R/jamba-matrix.R
In jmw86069/jamba: Jam Base Methods
#' Fix matrix dimension ratio
#'
#' Fix matrix dimension ratio
#'
#' This function is experimental, replicating the logic used inside
#' `imageDefault()` to ensure a numeric matrix is roughly 1:1 ratio
#' of nrow:ncol. It currently duplicates columns or rows `n` times
#' in an effort to make the resulting matrix less than a 2:1 ratio.
#' The purpose is to allow `rasterImage()` or `grid.raster()` with
#' argument `interpolate=TRUE` to produce an output raster image
#' that has interpolated the image with reasonably square pixels.
#' Without this adjustment, a matrix with 2,000 rows and 10 columns
#' would be interpolated much more on the x-axis than the y-axis,
#' blurring the data along the x-axis.
#'
#' The main goal is to enable arguments `useRaster=TRUE` and
#' `interpolate=TRUE` which allows an output image to contain
#' more rows than pixels, and still have the pixels represent
#' properly smoothed content.
#'
#' See the examples for visual examples of the effect, showing
#' `image.default()`, `jamba::imageDefault()`,
#' `graphics::rasterImage()`, and `grid::grid.raster()`.
#'
#' @param x `matrix` input
#' @param maxRatioFix integer value indicating the maximum multiple
#' used to duplicate columns or rows. This value is used to prevent
#' replicating a matrix with 1 million rows and 10 columns into
#' a 10 million by 10 million matrix. For example `maxRatioFix=100`
#' will not replicate columns or rows more than 100 times.
#' @param ratioThreshold numeric value indicating the ratio of nrow:ncol
#' above which this function will adjust the dimensions of the
#' output matrix. For example when `ratioThreshold=3` there must be
#' 3 times more rows than columns, or 3 times more columns than rows.
#' @param rasterTarget integer number reflecting the target minimum
#' number of rows and columns. This value is used to protect from
#' interpolating a 5x5 matrix, which yields a blurry result. When
#' `rasterTarget=200`, a 5x5 matrix will be expanded to 200x200,
#' and the 200x200 matrix will be interpolated to yield a sharp image.
#' @param minRasterMultiple integer vector of 1 or 2 values, referring
#' to the minimum number of times each row or column is replicated,
#' respectively. For example `minRasterMultiple=c(2,5)` will at minimum
#' replicate each row 2 times, and each column 5 times.
#' @param verbose logical indicating whether to print verbose output.
#' @param ... additional arguments are ignored.
#'
#' @examples
#' m <- matrix(rainbow(9), ncol=3);
#' m2 <- fix_matrix_ratio(m);
#' par("mfrow"=c(1,3));
#' imageByColors(m, useRaster=FALSE,
#' main="m\nuseRaster=FALSE");
#' imageByColors(m, useRaster=TRUE, fixRasterRatio=FALSE,
#' main="m\nuseRaster=FALSE\nfixRasterRatio=FALSE");
#' imageByColors(m2, useRaster=TRUE, fixRasterRatio=FALSE,
#' main="m2\nuseRaster=FALSE\nfixRasterRatio=FALSE");
#'
#' m <- matrix(colors()[1:90], ncol=3)
#' dim(m)
#' m2 <- fix_matrix_ratio(m);
#' dim(m2);
#' par("mfrow"=c(1,4));
#' imageByColors(m, useRaster=FALSE,
