R/subset_single_bracket.r
In adamlilith/fasterRaster: Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
#' Subset geometries of a GVector
#'
#' @description The `[` operator returns a subset or remove specific geometries of a `GVector`. You can get the number of geometries using [ngeom()]. Note that you cannot use this function to change the "order" in which geometries or their associated records in a data table appear. For example, `vector[1:3]` and `vector[3:1]` will yield the exact same results.
#'
#' Note that subsetting can take a very long time if you are retaining only a small number of geometries from a vector with many geometries. The routine selects geometries by removing those that are not in `i`. So if you can write code to remove fewer geometries (i.e., an "inverse" selection), it may go faster.
#'
#' @param x A `GVector`.
#'
#' @param i Numeric integer, integer, or logical vector: Indicates which geometry(ies) to obtain. Negative numeric or integer values will remove the given geometries from the output. If a logical vector is supplied and it is not the same length as the number of geometries, it will be recycled.
#'
#' @param j Numeric integer, integer, logical, or character: Indices or name(s) of the column(s) to obtain. You can see column names using [names()]. Negative numeric or integer values will remove the given columns from the output. If a logical vector is supplied and it is not the same length as the number of columns, it will be recycled.
#'
#' @returns A `GVector`.
#'
#' @example man/examples/ex_GRaster_GVector_subset_assign.r
#'
#' @seealso [subset()], [$], \code{\link[fasterRaster]{[[}}
#'
#' @name [
#' @aliases [,GVector,ANY,ANY-method
#' @docType methods
#' @rdname subset_single_bracket
#' @exportMethod [
methods::setMethod(
"[",
signature = c(x = "GVector", i = "ANY", j = "ANY"),
function(x, i, j) {
.locationRestore(x)
nGeoms <- ngeom(x)
if (missing(i) & missing(j)) {
out <- x
} else if (missing(i) & !missing(j)) {
out <- x[[i = j]]
} else if (all(1L:nGeoms %in% i) & !missing(j)) {
out <- x[[i = j]]
} else if (all(1L:nGeoms %in% i) & missing(j)) {
out <- x
} else if (!missing(i)) {
if (is.logical(i)) {
if (length(i) < nGeoms) i <- rep(i, length.out = nGeoms)
i <- which(i)
}
if (any(i > 0L) & any(i < 0L)) stop("Cannot mix positive and negative indices.")
# negative indices
if (all(i < 0L)) {
reverseRowSelect <- TRUE
iRev <- i
iSeq <- seq_len(nGeoms) # all possible i's
i <- iSeq[i] # retained i's
removeAll <- length(i) == 0L
} else {
reverseRowSelect <- removeAll <- FALSE
}
if (any(i > nGeoms) | any(i == 0L)) stop("Index out of bounds.")
i <- sort(i)
