h
@@ -30,9 +30,7 @@ f3b89c12d91297deee7a2b1cf27d41d7 *inst/include/niftilib/nifti2.h
 4e373c9b99d88d0019a2ea3da10e7330 *inst/include/niftilib/nifti2_image.h
 59a3d4d90a3c6f2f1577e59b130850fb *inst/include/niftilib/nifti2_io.h
 d3ab930e9ad209cc857a839d2e080ebc *inst/include/niftilib/nifti2_io_version.h
-5407d4c937d8f925665f71aad35c12fa *inst/include/zlib/zconf.h
-1c128a3b0a0fd84c1224754170ee7756 *inst/include/zlib/zlib.h
-b832290b2ff8ffe44114b4e86475f301 *inst/include/znzlib/znzlib.h
+e465fe9fd570402aba84704902ead0e4 *inst/include/znzlib/znzlib.h
 ee8949e3b781480b0201286063b5c2ac *man/ExtensionCodes.Rd
 8ecefba81cb4bce311f77e0cb0e7d865 *man/asNifti.Rd
 89095e599895dbb1547cfc9159d447f1 *man/channels.Rd
@@ -41,7 +39,7 @@ f62cda6e04dc9e2216c24227eac3c1c0 *man/extensions.Rd
 1ea9e61a79acb5999d259813d2213c0f *man/indexing.Rd
 b83a9399244f6c7de4ddf7775daf8a36 *man/internalImage.Rd
 42120833f7c250a1d4e56c649ef40ed4 *man/ndim.Rd
-f140c602ae576950196d1ce92e00d7b3 *man/niftiHeader.Rd
+858433f6367476a59330e16917d291d2 *man/niftiHeader.Rd
 7406628fc63edbf979ad6348dda8b9a7 *man/niftiVersion.Rd
 20c181da31a24521475e83eff3927f90 *man/pixdim.Rd
 bdff7a46d55ff74e148f797da7af245a *man/readNifti.Rd
@@ -50,40 +48,51 @@ dfef27c9fc33dc654e3e1cb2cdbb1464 *man/view.Rd
 7f366aa4296dae452fb39f3131e3cf38 *man/voxelToWorld.Rd
 d1e37db347a3cdf2329fe98282c554d5 *man/writeNifti.Rd
 cd7905d91c416d05dc58c980254711fb *man/xform.Rd
-8e06de557abf2608ef1d50c13753683c *src/Makevars.in
-49abe6af876df7ba9299e3eda904dc59 *src/Makevars.win
-2b76d04b3924ab31ced53f5e08491d5e *src/main.cpp
-ba4b75f46c445369ab22405a14947c88 *src/niftilib/nifti1_io.c
+56634e57ebb5d93a068d62acb48c6b1a *src/Makevars.in
+08367357a0cc57225d43002490f619fa *src/Makevars.win
+dc85947bdd5b359584b04c8e8e0486d6 *src/main.cpp
+3ec9b546cf310cdb253ec203693e4e8d *src/niftilib/nifti1_io.c
 5bbd85dfe9831c8cda38edcfa4a60cd9 *src/niftilib/nifti2_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
+1167fcfa3f77ffa597b4f5a5b42d8e2c *src/zlib/Makefile.in
+cea51e08d9b176c6bf8b5820169d4102 *src/zlib/adler32.c
+b0b5688c87d809bb32d0923dbef28ee6 *src/zlib/compress.c
+27b59d6e86c24acba698841021daf84b *src/zlib/configure
+47f7b459ecb8e1cc0240d9ae8dda8e6e *src/zlib/crc32.c
+0ce0ac9394905aa53ed0a915620d9e5d *src/zlib/crc32.h
+35a956fb82eee2a69cf298d455e727d4 *src/zlib/deflate.c
+c4e786a4cb9b55522c1d084388abcee5 *src/zlib/deflate.h
+83049e4eaab1319f7ed94f15e7de5c4c *src/zlib/gzclose.c
+262b6710ab626436ee7e7ebe18f47212 *src/zlib/gzguts.h
+f2ae48e6c40e5c92b1b0074e1cb08e5f *src/zlib/gzlib.c
+1c8f8dfe08e58d6088a3b6c9bf4160bd *src/zlib/gzread.c
+fc122bb96017e7a19828e04a1b3dd564 *src/zlib/gzwrite.c
+1b8a0a4ebb220896e2610d292b821ce0 *src/zlib/infback.c
+1846b459fac461ded03f741f4953dc00 *src/zlib/inffast.c
+6c907e4d7c65aff48183101b66a6133b *src/zlib/inffast.h
 7fa3e91804601b6618c915b76a8dc332 *src/zlib/inffixed.h
-ec1b347da6284c0661decb41d3c50955 *src/zlib/inflate.c
-8f1b05cdf36a269882a955071b140162 *src/zlib/inflate.h
-3d0a4fce4b156f064e9be2aef36a7897 *src/zlib/inftrees.c
-ec87be89b9bcca8ced80a70f857e823b *src/zlib/inftrees.h
-bc195d555c24fecff56af6c06bd55b1d *src/zlib/trees.c
+6b32d46536f8c9adc0378ab9b9251fa4 *src/zlib/inflate.c
+819fb5556d0c65ba2577ee379b4641c0 *src/zlib/inflate.h
+b6705992b276162d6ea76cc0442bcd28 *src/zlib/inftrees.c
+ca4636a86335f58971f7a8944e5519b7 *src/zlib/inftrees.h
+3f55761581cbf60586a2c6380721e41d *src/zlib/trees.c
 51fdcb3e2ccf60ca13c06920c89296a3 *src/zlib/trees.h
-eabe905cdd27f5b935e6378cd0253418 *src/zlib/uncompr.c
-fff257bc1656eb60fc585a7dc35f963d *src/zlib/zutil.c
-de91a463004fd5b944c3d37eab0c1794 *src/zlib/zutil.h
+c76e0f7b934ca6695d453b1b51aa3112 *src/zlib/uncompr.c
+63cdfd6798d79c3d181b59daa84c5df0 *src/zlib/win32/Makefile.bor
+14edf6fc0eb45b3e0ae5b73cef7300f5 *src/zlib/win32/Makefile.gcc
+4b7373caa4e587e84d56b3719bfcc288 *src/zlib/win32/Makefile.msc
+684d84fae62becb5ad9d0b4a95d262bd *src/zlib/win32/zlib.def
+6ebfda6f8e9db737af5af76b5f06faa8 *src/zlib/win32/zlib1.rc
+bf9c9b7ce8a0434dc4f3ae1efdd5c1c4 *src/zlib/zconf.h
+bf9c9b7ce8a0434dc4f3ae1efdd5c1c4 *src/zlib/zconf.h.in
+b0d674489d5c40c17a7ab66238737af4 *src/zlib/zlib.h
+60674eee456b5cab09b25a4bfd55d533 *src/zlib/zlib.pc.in
+ef9f3b09085209c0193ab0686e1edd5b *src/zlib/zutil.c
+1e2f8af01fcb13b9b32ded1340092d11 *src/zlib/zutil.h
 420a0b8e9d75cd936a6d08acd1e7bf34 *src/znzlib/znzlib.c
 2960da031fea46eaffe3e3abedb78f29 *src/zzz.c
 d4a2abbb6217055b8900c8d86ac6aa53 *tests/testthat.R
 284ecfcebb44440aaf575935eb8a37dc *tests/testthat/Rplots.pdf
-9b78b59582b4b2dfdab2c3124c705535 *tests/testthat/test-05-nifti.R
+8ee24bd56273bdd9e13749822b8cae8f *tests/testthat/test-05-nifti.R
 923f10fc2c56863736b67257909b4e19 *tests/testthat/test-08-composite.R
 f586c7912239dbe87e5d75cfba3b4aee *tests/testthat/test-10-xform.R
 9cefc1807eb2fc89f6dcf799ca4b6e0b *tests/testthat/test-12-viewer.R