#' main="m\nuseRaster=FALSE");
#' imageByColors(m, useRaster=TRUE, interpolate=FALSE,
#' main="m\nuseRaster=TRUE\ninterpolate=FALSE");
#' imageByColors(m, useRaster=TRUE, interpolate=TRUE, fixRasterRatio=FALSE,
#' main="m\nuseRaster=TRUE\ninterpolate=TRUE");
#' imageByColors(m2, useRaster=TRUE, fixRasterRatio=FALSE,
#' main="fix_matrix_ratio(m)\nuseRaster=TRUE\ninterpolate=TRUE");
#' par("mfrow"=c(1,1));
#'
#' ## Complicated example showing the effect of interpolate=TRUE
#' testHeatdata <- matrix(rnorm(90000), ncol=9)[,1:9];
#' testHeatdata <- testHeatdata[order(testHeatdata[,5]),];
#' g1 <- seq(from=10, to=10000, by=1000);
#' testHeatdata[g1+rep(1:3, each=length(g1)),] <- 9;
#' for (i in seq(from=125, to=235, by=3)) {
#' ix <- round(sin(deg2rad(i))*5+5);
#' iy <- round(-cos(deg2rad(i))*5500 + 3500);
#' testHeatdata[iy:(iy+4), ix] <- 10;
#' }
#' g2 <- 3011+c(1:12*90);
#' testHeatdata[g2+rep(1:3, each=length(g2)), c(3,7)] <- 10;
#' testHeatdata <- testHeatdata[10000:1,];
#' col <- getColorRamp("RdBu_r", n=15, lens=1, trimRamp=c(4,1));
#' par("mfrow"=c(1,2));
#' image.default(z=t(testHeatdata), col=col, useRaster=TRUE,
#' main="image.default(..., useRaster=TRUE,\ninterpolate=FALSE)");
#' imageDefault(z=t(testHeatdata), col=col, useRaster=TRUE,
#' main="imageDefault(..., useRaster=TRUE,\ninterpolate=TRUE)");
#' par("mfrow"=c(1,1));
#'
#' m2r <- as.raster(m2);
#' nullPlot(xaxs="i", yaxs="i",
#' main="using rasterImage()");
#' rasterImage(m2r, xleft=1, xright=2, ybottom=1, ytop=2);
#'
#' if (require(grid)) {
#' testHeatdata2 <- testHeatdata[10000:1,,drop=FALSE];
#' testHeatdata2[] <- circlize::colorRamp2(breaks=seq(from=-10, to=10, length.out=25),
#' colors=getColorRamp("RdBu_r", n=25))(testHeatdata2);
#' testHeatdata2 <- fix_matrix_ratio(testHeatdata2);
#' m2r <- as.raster(testHeatdata2);
#' par("mfrow"=c(1,1));
#' nullPlot(xaxs="i", yaxs="i",
#' doBoxes=FALSE);
#' grid::grid.raster(m2r,
#' x=grid::unit(0.5, "npc"),
#' y=grid::unit(0.5, "npc"),
#' height=grid::unit(1, "npc"),
#' width=grid::unit(1, "npc"),
#' interpolate=FALSE);
#' title(main="using grid.raster(..., interpolate=FALSE)")
#' nullPlot(xaxs="i", yaxs="i",
#' doBoxes=FALSE);
#' grid::grid.raster(m2r,
#' x=grid::unit(0.5, "npc"),
#' y=grid::unit(0.5, "npc"),
#' height=grid::unit(1, "npc"),
#' width=grid::unit(1, "npc"),
#' interpolate=TRUE);
#' title(main="using grid.raster(..., interpolate=TRUE)")
#' }
#'
#' ## Example showing usr coordinates for grid.raster()
#' if (require(gridBase)) {
#' nullPlot(xaxs="i", yaxs="i",
#' main="gridBase grid.raster(..., interpolate=TRUE)");
#' vps <- gridBase::baseViewports();
#' grid::pushViewport(vps$inner, vps$figure, vps$plot);
#' grid::grid.raster(m2r,
#' x=grid::unit(1.5, "native"),
#' y=grid::unit(1.5, "native"),
#' height=grid::unit(1, "native"),
#' width=grid::unit(1, "native"),
#' interpolate=TRUE);
#' grid::popViewport(3);
#' }
#'
#' @family jam numeric functions
#'
#' @export
fix_matrix_ratio <- function
(x,
maxRatioFix=10,
minRasterMultiple=NULL,
rasterTarget=200,
ratioThreshold=3,
verbose=FALSE,
...)
