updated all of it

.Rbuildignore

@@ -4,5 +4,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^appveyor.yml$
+^\.covrignore$
 ^standalone$
 ^revdep$

.covrignore

@@ -0,0 +1,2 @@
+src/zlib
+src/znzlib

.travis.yml

@@ -11,4 +11,4 @@ script:
 - 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(line_exclusions=as.list(list.files(file.path("src",c("zlib","znzlib")), full.names=TRUE)))'
+  - Rscript -e 'covr::coveralls()'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RNifti
-Version: 0.10.0
-Date: 2018-10-19
+Version: 0.11.0
+Date: 2019-06-17
 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"),
@@ -23,4 +23,4 @@ License: GPL-2
 URL: https://github.com/jonclayden/RNifti
 BugReports: https://github.com/jonclayden/RNifti/issues
 Encoding: UTF-8
-RoxygenNote: 6.1.1
+RoxygenNote: 6.1.0

Doxyfile

@@ -6,3 +6,4 @@ FILE_PATTERNS       = "NiftiImage.h"
 RECURSIVE           = NO
 GENERATE_LATEX      = NO
 JAVADOC_AUTOBRIEF   = YES
+EXCLUDE_SYMBOLS     = internal

NAMESPACE

@@ -2,6 +2,8 @@
 
 S3method("$",niftiImage)
 S3method("$<-",niftiImage)
+S3method("[",internalImage)
+S3method("[<-",internalImage)
 S3method("dim<-",internalImage)
 S3method("pixdim<-",default)
 S3method("pixunits<-",default)

NEWS

@@ -2,6 +2,33 @@ Significant changes to the RNifti package are laid out below for each release.
 
 ===============================================================================
 
+VERSION 0.11.0
+
+R interface
+
+- It is now possible to index directly into objects of class `internalImage`,
+  meaning that individual elements or arbitrary blocks may be converted to R
+  vectors or arrays, without needing to convert everything. This can save
+  significant amounts of memory for large images.
+
+API changes
+
+- This release introduces the `NiftiImageData` C++ class as the main way to
+  encapsulate the data in a NIfTI image. This class handles datatypes and data
+  scaling, and provides indexing, iterators and other niceties. The doxygen
+  documentation has full details.
+- As a result of this new introduction, the templated `getData()` method within
+  `NiftiImage` is deprecated in favour of `data()`, which returns a (constant
+  or mutable) object of class `NiftiImageData` rather than a standard `vector`.
+
+Bug fixes
+
+- The slope and intercept fields in `nifti` objects (from the `oro.nifti`
+  package) are now ignored, since that package does its own scaling. (Reported
+  by John Muschelli, issue #13.)
+
+===============================================================================
+
 VERSION 0.10.0
 
 R interface

R/image.R

@@ -7,9 +7,14 @@
 #' 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.
+#' @param value Not used. Changing the dimensions of (or data in) an internal
+#'   image is invalid, and will produce an error. Convert to an array first.
+#' @param i,j Index vectors. May be missing, which indicates that the whole of
+#'   the relevant dimension should be obtained.
+#' @param ... Additional parameters to methods. Only used for additional
+#'   indices.
+#' @param drop If \code{TRUE} (the default), unitary indices in the result will
+#'   be dropped. This mirrors the behaviour of standard array indexing.
 #' 
 #' @author Jon Clayden <code@@clayden.org>
 #' @rdname internalImage
@@ -34,6 +39,74 @@ as.array.internalImage <- function (x, ...)
     return (.Call("pointerToArray", x, PACKAGE="RNifti"))
 }
 
+#' @rdname internalImage
+#' @export
+"[.internalImage" <- function (x, i, j, ..., drop = TRUE)
+{
+    nArgs <- nargs() - as.integer(!missing(drop))
+    if (nArgs < 2)
+        return (as.array(x))
+
+    # Evaluate the indices, replacing missing values with -1
+    if (nArgs == 2)
+        indices <- substitute(list(i))
+    else
+        indices <- substitute(list(i,j,...))
+    present <- (sapply(indices, as.character)[-1] != "")
+    if (any(!present))
+        indices[which(!present)+1] <- -1
+    indices <- eval(indices, parent.frame())
+    lengths <- rep(-1L, nArgs - 1)
+    lengths[present] <- sapply(indices[present], length)
+
+    dims <- dim(x)
+    data <- NULL
+
+    if (all(lengths == -1))
+        return (as.array(x))
+    else if (any(lengths == 0))
+        return (numeric(0))
+    else if (nArgs == 2 && present[1])
+    {
+        if (is.matrix(i))
+        {
+            if (ncol(i) != length(dims))
+                stop("Index matrix should have as many columns as the image has dimensions")
+            strides <- c(1, cumprod(dims)[-length(dims)])
+            locs <- apply(i, 1, function(n) sum((n-1)*strides) + 1)
+        }
+        else
+            locs <- as.integer(i)
+
+        return (.Call("indexVector", x, locs, PACKAGE="RNifti"))
+    }
+    else if (nArgs != length(dims) + 1)
+        stop("Number of indices (", nArgs-1, ") not equal to the dimensionality of the image (", length(dims), ")")
+    else
+    {
+        data <- .Call("indexList", x, lapply(seq_along(indices), function(l) {
+            if (length(indices[[l]]) == 1 && indices[[l]] == -1)
+                seq_len(dims[l])
+            else if (is.logical(indices[[l]]))
+                which(indices[[l]])
+            else
+                indices[[l]]
+        }), PACKAGE="RNifti")
+        dim(data) <- ifelse(present, lengths, dims)
+    }
+
+    if (drop)
+        data <- drop(data)
+    return (data)
+}
+
+#' @rdname internalImage
+#' @export
+"[<-.internalImage" <- function (x, i, j, ..., value)
+{
+    stop("The data in an internal image cannot be changed - convert to array first")
+}
+
 #' @export
 print.niftiImage <- function (x, ...)
 {