if (removeAll) {
out <- NULL # removed all
} else if (all(1L:nGeoms %in% i) & missing(j)) {
out <- x
} else {
# # # # will be deleting geometries from this copy
# # # src <- .copyGSpatial(x)
# # # cats <- .vCats(src)
# # # cats <- sort(unique(cats))
# # # iNot <- seq_len(nGeoms)
# # # iNot <- iNot[!(iNot %in% i)]
# # # cats <- cats[iNot] # will be removed
# # # # delete geometries in subsets bc removing large numbers of geometries at a time is inefficient
# # # done <- FALSE
# # # n <- 200000L # maximum number of cats to delete at a time (seqToSQL() usually stops far short)
# # # # n <- 10L # maximum number of cats to delete at a time (seqToSQL() usually stops far short)
# # # startFrom <- 1L
# # # numRemoved <- 0L
# # # stopAt <- min(length(cats), startFrom + n - 1L)
# # # while (!done) {
# # # thisCats <- cats[startFrom:stopAt]
# # # thisCats <- seqToSQL(thisCats)
# # # # <<< ORIGINAL -- selecting by deleting unwanted... VERY slow for large vectors >>>
# # # rgrass::execGRASS(
# # # cmd = "v.edit",
# # # map = src,
# # # # type = gtype, # breaks
# # # tool = "delete",
# # # cats = thisCats,
# # # flags = c(.quiet(), "overwrite")
# # # )
# # # # <<< end ORIGINAL >>>
# # # # args <- list(
# # # # cmd = "v.edit",
# # # # map = src,
# # # # # type = gtype, # breaks
# # # # tool = "delete",
# # # # cats = thisCats,
# # # # flags = c(.quiet(), "overwrite")
# # # # )
# # # # # if (geomtype(x) == "polygons") args$type <- "area"
# # # # # if (geomtype(x) == "points") args$flags <- c(args$flags, "b")
# # # # do.call(rgrass::execGRASS, args = args)
# # # # rgrass::execGRASS("v.build", map = src, option = "build", flags = c(.quiet(), "overwrite"))
# # # numRemoved <- numRemoved + attr(thisCats, "lastIndex")
# # # if (numRemoved == length(cats)) {
# # # done <- TRUE
# # # } else {
# # # startFrom <- startFrom + attr(thisCats, "lastIndex") # what was the index of the last used cat?
# # # stopAt <- min(length(cats), startFrom + n)
# # # }
# # # } # next removal
# # # # check to see if all cats have been removed
# # # # a hack... for some reason, seqToSQL may not list all cats
# # # newCats <- .vCats(src)
# # # badCats <- cats[cats %in% newCats]
# # # if (length(badCats) > 0L) {
# # # badCats <- cats[cats %in% newCats]
# # # thisCats <- seqToSQL(badCats)
# # # rgrass::execGRASS(
# # # cmd = "v.edit",
# # # map = src,
# # # # type = gtype, # breaks
# # # tool = "delete",
# # # cats = thisCats,
# # # flags = c(.quiet(), "overwrite")
# # # )
# # # newCats <- newCats[!(newCats %in% badCats)]
# # # }
# ### WORKS!!!!! Keeping copy.
# src <- .makeSourceName("subset_single_bracket_v_extract", "vector")
# cats <- .vCats(sources(x))
# cats <- unique(cats)
# cats <- cats[cats %in% i] # selects same as GVector but wrong geometry
# sqlCats <- seqToSQL(cats)
# sqlCats <- as.character(sqlCats)
# gtype <- geomtype(x, grass = TRUE)
# ### ^^^ WORKS!!!!! Keeping copy.
gtype <- geomtype(x, grass = TRUE)
src <- .makeSourceName("subset_single_bracket_v_extract", "vector")
cats <- .vCats(sources(x))
cats <- unique(cats)
keepCats <- cats[cats %in% i] # selects same as GVector but wrong geometry
args <- list(
cmd = "v.extract",
input = sources(x),
output = src,
type = gtype,
flags = c(.quiet(), "overwrite")
)
if (gtype == "point") {
# selecting geometries using database method
qid <- rep(0L, nGeoms)
qid[keepCats] <- 1L
db <- data.table::data.table(cat = cats, qid = qid)
.vAttachDatabase(x, db)
args$where <- "qid = 1" # will not work with inequalities
} else if (gtype %in% c("area", "line")) {
sqlCats <- seqToSQL(keepCats)
sqlCats <- as.character(sqlCats)
args$cats <- sqlCats
}
do.call(rgrass::execGRASS, args = args)
src <- .vRecat(src, gtype = gtype, cats = keepCats)
# srcs <- character()
# trim <- TRUE
# j <- 1L
# while (trim) {
# if (j > 1L) {
# thisKeepCats <- seqToSQL(keepCats[(stoppedAt + 1):length(i)])
# stoppedAt <- attr(thisKeepCats, "lastIndex")
# trim <- attr(thisKeepCats, "trim")
# }
# thisKeepCats <- as.character(thisKeepCats)
# srcs[j] <- .makeSourceName("single_bracket_select_v_extract", "vector")
# rgrass::execGRASS(
# cmd = "v.extract",
# input = sources(x),
# output = srcs[j],
# cats = thisKeepCats,
# type = gtype,
# flags = c(.quiet(), "overwrite")
# )
# j <- j + 1L
# }
# }
# renumber cats so they start from 1 and are sequential
} # not removing all and not removing nothing
### select data table rows and columns
if (nrow(x) == 0L) {
table <- NULL
} else if (!removeAll) {
table <- x@table
# select columns
if (missing(j)) {
removeAllCols <- FALSE
} else {
nc <- ncol(table)
if (is.character(j)) {
j <- match(j, names(table))
} else if (is.logical(j)) {
if (length(j) < nc) j <- rep(j, length.out = nc)
j <- which(j)
}
if (all(j < 0L)) {
reverseColSelect <- TRUE
j <- j * -1L
removeAllCols <- (all(sort(j) == seq_len(ncol(x))))
} else {
reverseColSelect <- removeAllCols <- FALSE
}
if (any(j > nc)) stop("Index out of bounds.")