{
if (!is.matrix(x)) {
stop("x must be a matrix");
}
if (length(x) == 0) {
return(x);
}
if (length(ratioThreshold) == 0) {
ratioThreshold <- 3;
}
ratioThreshold <- head(ratioThreshold, 1);
if (ratioThreshold < 1) {
stop("ratioThreshold must be higher than 1.");
}
rasterTarget <- rep(rasterTarget, length.out=2);
if (length(minRasterMultiple) == 0) {
if (length(rasterTarget) > 0) {
minRasterMultiple <- c(ceiling(rasterTarget[1]/nrow(x)),
ceiling(rasterTarget[2]/ncol(x)));
} else {
minRasterMultiple <- c(1,1);
}
} else {
minRasterMultiple <- rep(minRasterMultiple, length.out=2);
}
if (verbose) {
printDebug("minRasterMultiple:", minRasterMultiple);
}
if (!is.null(maxRatioFix)) {
maxRatioFix <- rep(maxRatioFix, length.out=2);
}
if (any(minRasterMultiple > 1) ||
(nrow(x)-1) > ratioThreshold * (ncol(x)-1) ||
(ncol(x) > ratioThreshold * nrow(x)) ) {
if (verbose) {
printDebug("fix_matrix_ratio(): ",
c("Fixing the matrix ratio."));
}
dimRange <- range(c(ncol(x), nrow(x)));
if (ncol(x) > ratioThreshold * nrow(x)) {
dupRowX <- floor((ncol(x)-1)/(nrow(x)-1));
dupRowX <- min(c(dupRowX, maxRatioFix[1]));
dupColX <- 1;
} else {
dupColX <- floor((nrow(x)-1)/(ncol(x)-1));
dupColX <- min(c(dupColX, maxRatioFix[2]));
dupRowX <- 1;
}
if (verbose) {
printDebug("fix_matrix_ratio(): ",
"dupColX: ",
dupColX);
printDebug("fix_matrix_ratio(): ",
"dupRowX: ",
dupRowX);
}
## Ensure that minRasterMultiple is applied
dupColX <- min(c(maxRatioFix[2],
max(c(dupColX, minRasterMultiple[2]))));
dupRowX <- min(c(maxRatioFix[1],
max(c(dupRowX, minRasterMultiple[1]))));
if (verbose) {
printDebug("fix_matrix_ratio(): ",
"minRasterMultiple:",
minRasterMultiple);
printDebug("fix_matrix_ratio(): ",
"maxRatioFix:",
maxRatioFix);
printDebug("fix_matrix_ratio(): ",
"dupColX: ",
dupColX);
printDebug("fix_matrix_ratio(): ",
"dupRowX: ",
dupRowX);
}
newCols <- rep(1:(ncol(x)-0), each=dupColX);
newRows <- rep(1:(nrow(x)-0), each=dupRowX);
x <- x[newRows,newCols,drop=FALSE];
} else if (ncol(x) > ratioThreshold * nrow(x)) {
if (verbose) {
printDebug("fix_matrix_ratio(): ",
"ncol(x) is more than ", ratioThreshold, "x nrow(x).");
}
dupRowX <- floor((ncol(x)-0)/(nrow(x)-0));
newRows <- rep(1:(nrow(x)-0), each=dupRowX);
x <- x[newRows,,drop=FALSE];
}
return(x);
}
jmw86069/jamba documentation built on March 26, 2024, 5:26 a.m.
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#' Fix matrix dimension ratio
#'
#' Fix matrix dimension ratio
#'
#' This function is experimental, replicating the logic used inside
#' `imageDefault()` to ensure a numeric matrix is roughly 1:1 ratio
#' of nrow:ncol. It currently duplicates columns or rows `n` times
#' in an effort to make the resulting matrix less than a 2:1 ratio.
#' The purpose is to allow `rasterImage()` or `grid.raster()` with
#' argument `interpolate=TRUE` to produce an output raster image
#' that has interpolated the image with reasonably square pixels.
#' Without this adjustment, a matrix with 2,000 rows and 10 columns
#' would be interpolated much more on the x-axis than the y-axis,
#' blurring the data along the x-axis.
#'
#' The main goal is to enable arguments `useRaster=TRUE` and
#' `interpolate=TRUE` which allows an output image to contain
#' more rows than pixels, and still have the pixels represent
#' properly smoothed content.
#'
#' See the examples for visual examples of the effect, showing
#' `image.default()`, `jamba::imageDefault()`,
#' `graphics::rasterImage()`, and `grid::grid.raster()`.
#'
#' @param x `matrix` input
#' @param maxRatioFix integer value indicating the maximum multiple
#' used to duplicate columns or rows. This value is used to prevent
#' replicating a matrix with 1 million rows and 10 columns into
#' a 10 million by 10 million matrix. For example `maxRatioFix=100`
#' will not replicate columns or rows more than 100 times.
#' @param ratioThreshold numeric value indicating the ratio of nrow:ncol
#' above which this function will adjust the dimensions of the
#' output matrix. For example when `ratioThreshold=3` there must be
#' 3 times more rows than columns, or 3 times more columns than rows.