README.md

@@ -195,7 +195,12 @@ This arrangement is efficient and generally works well, but many R operations st
 
 ## API
 
-It is possible to use the package's NIfTI-handling code in other R packages' compiled code, thereby obviating the need to duplicate the reference implementation. Moreover, `RNifti` provides a C++ wrapper class, `NiftiImage`, which simplifies memory management, supports the package's internal image pointers and persistence, and provides syntactic sugar. Full doxygen documentation for this class is available at <http://doxygen.flakery.org/RNifti/>, and is also provided with package releases.
+It is possible to use the package's NIfTI-handling code in other R packages' compiled code, thereby obviating the need to duplicate the reference implementation. Moreover, `RNifti` provides two key C++ wrapper classes:
+
+- `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.
 
 A third-party package can use the `NiftiImage` class by including
 
@@ -254,7 +259,7 @@ Thanks to contributions from [@soolijoo](https://github.com/soolijoo), it is pos
 | `src/znzlib/znzlib.c`           | Source for I/O functions from the NIfTI-1 reference implementation                                  |
 | `src/zlib/*`                    | `zlib` source files for reading and writing gzipped files (optional, as above)                      |
 
-Note that the `NiftiImage` class is header-only, but C code from the NIfTI-1 reference implementation will need to be compiled and linked into the project. The `print.h` header should be included before including `NiftiImage.h`, so that the R API is not used for printing error messages. The [`standalone` directory](https://github.com/jonclayden/RNifti/tree/master/standalone) provides a minimal example.
+Note that the `NiftiImage` and `NiftiImageData` classes are header-only, but C code from the NIfTI-1 reference implementation will need to be compiled and linked into the project. The `NiftiImage_print.h` header should be included before including `NiftiImage.h`, so that the R API is not used for printing error messages. The [`standalone` directory](https://github.com/jonclayden/RNifti/tree/master/standalone) provides a minimal example.
 
 ## The NIfTI-2 format
 

inst/include/RNifti.h

@@ -9,7 +9,7 @@
 // Defined since RNifti v0.10.0
 // Equal to 100 * (major version) + (minor version)
 // Does not change with patch level, since the API should not change
-#define RNIFTI_VERSION 10
+#define RNIFTI_VERSION 11
 
 #include "niftilib/nifti1_io.h"
 

inst/include/RNiftiAPI.h

@@ -18,6 +18,7 @@ static int(*_nifti_copy_extensions)(nifti_image*, const nifti_image*) = NULL;
 static void(*_nifti_image_unload)(nifti_image*) = NULL;
 static void(*_nifti_image_free)(nifti_image*) = NULL;
 
+static int(*_nifti_is_inttype)(int) = NULL;
 static void(*_nifti_datatype_sizes)(int, int*, int*) = NULL;
 static char const *(*_nifti_datatype_string)(int) = NULL;
 static char const *(*_nifti_units_string)(int) = NULL;
@@ -61,6 +62,7 @@ void niftilib_register_all ()
         _nifti_image_unload = (void(*)(nifti_image*)) R_GetCCallable("RNifti","nii_image_unload");
         _nifti_image_free = (void(*)(nifti_image*)) R_GetCCallable("RNifti","nii_image_free");
 
+        _nifti_is_inttype = (int(*)(int)) R_GetCCallable("RNifti","nii_is_inttype");
         _nifti_datatype_sizes = (void(*)(int, int*, int*)) R_GetCCallable("RNifti","nii_datatype_sizes");
         _nifti_datatype_string = (char const *(*)(int)) R_GetCCallable("RNifti","nii_datatype_string");
         _nifti_units_string = (char const *(*)(int)) R_GetCCallable("RNifti","nii_units_string");
@@ -146,6 +148,13 @@ void nifti_image_free (nifti_image *nim)
     _nifti_image_free(nim);
 }
 
+int nifti_is_inttype (int dt)
+{
+    if (_nifti_is_inttype == NULL)
+        niftilib_register_all();
+    return _nifti_is_inttype(dt);
+}
+
 void nifti_datatype_sizes (int datatype, int *nbyper, int *swapsize)
 {
     if (_nifti_datatype_sizes == NULL)