if (removeAllCols) {
table <- data.table::data.table(NULL)
} else {
# ..j <- NULL
if (reverseColSelect) {
j <- setdiff(names(x), names(x)[j])
} else {
j <- names(x)[j]
}
table <- table[ , ..j, with = FALSE]
}
}
# select rows
if (!removeAllCols) {
if (reverseRowSelect) {
table <- table[iRev]
} else {
table <- table[i]
}
}
} # vector has table
if (removeAll) {
out <- NULL
} else {
# out <- .makeGVector(src, table = table, cats = newCats)
out <- .makeGVector(src, table = table)
}
}
out
} # EOF
)
#' @name [
#' @aliases [,GRaster,GRaster,ANY-method
#' @docType methods
#' @rdname subset_single_bracket
#' @exportMethod [
methods::setMethod(
"[",
signature = c(x = "GRaster", i = "GRaster", j = "ANY"),
function(x, i, j) {
.locationRestore(x)
.region(x)
if (missing(j)) j <- NULL
nLayers <- nlyr(x)
nLayersI <- nlyr(i)
if (nLayersI != nLayers) {
if (nlyr(i) != 1L) warning("The number of layers in the subset raster (inside the `[]`) does not have\n the same number of layers as the raster to be subset. The layers inside\n the square brackets will be recycled.")
iIndex <- rep(seq_len(nLayersI), length.out = nLayers)
i <- i[[iIndex]]
}
srcs <- .makeSourceName("subset_single_bracket", "raster", nLayers)
for (count in seq_len(nLayers)) {
if (!(.minVal(i)[count] %in% c(NA, 0, 1)) & !(.maxVal(i)[count] %in% c(NA, 0, 1))) stop("The GRaster in `i` must 0, 1, or NA values.")
ex <- paste0(srcs[count], " = if(", sources(i)[count], " == 1, ", sources(x)[count], ", 0)")
rgrass::execGRASS("r.mapcalc", expression = ex, flags = c(.quiet(), "overwrite"))
}
.makeGRaster(srcs, names(x), levels = cats(x), ac = activeCats(x))
} # EOF
)
adamlilith/fasterRaster documentation built on Oct. 26, 2024, 4:06 p.m.
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#' Subset geometries of a GVector
#'
#' @description The `[` operator returns a subset or remove specific geometries of a `GVector`. You can get the number of geometries using [ngeom()]. Note that you cannot use this function to change the "order" in which geometries or their associated records in a data table appear. For example, `vector[1:3]` and `vector[3:1]` will yield the exact same results.
#'
#' Note that subsetting can take a very long time if you are retaining only a small number of geometries from a vector with many geometries. The routine selects geometries by removing those that are not in `i`. So if you can write code to remove fewer geometries (i.e., an "inverse" selection), it may go faster.
#'
#' @param x A `GVector`.
#'
#' @param i Numeric integer, integer, or logical vector: Indicates which geometry(ies) to obtain. Negative numeric or integer values will remove the given geometries from the output. If a logical vector is supplied and it is not the same length as the number of geometries, it will be recycled.
#'
#' @param j Numeric integer, integer, logical, or character: Indices or name(s) of the column(s) to obtain. You can see column names using [names()]. Negative numeric or integer values will remove the given columns from the output. If a logical vector is supplied and it is not the same length as the number of columns, it will be recycled.
#'
#' @returns A `GVector`.
#'
#' @example man/examples/ex_GRaster_GVector_subset_assign.r
#'
#' @seealso [subset()], [$], \code{\link[fasterRaster]{[[}}
#'
#' @name [
#' @aliases [,GVector,ANY,ANY-method
#' @docType methods
#' @rdname subset_single_bracket
#' @exportMethod [
methods::setMethod(
"[",
signature = c(x = "GVector", i = "ANY", j = "ANY"),
function(x, i, j) {
.locationRestore(x)
nGeoms <- ngeom(x)
if (missing(i) & missing(j)) {
out <- x
} else if (missing(i) & !missing(j)) {
out <- x[[i = j]]
} else if (all(1L:nGeoms %in% i) & !missing(j)) {
out <- x[[i = j]]
} else if (all(1L:nGeoms %in% i) & missing(j)) {
out <- x
} else if (!missing(i)) {
if (is.logical(i)) {
if (length(i) < nGeoms) i <- rep(i, length.out = nGeoms)
i <- which(i)
}
if (any(i > 0L) & any(i < 0L)) stop("Cannot mix positive and negative indices.")
