Nicer default output name for cmtk.reformatx

* closes https://github.com/jefferis/nat/issues/198
make cmtk.reformatx return output path

* since it can construct this when output is not specified
Initial work on xformimage and xform.character

* xform.character will call xformimage if it sees some image data
* at the moment this will not check image type
* xform.character could in theory handle other file types,
  e.g. neurons etc, but does not presently do this.
Fix test baseline for return val in cmtk.reformatx
Add xform(image) test
additional test for xformimage
Doc fixes
affine only registration not yet implemented
new cmtk.extract_affine function
cmtkreglist returns object with class cmtkreg
doc: cross-ref to cmtkreg
fix handling of affine matrix by xformimage

* nb makes use of tweaked behaviour of cmtkreglist
* fixes NOTE since as.cmtkreglist does not exist
cmtk.reforamtx passes ... args to cmtk.call

* also test this behaviour using interpolation
test that xformimage can use nn interpolation
Give cmtk.reformatx an explicit interpolation arg

* seems important enough to document due to behaviour re masks
* this is half of #201
e.g. of command line help for cmtk reformatx tool
give cmtk.reformatx a mask arg

* closes #201
better ordering of cmtk.reformatx args
fix cmtk.call handling of logical FALSE args

* should be omitted I think – could also use
  no-xxx but not sure this behaviour is consistent
* fixes a broken example revealed in 9c6d25c8a067e0e9bf005be81c23a3e71f3db8e1
Merge branch 'fix/xformimage'

* closes #143 amongst others
* fix/xformimage:
  fix cmtk.call handling of logical FALSE args
  better ordering of cmtk.reformatx args
  give cmtk.reformatx a mask arg
  e.g. of command line help for cmtk reformatx tool
  Give cmtk.reformatx an explicit interpolation arg
  test that xformimage can use nn interpolation
  cmtk.reforamtx passes ... args to cmtk.call
  fix handling of affine matrix by xformimage
  doc: cross-ref to cmtkreg
  cmtkreglist returns object with class cmtkreg
  new cmtk.extract_affine function
  affine only registration not yet implemented
  Doc fixes
  additional test for xformimage
  Add xform(image) test
  Fix test baseline for return val in cmtk.reformatx
  Initial work on xformimage and xform.character
  make cmtk.reformatx return output path
  Nicer default output name for cmtk.reformatx