#' @param rasterTarget integer number reflecting the target minimum
#' number of rows and columns. This value is used to protect from
#' interpolating a 5x5 matrix, which yields a blurry result. When
#' `rasterTarget=200`, a 5x5 matrix will be expanded to 200x200,
#' and the 200x200 matrix will be interpolated to yield a sharp image.
#' @param minRasterMultiple integer vector of 1 or 2 values, referring
#' to the minimum number of times each row or column is replicated,
#' respectively. For example `minRasterMultiple=c(2,5)` will at minimum
#' replicate each row 2 times, and each column 5 times.
#' @param verbose logical indicating whether to print verbose output.
#' @param ... additional arguments are ignored.
#'
#' @examples
#' m <- matrix(rainbow(9), ncol=3);
#' m2 <- fix_matrix_ratio(m);
#' par("mfrow"=c(1,3));
#' imageByColors(m, useRaster=FALSE,
#' main="m\nuseRaster=FALSE");
#' imageByColors(m, useRaster=TRUE, fixRasterRatio=FALSE,
#' main="m\nuseRaster=FALSE\nfixRasterRatio=FALSE");
#' imageByColors(m2, useRaster=TRUE, fixRasterRatio=FALSE,
#' main="m2\nuseRaster=FALSE\nfixRasterRatio=FALSE");
#'
#' m <- matrix(colors()[1:90], ncol=3)
#' dim(m)
#' m2 <- fix_matrix_ratio(m);
#' dim(m2);
#' par("mfrow"=c(1,4));
#' imageByColors(m, useRaster=FALSE,
#' main="m\nuseRaster=FALSE");
#' imageByColors(m, useRaster=TRUE, interpolate=FALSE,
#' main="m\nuseRaster=TRUE\ninterpolate=FALSE");
#' imageByColors(m, useRaster=TRUE, interpolate=TRUE, fixRasterRatio=FALSE,
#' main="m\nuseRaster=TRUE\ninterpolate=TRUE");
#' imageByColors(m2, useRaster=TRUE, fixRasterRatio=FALSE,
#' main="fix_matrix_ratio(m)\nuseRaster=TRUE\ninterpolate=TRUE");
#' par("mfrow"=c(1,1));
#'
#' ## Complicated example showing the effect of interpolate=TRUE
#' testHeatdata <- matrix(rnorm(90000), ncol=9)[,1:9];
#' testHeatdata <- testHeatdata[order(testHeatdata[,5]),];
#' g1 <- seq(from=10, to=10000, by=1000);
#' testHeatdata[g1+rep(1:3, each=length(g1)),] <- 9;
#' for (i in seq(from=125, to=235, by=3)) {
#' ix <- round(sin(deg2rad(i))*5+5);
#' iy <- round(-cos(deg2rad(i))*5500 + 3500);
#' testHeatdata[iy:(iy+4), ix] <- 10;
#' }
#' g2 <- 3011+c(1:12*90);
#' testHeatdata[g2+rep(1:3, each=length(g2)), c(3,7)] <- 10;
#' testHeatdata <- testHeatdata[10000:1,];
#' col <- getColorRamp("RdBu_r", n=15, lens=1, trimRamp=c(4,1));
#' par("mfrow"=c(1,2));
#' image.default(z=t(testHeatdata), col=col, useRaster=TRUE,
#' main="image.default(..., useRaster=TRUE,\ninterpolate=FALSE)");
#' imageDefault(z=t(testHeatdata), col=col, useRaster=TRUE,
#' main="imageDefault(..., useRaster=TRUE,\ninterpolate=TRUE)");
#' par("mfrow"=c(1,1));
#'
#' m2r <- as.raster(m2);
#' nullPlot(xaxs="i", yaxs="i",
#' main="using rasterImage()");
#' rasterImage(m2r, xleft=1, xright=2, ybottom=1, ytop=2);
#'
#' if (require(grid)) {
#' testHeatdata2 <- testHeatdata[10000:1,,drop=FALSE];
#' testHeatdata2[] <- circlize::colorRamp2(breaks=seq(from=-10, to=10, length.out=25),
#' colors=getColorRamp("RdBu_r", n=25))(testHeatdata2);
#' testHeatdata2 <- fix_matrix_ratio(testHeatdata2);
#' m2r <- as.raster(testHeatdata2);
#' par("mfrow"=c(1,1));
