Significant changes to the RNifti package are laid out below for each release.

===============================================================================

VERSION 0.10.0

R interface

- Objects of class `niftiHeader`, created by the function of the same name,
  now also have core attributes such as `pixdim` and `pixunits`.
- Passing objects without a `dim` or `class` attribute to functions expecting
  an image will now produce a more informative error message.

API changes

- The `NiftiImage` class now uses a reference counting scheme, rather than
  relying on a simple persistence flag. (See the doxygen documentation for more
  details.) The `isPersistent` and `setPersistence` methods are therefore
  deprecated, with the former replaced by `isShared`.
- Images are no longer internally duplicated when being passed back to R. This
  improves the package's memory footprint, but performing an explicit copy may
  now be necessary in some circumstances, e.g., if the image's memory will be
  freed elsewhere.
- The `RNIFTI_VERSION` constant is now defined, as 100 * (major version) +
  (minor version). Its current value is therefore 10.
- The `niftilib` function `nifti_strdup` is now part of the package API.

Bug fixes

- The `pixdim()` and `pixunits()` functions will now work properly for path
  strings and other objects acceptable to `niftiHeader()`. (Reported by John
  Muschelli.)
- Other, smaller memory leaks have been resolved.

===============================================================================

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
  integer types.
- Usage of the R API has been updated for forwards compatibility.

===============================================================================

VERSION 0.7.0

- The new orientation() function can be used to identify the approximate
  storage orientation of an image. A replacement version allows the image
  data and metadata dimensions to be permuted and/or reversed.
- Image reorientation is similarly available through the C++ API.
- The sform and qform replacement methods should now follow R's usual
  semantics, and no longer modify the object in place if it is referred to by
  more than one name.
- The NiftiImage class is now suitable for use in standalone C++ projects.
  (Thanks to Matt Hall.)

===============================================================================

VERSION 0.6.0

- Slope and intercept values in a NIfTI-1 header are now applied to the image
  data when converting it to an R array (which will in this case always be of
  mode double), or a C++ vector.
- The slope and intercept will be reset to zero when updating the data in an
  internal image object.

===============================================================================

VERSION 0.5.1

- A potential crash and/or memory leak in the C++ NiftiImage copy assignment
  methods has been fixed.

===============================================================================

VERSION 0.5.0

- The NiftiImage class gains methods to drop or replace the image data, and to
  mutate its datatype in-place. A datatype no longer needs to be specified when
  writing an image to file using the toFile() C++ method.
- The niftilib functions nifti_image_unload() and nifti_mat44_to_orientation()
  are now exposed through the RNifti API.
- Some minor compiler warnings that would affect packages linking to RNifti
  have been resolved.
- Additional tests have been added, to exercise the package more thoroughly.

===============================================================================

VERSION 0.4.0

- Additional public methods have been added to the NiftiImage C++ class. Please
  see the API documentation at <http://doxygen.flakery.org/RNifti/> for
  details.
- The new origin() R function is a convenience wrapper for worldToVoxel(),
  which returns the voxel coordinates of the image origin.
- The package now produces an error when passed an "anlz" class object (from
  package "oro.nifti"), rather than mishandling it.

===============================================================================

VERSION 0.3.0

- C++ API change: the NiftiImage class is now defined within an RNifti
  namespace. This will break existing uses of the class, but compatibility with
  older versions of the package can be preserved if desired, by checking for
  the compile-time constant HAVE_RNIFTI_NAMESPACE, which will be defined from
  now on.
- Additional niftilib functions for calculating matrix norms and byte swapping
  are now exposed through the RNifti API.
- Calling the C/C++ function niftilib_register_all() more than once should no
  longer result in repeated re-registration of functions.

===============================================================================

VERSION 0.2.2

- The voxelToWorld() and worldToVoxel() functions now handle 2D points, rather
  than producing an error. (Reported by Takeo Katsuki.)

===============================================================================

VERSION 0.2.1

- Examples have been added to the R-level documentation.
- Image pixel dimensions are now used to return a more sensible xform matrix in
  the case where the NIfTI-1 sform and qform are both marked unknown.

===============================================================================

VERSION 0.2.0

- The writeNifti() function now performs path expansion on its argument,
  matching the behaviour of readNifti(). (Reported by John Muschelli.)
- Calling as.array() on an internal image containing no data now returns an
  array full of NAs (with a warning), rather than crashing R. (Reported by Tim
  Tierney.)
- The package should now work correctly with sparse MriImage objects, from
  first-party package "tractor.base".
- Images with invalid internal pointers are now handled (with a warning) by
  attempting to reconstruct the missing data structure. This should not happen
  in regular use, but can occur when external pointers are handed back to the
  main thread by worker threads when working in parallel. (Reported by Takeo
  Katsuki.)
- Calling the RNifti API from within OpenMP threads could previously lead to a
  stack imbalance. This is now guarded against, and a new C function,
  niftilib_register_all(), has been added as the recommended way to preregister
  all NIfTI-1 library functions wrapped by RNifti, particularly in threaded
  applications.
- Doxygen comments have been added to the C++ code to document the low-level
  API. A Doxyfile has also been added to the package root directory.

===============================================================================

VERSION 0.1.0

- First public release. Package code has been split off from "RNiftyReg".

===============================================================================
