dotprops | R Documentation |
dotprops
makes dotprops representation from raw 3D points
(extracting vertices from S3 objects that have them)
dotprops.character
makes dotprops objects from one or
more files on disk (typically binary segmentations saved as NRRDs).
x
can a vector of paths or be a directory (in which case
pattern
can be used to restrict the files to read). The ...
argument is passed first to nlapply
(if there is more than
one file) and then to dotprops.default
.
dotprops.dotprops
will default to the original vale of
k
and copy over all attributes that are not set by
dotprops.default
.
dotprops.neuronlist
will run for every object in the
neuronlist using nlapply
. ...
arguments will be passed to
nlapply
in addition to the named argument OmitFailures
.
is.dotprops(x)
as.dotprops(x, ...)
dotprops(x, ...)
## S3 method for class 'character'
dotprops(x, pattern = NULL, OmitFailures = NA, ...)
## S3 method for class 'dotprops'
dotprops(x, k = attr(x, "k"), ...)
## S3 method for class 'im3d'
dotprops(x, ...)
## S3 method for class 'neuronlist'
dotprops(x, ..., OmitFailures = NA)
## S3 method for class 'neuron'
dotprops(x, Labels = NULL, resample = NA, topo = FALSE, ...)
## Default S3 method:
dotprops(x, k = NULL, Labels = NULL, na.rm = FALSE, topo_features = NULL, ...)
x |
Object to be tested/converted |
... |
Additional arguments passed to methods |
pattern |
an optional regular expression. Only file names which match the regular expression will be returned. |
OmitFailures |
Whether to omit neurons for which |
k |
Number of nearest neighbours to use for tangent vector calculation (set to k=20 when passed NULL) |
Labels |
Vector of labels for each point e.g. identifying axon vs
dendrite. The default value |
resample |
When finite, a new length to which all segmented edges will
be resampled. See |
topo |
flag that says whether or not to add topological features (reversed Strahler Order and distance from soma) |
na.rm |
Whether to remove |
topo_features |
topological features of each dotprops |
k
will default to 20 nearest neighbours when unset (i.e. when
it has default value of NA) unless x
is a dotprops object (when the
original value of k
is reused).
The dotprops format is essentially identical to that developed in:
Masse N.Y., Cachero S., Ostrovsky A., and Jefferis G.S.X.E. (2012). A mutual information approach to automate identification of neuronal clusters in Drosophila brain images. Frontiers in Neuroinformatics 6 (00021). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3389/fninf.2012.00021")}
nlapply
## Not run:
# process a single file on disk
dp=dotprops.character('~/skeleton-nrrds/file01.nrrd', k=5)
# process a whole directory of files
dps=dotprops.character('~/skeleton-nrrds/', OmitFailures=T, k=5)
## End(Not run)
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