jefferis/nat: nat 1.9.0

We are bumping a whole version point because of some changes in the default behaviour of nat. We do not expect to submit this first version in the 1.9.x series to CRAN without further testing, but it is our current recommended version for general use.

Significant changes:

• read.neurons will name neurons in the neuronlist that it returns by their filename after removing the file extension. So the neuron read from file "n1.swc" will now be named "n1" not "n1.swc". (#383)

• write.swc normalises SWC files to maximise external compatibility. The canonical SWC form gives each point a numbered identifier increasing from 1 to the number of points. However many SWC files in the wild do not respect such an ordering. The new behaviour will result in cases where SWC files will be written out with a different point ordering from earlier versions of nat; nevertheless we prefer this behaviour since it is a source of confusion for new users since many external programs cannot read SWC files where this is not the case. The original behaviour can still be requested (#358).

• The use of operators e.g. adding or multiplying neurons by a constant is now provided by the Ops approach (see ?groupGeneric in main R help). This is a fairly large change under the hood, but should not have any user visible effects other than the fact that it is now possible to use the same functionality for hxsurf and mesh3d objects.

New vignettes:

• Working with Individual Neurons as Graph Structures
• NeuroGeometry: Analysing 3D Morphology of Neurons

Additional changes:

• Support for CMTK deformation fields
• Always pass on ... for reglists in xform() and friends. This ensures that nat.templatebrains::xform_brain can fall back to an affine registration when a non-rigid registration fails (#365)
• Fix thinko in re-ordering vertex ids for SWC files (#366)
• Add makeboundingbox() for constructing a boundingbox explicitly rather than from an object. This allows boundingbox() to work for matrices of 3D points (#222)
• Export nrrd.datafiles() + nrrd doc fixes (#316)
• Teach materials() to return col for amiramesh/im3d (#284)
• Fix nview3d() "oblique_right"
• Pass ... on to spheres3d to plot somata with alpha transparency (#370)
• as.data.frame.neuronlist() makes autonames when none present (#371)
• Check that ngraph() edgelist references valid vertices to avoid segfaults in igraph library (#363)
• Fix bug in constructing im3d() with image bounds (#205)
• Allow dotprops objects to be plotted in 2D (#112)
• Speed up spine() by only considering endpoints (#372)
• Export graph.nodes() and improve docs for root points (#373)
• Speed up pointsinside() by checking if inside bounding box of surface mesh (progress on #353)
• Teach read.neurons() to read remote zip file (#381)
• Fix invert_reglist() for mix of swapped/unswapped regs
• Fix bug in write.im3d()/write.nrrd() for raw detached nrrd (#384)
• Export is.im3d()