NEWS

@@ -2,6 +2,38 @@ Significant changes to the RNifti package are laid out below for each release.
 
 ===============================================================================
 
+VERSION 1.6.0
+
+R interface
+
+- The `niftiHeader()` function gains an "unused" argument. If `TRUE`, the
+  function's return value includes those legacy ANALYZE-7.5 fields that are
+  formally unused by the NIfTI-1 standard (or the last few bytes of a NIfTI-2
+  header). These fields cannot be set, however, as the `niftilib` I/O functions
+  discard them, and the core `nifti_image` structure does not represent them.
+  They also cannot be accessed with the `$` operator shorthand. The option is
+  therefore only useful to inspect file headers created by other software.
+
+API changes
+
+- The `NiftiImage` class now has constructors taking a NIfTI header structure.
+
+Other changes
+
+- The `NiftiImageData::Iterator` inner class now holds a pointer, not a
+  reference, to its parent. This doesn't really change the API, but ensures
+  that iterator objects are mutable, which is formally required by the C++
+  standard. (Prompted by Timothy Anderson, issue #31.)
+- There is now support for standalone use on Windows with the Visual C++
+  toolchain, including an `nmake`-compatible makefile, and this is now tested
+  as part of package CI. The package also no longer includes symlinks, for
+  better portability. (Prompted by Timothy Anderson, issue #31.)
+- The bundled `zlib` is now version 1.3. The included `zlib` headers are no
+  longer exposed to client packages if the system `zlib` is used for linkage,
+  as the two may be incompatible.
+
+===============================================================================
+
 VERSION 1.5.1
 
