Gregory Jefferis

cmtk.streamxform and xform.default inconsistent with affine matrices

3

```r scalemat=rgl::scaleMatrix(8/1e3,8/1e3,8/1e3) pts=structure(c(23244, 23376, 23384, 22364, 23354, 4566, 23684, 23195.5, 23728, 23750, 31140, 31690, 31306, 33230, 32284, 20140, 32966, 33498.6, 31998, 32328, 26474, 26540, 25610, 26584, 25506, 8346, 26034, 26241.1,...

teach xform to scale neuron diameter when appropriate

5

Although neurons can easily be scaled with both points/radius information `xform` and friends (e.g. `xform_brain` currently can only transform point locations.

The key issue is that the `space dimensions` is assumed to consist of 3 vectors at various locations in the code, but in these 4D fields contains a `none` entry....

Currently only works for the main tree.

For neurons we return the node indices, for igraph/ngraph objects the node identifiers (aka names/PointNo). This is bad. However there is likely to be code in the wild that depends...

analogous to plot3d.hxsurf

add function to reroot neuron

2

and list it under [ngraph type functions](http://jefferis.github.io/nat/reference/index.html#section-neurons-as-graphs-). Simplest form: ```r reroot

simplify_reglist treats rds files on disk as cmtk reg files

1

e.g. ```r fcwb_chiangf fcwb_chiangf [[1]] [1] "/GD/dev/R/catnat/inst/extdata/CMTKreg/InitialAffine/initialiseCMTKreg_ChiangFemaleTowardsFCWB.rds" [[2]] [1] "/GD/dev/R/catnat/inst/extdata/CMTKreg/Registration/warp/FCWB_typicalbrainfemale_01_warp_m0g80c8e1e-1x26r4.list" attr(,"class") [1] "cmtkreg" "character" [[3]] [1] "/GD/dev/R/catnat/inst/extdata/CMTKreg/InitialAffine/finalaffine_ChiangFemaleTowardsFCWB.rds" attr(,"class") [1] "reglist" > > simplify_reglist(fcwb_chiangf) [1] "/GD/dev/R/catnat/inst/extdata/CMTKreg/InitialAffine" [2] "/GD/dev/R/catnat/inst/extdata/CMTKreg/Registration/warp/FCWB_typicalbrainfemale_01_warp_m0g80c8e1e-1x26r4.list" [3] "/GD/dev/R/catnat/inst/extdata/CMTKreg/InitialAffine" attr(,"class")...

Teach plot3d to plot soma radius

3

We could fetch the radius from the point tagged as soma

Several of the sample neurons have a loop due to a tracing error ``` > table(sapply(Cell07PNs, function(x) igraph::is.dag(as.ngraph(x)))) FALSE TRUE 9 31 ``` i.e. 9/40 neurons have cycles. This is...