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WIP read in metadata #487

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WIP read in metadata #487

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37 changes: 36 additions & 1 deletion R/neuron-io.R
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Original file line number Diff line number Diff line change
Expand Up @@ -268,6 +268,7 @@ read.neurons<-function(paths, pattern=NULL, neuronnames=NULL, format=NULL,
total = length(paths),
show_after=2)

mdl=list()
for(n in nn){
if(interactive())
pb$tick()
Expand All @@ -287,6 +288,11 @@ read.neurons<-function(paths, pattern=NULL, neuronnames=NULL, format=NULL,
nl=x
break
}
md <- attr(x, 'metadata')
if(!is.null(md)) {
mdl[[n]]=md
attr(x, 'metadata')=NULL
}
nl[[n]]=x
}

Expand All @@ -305,6 +311,10 @@ read.neurons<-function(paths, pattern=NULL, neuronnames=NULL, format=NULL,
}
# nb only keep dataframe rows for neurons that were successfully read in
# Look after the attached dataframe
if(is.null(df) && length(mdl)>0) {
df <- do.call(rbind, mdl)
rownames(df) <- names(mdl)
}
if(!is.null(df)){
data.frame(nl)=df
}
Expand Down Expand Up @@ -548,7 +558,11 @@ read.neuron.swc<-function(f, ...){
d=read.swc(f)
# multiply by 2 to get diam which is what I work with internally
d$W=d$W*2
as.neuron(d, InputFileName=f, ...)
d=as.neuron(d, InputFileName=f, ...)
metadata=read_swc_meta(f)
if(!is.null(metadata))
attr(d, 'metadata')=metadata
d
}

# internal function that just reads a table of SWC format data
Expand All @@ -566,6 +580,27 @@ read.swc<-function(f){
d
}

read_swc_comments <- function(f) {
con=file(f, open='r')
on.exit(close(con))
header=character()
while(TRUE) {
l=try(readLines(con = con, n=1), silent = T)
if(inherits(l, 'try-error') || nchar(l)<1 || substr(l,1,1)!="#")
break;
header=c(header, l)
}
header
}

read_swc_meta <- function(f, parse=TRUE) {
h=read_swc_comments(f)
if(!isTRUE(any(nchar(metal <- grep("^# Meta: ", h, value = TRUE))>0)))
return(NULL)
meta=substr(metal, nchar("# Meta: ")+1, nchar(metal))
if(isTRUE(parse)) jsonlite::fromJSON(meta, simplifyVector = F) else meta
}

#' @rdname read.neuron.swc
#' @inheritParams ngraph
#' @export
Expand Down