 - Several warnings from recent compilers relating to printf-style format

R/nifti.R

@@ -217,6 +217,9 @@ updateNifti <- function (image, template = NULL, datatype = "auto")
 #' @param image An image, in any acceptable form (see \code{\link{asNifti}}).
 #'   A list containing partial header information is acceptable, including an
 #'   empty list, which returns defaults for every field.
+#' @param unused Logical value. If \code{TRUE}, legacy ANALYZE and padding
+#'   fields that are unused by the relevant NIfTI standard are included in the
+#'   return value. These are occasionally used by software packages.
 #' @param x A \code{"niftiHeader"} object.
 #' @param ... Ignored.
 #' @return For \code{niftiHeader}, a list of class \code{"niftiHeader"}, with
@@ -246,13 +249,13 @@ updateNifti <- function (image, template = NULL, datatype = "auto")
 #' @references The NIfTI-1 standard (\url{https://www.nitrc.org/docman/view.php/26/64/nifti1.h}).
 #' @aliases dumpNifti
 #' @export niftiHeader dumpNifti
-niftiHeader <- dumpNifti <- function (image = list())
+niftiHeader <- dumpNifti <- function (image = list(), unused = FALSE)
 {
     # Special case to avoid expensively reading image data from file when only metadata is needed
     if (is.character(image) && length(image) == 1 && !inherits(image,"internalImage"))
-        .Call("niftiHeader", image, PACKAGE="RNifti")
+        .Call("niftiHeader", image, unused, PACKAGE="RNifti")
     else
-        .Call("niftiHeader", asNifti(image,internal=TRUE), PACKAGE="RNifti")
+        .Call("niftiHeader", asNifti(image,internal=TRUE), unused, PACKAGE="RNifti")
 }
 
 #' @rdname niftiHeader

README.md

@@ -1,6 +1,6 @@
 
 
-[![CRAN version](http://www.r-pkg.org/badges/version/RNifti)](https://cran.r-project.org/package=RNifti) [![CI](https://github.com/jonclayden/RNifti/actions/workflows/ci.yaml/badge.svg)](https://github.com/jonclayden/RNifti/actions/workflows/ci.yaml) [![Coverage Status](https://coveralls.io/repos/github/jonclayden/RNifti/badge.svg?branch=master)](https://coveralls.io/github/jonclayden/RNifti?branch=master)
+[![CRAN version](http://www.r-pkg.org/badges/version/RNifti)](https://cran.r-project.org/package=RNifti) [![CI](https://github.com/jonclayden/RNifti/actions/workflows/ci.yaml/badge.svg)](https://github.com/jonclayden/RNifti/actions/workflows/ci.yaml) [![codecov](https://codecov.io/gh/jonclayden/RNifti/graph/badge.svg?token=WTwyfvbbfL)](https://app.codecov.io/gh/jonclayden/RNifti) [![Dependencies](https://tinyverse.netlify.com/badge/RNifti)](https://tinyverse.netlify.app)
 
 # RNifti: Fast R and C++ Access to NIfTI Images
 
@@ -283,7 +283,7 @@ Moreover, when reading the file into an "internal" image, which does not copy th
 
 ## Implementation details
 
-The package does not fully duplicate the NIfTI structure's contents in R-visible objects. Instead, it passes key metadata back to R, such as the image dimensions and pixel dimensions, and it also passes back the pixel values where they are needed. Finally, it creates an [external pointer](http://r-manuals.flakery.org/R-exts.html#External-pointers-and-weak-references) to the native data structure, which is stored in an attribute. This pointer is dereferenced whenever the object is passed back to the C++ code, thereby avoiding unnecessary duplication and ensuring that all metadata remains intact. The full NIfTI-1 header can be obtained using the `niftiHeader` R function, if it is needed.
+The package does not fully duplicate the NIfTI structure's contents in R-visible objects. Instead, it passes key metadata back to R, such as the image dimensions and pixel dimensions, and it also passes back the pixel values where they are needed. Finally, it creates an [external pointer](https://r-manuals.flakery.org/R-exts.html#External-pointers-and-weak-references) to the native data structure, which is stored in an attribute. This pointer is dereferenced whenever the object is passed back to the C++ code, thereby avoiding unnecessary duplication and ensuring that all metadata remains intact. The full NIfTI-1 header can be obtained using the `niftiHeader` R function, if it is needed.
 
 This arrangement is efficient and generally works well, but certain R operations strip attributes—in which case the external pointer will be removed. The internal structure will be built again when necessary, but using default metadata. In these cases, if it is important to keep the original metadata, the `asNifti` function should be called explicitly, with a template object. This reconstructs the NIfTI data structure, using the template as a starting point.
 
@@ -294,7 +294,7 @@ It is possible to use the package's NIfTI-handling code in other R packages' com
 - `NiftiImage`, which simplifies memory management and supports the package's internal image pointers and associated reference counting, and
 - `NiftiImageData`, which encapsulates the pixel data within an image, and handles datatype multiplexing and data scaling, as well as providing indexing, iterators and other niceties.
 
-Full doxygen documentation for these classes is available at <http://doxygen.flakery.org/RNifti/>, and is also provided with package releases.
+Full doxygen documentation for these classes is available at <https://doxygen.flakery.org/RNifti/>, and is also provided with package releases.
 
 A third-party package can use the `NiftiImage` class by including
 

cleanup

@@ -1,3 +1,4 @@
 #!/bin/sh
 
-rm -f src/Makevars src/*.o src/niftilib/*.o src/zlib/*.o src/znzlib/*.o
+rm -f src/Makevars src/*.o src/niftilib/*.o src/znzlib/*.o inst/include/zlib.h inst/include/zconf.h
+rm -f src/zlib/*.o src/zlib/libz.*