# negative indices
if (all(i < 0L)) {
reverseRowSelect <- TRUE
iRev <- i
iSeq <- seq_len(nGeoms) # all possible i's
i <- iSeq[i] # retained i's
removeAll <- length(i) == 0L
} else {
reverseRowSelect <- removeAll <- FALSE
}
if (any(i > nGeoms) | any(i == 0L)) stop("Index out of bounds.")
i <- sort(i)
if (removeAll) {
out <- NULL # removed all
} else if (all(1L:nGeoms %in% i) & missing(j)) {
out <- x
} else {
# # # # will be deleting geometries from this copy
# # # src <- .copyGSpatial(x)
# # # cats <- .vCats(src)
# # # cats <- sort(unique(cats))
# # # iNot <- seq_len(nGeoms)
# # # iNot <- iNot[!(iNot %in% i)]
# # # cats <- cats[iNot] # will be removed
# # # # delete geometries in subsets bc removing large numbers of geometries at a time is inefficient
# # # done <- FALSE
# # # n <- 200000L # maximum number of cats to delete at a time (seqToSQL() usually stops far short)
# # # # n <- 10L # maximum number of cats to delete at a time (seqToSQL() usually stops far short)
# # # startFrom <- 1L
# # # numRemoved <- 0L
# # # stopAt <- min(length(cats), startFrom + n - 1L)
# # # while (!done) {
# # # thisCats <- cats[startFrom:stopAt]
# # # thisCats <- seqToSQL(thisCats)
# # # # <<< ORIGINAL -- selecting by deleting unwanted... VERY slow for large vectors >>>
# # # rgrass::execGRASS(
# # # cmd = "v.edit",
# # # map = src,
# # # # type = gtype, # breaks
# # # tool = "delete",
# # # cats = thisCats,
# # # flags = c(.quiet(), "overwrite")
# # # )
# # # # <<< end ORIGINAL >>>
# # # # args <- list(
# # # # cmd = "v.edit",
# # # # map = src,
# # # # # type = gtype, # breaks
# # # # tool = "delete",
# # # # cats = thisCats,
# # # # flags = c(.quiet(), "overwrite")
# # # # )
# # # # # if (geomtype(x) == "polygons") args$type <- "area"
# # # # # if (geomtype(x) == "points") args$flags <- c(args$flags, "b")
# # # # do.call(rgrass::execGRASS, args = args)
# # # # rgrass::execGRASS("v.build", map = src, option = "build", flags = c(.quiet(), "overwrite"))
# # # numRemoved <- numRemoved + attr(thisCats, "lastIndex")
# # # if (numRemoved == length(cats)) {
# # # done <- TRUE
# # # } else {
# # # startFrom <- startFrom + attr(thisCats, "lastIndex") # what was the index of the last used cat?
# # # stopAt <- min(length(cats), startFrom + n)
# # # }
# # # } # next removal
# # # # check to see if all cats have been removed
# # # # a hack... for some reason, seqToSQL may not list all cats
# # # newCats <- .vCats(src)
# # # badCats <- cats[cats %in% newCats]
# # # if (length(badCats) > 0L) {
# # # badCats <- cats[cats %in% newCats]
# # # thisCats <- seqToSQL(badCats)
# # # rgrass::execGRASS(
# # # cmd = "v.edit",
# # # map = src,
# # # # type = gtype, # breaks
# # # tool = "delete",
# # # cats = thisCats,
# # # flags = c(.quiet(), "overwrite")
# # # )
# # # newCats <- newCats[!(newCats %in% badCats)]
# # # }
# ### WORKS!!!!! Keeping copy.
# src <- .makeSourceName("subset_single_bracket_v_extract", "vector")
# cats <- .vCats(sources(x))
# cats <- unique(cats)
# cats <- cats[cats %in% i] # selects same as GVector but wrong geometry
# sqlCats <- seqToSQL(cats)
# sqlCats <- as.character(sqlCats)
# gtype <- geomtype(x, grass = TRUE)
# ### ^^^ WORKS!!!!! Keeping copy.
gtype <- geomtype(x, grass = TRUE)
src <- .makeSourceName("subset_single_bracket_v_extract", "vector")
cats <- .vCats(sources(x))
cats <- unique(cats)
keepCats <- cats[cats %in% i] # selects same as GVector but wrong geometry
args <- list(
