Improve view specification for plot.neuron

[jdmanton]

Currently, only the views "XY", "YZ", "XZ" and "ZY" can be specified, and it is not clear what orientation they correspond to. Possible alternatives include:

1. Specifying which axis the view should look along and which axis should point to the right of the plot (allowing Along="Z", ToTheRight="-X", etc.).
2. Named views, perhaps constructed in such a way as to give the direction of the camera and its on-axis rotation with respect to anatomical directions, such as anterior-dorsal for the 'canonical' frontal view, left-ventral for a view from the brain's left with the ventral-most part of the brain at the top of the plot, posterior-right for a view from the 'back' of the brain, with the right-most parts at the top of the plot, etc.
3. Specifying the full vectors that correspond to the horizontal and vertical axes, such that the 'canonical' frontal view would be specified as Hori=c(1,0,0), Vert=c(0,-1,0).

1 and 3 require the user to understand that the coordinates correspond to a right-handed basis in which z recedes from the viewer, while 2 does not and is anatomically unambiguous.

While it would be possible to implement a system in which an arbitrary view could be specified, users should probably be pointed to plot3d.neuron instead...

[jefferis]

For "XY", "YZ", "XZ" compare with e.g. Amira Orthoslice. ZY has the Z and Y axes switched. YX and ZX are also possible but I never wanted them.

plot(Cell07PNs[[1]],PlotAxes = 'XY')
plot(Cell07PNs[[1]],PlotAxes = 'XZ')
plot(Cell07PNs[[1]],PlotAxes = 'YZ')
plot(Cell07PNs[[1]],PlotAxes = 'ZY')

something more explicit might be good, but I think 1 and 3 are a little complicated. 2 does sound interesting, but I wonder if we would need to have anatomical coords set in the input neurons or images.

[jefferis]

Incidentally, I don't know if nat needs to know about anatomical coordinate systems or not (see e.g. http://www.slicer.org/slicerWiki/index.php/Coordinate_systems). We do want to keep it general i.e. not tie it to any particular organism's anatomical conventions.

[jefferis]

Just a thought w.r.t. anatomical coordinate systems. It would be nice if we could tag data as belonging to a particular template (e.g. from nat.flybrains).