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- changed in r.apply the handling of missing dim / dim.spec: now returns
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the 1-dimensional scidb array with the renamed attributes
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@flahn
flahn committed Dec 22, 2016
1 parent 3d4e375 commit 01c3012
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Showing 2 changed files with 80 additions and 64 deletions.
4 changes: 2 additions & 2 deletions R/TRS-class-decl.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,12 @@
#' @rdname TRS-class
#' @name TRS
#' @slot t0 POSIXt derivative as the datum for this TRS
#' @slot tUnit character - The unit definition as used in \link{\code{difftime}}
#' @slot tUnit character - The unit definition as used in \code{\link{difftime}}
#' @slot tResolution numeric - The amount of tUnits that make up the resolution
#' @slot dimname character - The dimension name

#'
#' @details The tUnit is mostly used in cases where the function \link{\code{difftime}} is called. Therefore tUnit can either be "secs", "mins",
#' @details The tUnit is mostly used in cases where the function \code{\link{difftime}} is called. Therefore tUnit can either be "secs", "mins",
#' "hours", "days" or "weeks".
#'
#' @exportClass TRS
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140 changes: 78 additions & 62 deletions R/apply.R
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Original file line number Diff line number Diff line change
Expand Up @@ -239,27 +239,30 @@ if(!isGeneric("r.apply")) {
.apply.scidbst.fun = function(x,f,array,packages,parallel=FALSE,cores=1,aggregates,output,logfile,dim,dim.spec, method="rexec",...) {
dimMissing = missing(dim)

# checking the parameter for correctness
if (!is.list(dim)) {
if (is.character(dim)) {
l = length(dim)
n = dim
dim = vector("list",l)
names(dim) = n
} else {
stop("Parameter 'dim' is no character vector or named list.")
}
}
if (is.null(names(dim))) {
stop("Cannot infer dimension names, please state the names by assigning 'names(dim)'")
if (!dimMissing) {
# checking the parameter for correctness
if (!is.list(dim)) {
if (is.character(dim)) {
l = length(dim)
n = dim
dim = vector("list",l)
names(dim) = n
} else {
stop("Parameter 'dim' is no character vector or named list.")
}
}
if (is.null(names(dim))) {
stop("Cannot infer dimension names, please state the names by assigning 'names(dim)'")
}
# if dim is unlisted later, then null values disappear
dim = .nullToNA(dim)

# compare if all dimensions are in the output
if (!all(names(dim) %in% names(output))) {
stop("Cannot find dimensions in the output.")
}
}
# if dim is unlisted later, then null values disappear
dim = .nullToNA(dim)

# compare if all dimensions are in the output
if (!all(names(dim) %in% names(output))) {
stop("Cannot find dimensions in the output.")
}
###

attr = scidb_attributes(x)
Expand Down Expand Up @@ -293,40 +296,50 @@ if(!isGeneric("r.apply")) {
out = scidb(temp_name)

#execute the transform statement
outlist = .renameAndConvertArray(out,dim,output)
if (dimMissing) {
outlist = .renameAndConvertArray(out,dim=NULL,output)
} else {
outlist = .renameAndConvertArray(out,dim,output)
}

renamed = outlist$arr
output = outlist$output

if (!missing(dim.spec)) {
if (!dimMissing && !missing(dim.spec)) {
redim = .redimensionArray(renamed,dim, dim.spec,output)
} else {
# check if dimension names are already in the source array, if yes then pick schema of them

# create a complete vector of dimension names ( how they are called in the end)
newDims = unlist(dim)
newDims[is.na(newDims)] = names(dim)[is.na(newDims)]
names(newDims) = c()

if (all(newDims %in% dimensions(x))) {
# if all potentially renamed dimensions are already used in scidbst array "x", then take the schema from there
dim.spec = vector("list",length(newDims))
names(dim.spec) = newDims

oldDimsSpec = cbind(min=scidb_coordinate_start(x),
max=scidb_coordinate_end(x),
chunk = scidb_coordinate_chunksize(x),
overlap = scidb_coordinate_overlap(x))
rownames(oldDimsSpec) = dimensions(x)
for (dimname in newDims) {
dim.spec[[dimname]] = oldDimsSpec[dimname,]
}
redim = .redimensionArray(renamed,dim, dim.spec,output)
if (missing(dim)) {
return(scidb::project(renamed,names(output)))
} else {
#don't redimension, because we don't know what the new dimensions are...
warning("Cannot redimension the array processed by r_exec. Returned the renamed and projected array.")
# check if dimension names are already in the source array, if yes then pick schema of them

# create a complete vector of dimension names ( how they are called in the end)
newDims = unlist(dim)
newDims[is.na(newDims)] = names(dim)[is.na(newDims)]
names(newDims) = c()

if (all(newDims %in% dimensions(x))) {
# if all potentially renamed dimensions are already used in scidbst array "x", then take the schema from there
dim.spec = vector("list",length(newDims))
names(dim.spec) = newDims

oldDimsSpec = cbind(min=scidb_coordinate_start(x),
max=scidb_coordinate_end(x),
chunk = scidb_coordinate_chunksize(x),
overlap = scidb_coordinate_overlap(x))
rownames(oldDimsSpec) = dimensions(x)
for (dimname in newDims) {
dim.spec[[dimname]] = oldDimsSpec[dimname,]
}
redim = .redimensionArray(renamed,dim, dim.spec,output)
} else {
#don't redimension, because we don't know what the new dimensions are...
warning("Cannot redimension the array processed by r_exec. Returned the renamed and projected array.")

return(project(renamed),names(output))
return(scidb::project(renamed,names(output)))
}
}

}


Expand Down Expand Up @@ -362,29 +375,32 @@ if(!isGeneric("r.apply")) {

# transform call
.renameAndConvertArray = function(arr, dim, output) {
# requires dim to be contained completely in output
# find dimensions in output
dim.pos = which(names(dim) %in% names(output))
new.dim.names = unlist(dim[dim.pos])
renamingDims = new.dim.names[!is.na(new.dim.names)]
n = names(output)
n[which(n %in% names(renamingDims))] = renamingDims
if (!is.null(dim)) {
# requires dim to be contained completely in output
# find dimensions in output
dim.pos = which(names(dim) %in% names(output))
new.dim.names = unlist(dim[dim.pos])
renamingDims = new.dim.names[!is.na(new.dim.names)]
n = names(output)
n[which(n %in% names(renamingDims))] = renamingDims

names(output) = n
#make sure dimension are forced to be int64 values
output[dim.pos] = "int64"
}
expr.attr.name = paste("expr_value_",0:(length(output)-1),sep="")
transforms = paste(output[],"(",expr.attr.name,")",sep="")
names(transforms) = names(output)

names(output) = n
#make sure dimension are forced to be int64 values
output[dim.pos] = "int64"
# create an argument list for the do.call
calls = unlist(list(`_data`=arr,transforms))

expr.attr.name = paste("expr_value_",0:(length(output)-1),sep="")
transforms = paste(output[],"(",expr.attr.name,")",sep="")
names(transforms) = names(output)
renamed = do.call(transform,args=calls)

# create an argument list for the do.call
calls = unlist(list(`_data`=arr,transforms))

renamed = do.call(transform,args=calls)
return(list(arr=renamed,output=output))


return(list(arr=renamed,output=output))
}

.redimensionArray = function(arr,dim,dim.spec,output) {
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