cmd = "v.extract",
input = sources(x),
output = src,
type = gtype,
flags = c(.quiet(), "overwrite")
)
if (gtype == "point") {
# selecting geometries using database method
qid <- rep(0L, nGeoms)
qid[keepCats] <- 1L
db <- data.table::data.table(cat = cats, qid = qid)
.vAttachDatabase(x, db)
args$where <- "qid = 1" # will not work with inequalities
} else if (gtype %in% c("area", "line")) {
sqlCats <- seqToSQL(keepCats)
sqlCats <- as.character(sqlCats)
args$cats <- sqlCats
}
do.call(rgrass::execGRASS, args = args)
src <- .vRecat(src, gtype = gtype, cats = keepCats)
# srcs <- character()
# trim <- TRUE
# j <- 1L
# while (trim) {
# if (j > 1L) {
# thisKeepCats <- seqToSQL(keepCats[(stoppedAt + 1):length(i)])
# stoppedAt <- attr(thisKeepCats, "lastIndex")
# trim <- attr(thisKeepCats, "trim")
# }
# thisKeepCats <- as.character(thisKeepCats)
# srcs[j] <- .makeSourceName("single_bracket_select_v_extract", "vector")
# rgrass::execGRASS(
# cmd = "v.extract",
# input = sources(x),
# output = srcs[j],
# cats = thisKeepCats,
# type = gtype,
# flags = c(.quiet(), "overwrite")
# )
# j <- j + 1L
# }
# }
# renumber cats so they start from 1 and are sequential
} # not removing all and not removing nothing
### select data table rows and columns
if (nrow(x) == 0L) {
table <- NULL
} else if (!removeAll) {
table <- x@table
# select columns
if (missing(j)) {
removeAllCols <- FALSE
} else {
nc <- ncol(table)
if (is.character(j)) {
j <- match(j, names(table))
} else if (is.logical(j)) {
if (length(j) < nc) j <- rep(j, length.out = nc)
j <- which(j)
}
if (all(j < 0L)) {
reverseColSelect <- TRUE
j <- j * -1L
removeAllCols <- (all(sort(j) == seq_len(ncol(x))))
} else {
reverseColSelect <- removeAllCols <- FALSE
}
if (any(j > nc)) stop("Index out of bounds.")
if (removeAllCols) {
table <- data.table::data.table(NULL)
} else {
# ..j <- NULL
if (reverseColSelect) {
j <- setdiff(names(x), names(x)[j])
} else {
j <- names(x)[j]
}
table <- table[ , ..j, with = FALSE]
}
}
# select rows
if (!removeAllCols) {
if (reverseRowSelect) {
table <- table[iRev]
} else {
table <- table[i]
}
}
} # vector has table
if (removeAll) {
out <- NULL
} else {
# out <- .makeGVector(src, table = table, cats = newCats)
out <- .makeGVector(src, table = table)
}
}
out
} # EOF
)
#' @name [
#' @aliases [,GRaster,GRaster,ANY-method
#' @docType methods
#' @rdname subset_single_bracket
#' @exportMethod [
methods::setMethod(
"[",
signature = c(x = "GRaster", i = "GRaster", j = "ANY"),
function(x, i, j) {
.locationRestore(x)
.region(x)
if (missing(j)) j <- NULL
nLayers <- nlyr(x)
nLayersI <- nlyr(i)
if (nLayersI != nLayers) {
if (nlyr(i) != 1L) warning("The number of layers in the subset raster (inside the `[]`) does not have\n the same number of layers as the raster to be subset. The layers inside\n the square brackets will be recycled.")
iIndex <- rep(seq_len(nLayersI), length.out = nLayers)
i <- i[[iIndex]]
}
srcs <- .makeSourceName("subset_single_bracket", "raster", nLayers)
for (count in seq_len(nLayers)) {
if (!(.minVal(i)[count] %in% c(NA, 0, 1)) & !(.maxVal(i)[count] %in% c(NA, 0, 1))) stop("The GRaster in `i` must 0, 1, or NA values.")
ex <- paste0(srcs[count], " = if(", sources(i)[count], " == 1, ", sources(x)[count], ", 0)")
rgrass::execGRASS("r.mapcalc", expression = ex, flags = c(.quiet(), "overwrite"))
}
.makeGRaster(srcs, names(x), levels = cats(x), ac = activeCats(x))
} # EOF
)
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