#' nullPlot(xaxs="i", yaxs="i",
#' doBoxes=FALSE);
#' grid::grid.raster(m2r,
#' x=grid::unit(0.5, "npc"),
#' y=grid::unit(0.5, "npc"),
#' height=grid::unit(1, "npc"),
#' width=grid::unit(1, "npc"),
#' interpolate=FALSE);
#' title(main="using grid.raster(..., interpolate=FALSE)")
#' nullPlot(xaxs="i", yaxs="i",
#' doBoxes=FALSE);
#' grid::grid.raster(m2r,
#' x=grid::unit(0.5, "npc"),
#' y=grid::unit(0.5, "npc"),
#' height=grid::unit(1, "npc"),
#' width=grid::unit(1, "npc"),
#' interpolate=TRUE);
#' title(main="using grid.raster(..., interpolate=TRUE)")
#' }
#'
#' ## Example showing usr coordinates for grid.raster()
#' if (require(gridBase)) {
#' nullPlot(xaxs="i", yaxs="i",
#' main="gridBase grid.raster(..., interpolate=TRUE)");
#' vps <- gridBase::baseViewports();
#' grid::pushViewport(vps$inner, vps$figure, vps$plot);
#' grid::grid.raster(m2r,
#' x=grid::unit(1.5, "native"),
#' y=grid::unit(1.5, "native"),
#' height=grid::unit(1, "native"),
#' width=grid::unit(1, "native"),
#' interpolate=TRUE);
#' grid::popViewport(3);
#' }
#'
#' @family jam numeric functions
#'
#' @export
fix_matrix_ratio <- function
(x,
maxRatioFix=10,
minRasterMultiple=NULL,
rasterTarget=200,
ratioThreshold=3,
verbose=FALSE,
...)
{
if (!is.matrix(x)) {
stop("x must be a matrix");
}
if (length(x) == 0) {
return(x);
}
if (length(ratioThreshold) == 0) {
ratioThreshold <- 3;
}
ratioThreshold <- head(ratioThreshold, 1);
if (ratioThreshold < 1) {
stop("ratioThreshold must be higher than 1.");
}
rasterTarget <- rep(rasterTarget, length.out=2);
if (length(minRasterMultiple) == 0) {
if (length(rasterTarget) > 0) {
minRasterMultiple <- c(ceiling(rasterTarget[1]/nrow(x)),
ceiling(rasterTarget[2]/ncol(x)));
} else {
minRasterMultiple <- c(1,1);
}
} else {
minRasterMultiple <- rep(minRasterMultiple, length.out=2);
}
if (verbose) {
printDebug("minRasterMultiple:", minRasterMultiple);
}
if (!is.null(maxRatioFix)) {
maxRatioFix <- rep(maxRatioFix, length.out=2);
}
if (any(minRasterMultiple > 1) ||
(nrow(x)-1) > ratioThreshold * (ncol(x)-1) ||
(ncol(x) > ratioThreshold * nrow(x)) ) {
if (verbose) {
printDebug("fix_matrix_ratio(): ",
c("Fixing the matrix ratio."));
}
dimRange <- range(c(ncol(x), nrow(x)));
if (ncol(x) > ratioThreshold * nrow(x)) {
dupRowX <- floor((ncol(x)-1)/(nrow(x)-1));
dupRowX <- min(c(dupRowX, maxRatioFix[1]));
dupColX <- 1;
} else {
dupColX <- floor((nrow(x)-1)/(ncol(x)-1));
dupColX <- min(c(dupColX, maxRatioFix[2]));
dupRowX <- 1;
}
if (verbose) {
printDebug("fix_matrix_ratio(): ",
"dupColX: ",
dupColX);
printDebug("fix_matrix_ratio(): ",
"dupRowX: ",
dupRowX);
}
## Ensure that minRasterMultiple is applied
dupColX <- min(c(maxRatioFix[2],
max(c(dupColX, minRasterMultiple[2]))));
dupRowX <- min(c(maxRatioFix[1],
max(c(dupRowX, minRasterMultiple[1]))));
if (verbose) {
printDebug("fix_matrix_ratio(): ",
"minRasterMultiple:",
minRasterMultiple);
printDebug("fix_matrix_ratio(): ",
"maxRatioFix:",
maxRatioFix);
printDebug("fix_matrix_ratio(): ",
"dupColX: ",
dupColX);
printDebug("fix_matrix_ratio(): ",
"dupRowX: ",
dupRowX);
}
newCols <- rep(1:(ncol(x)-0), each=dupColX);
newRows <- rep(1:(nrow(x)-0), each=dupRowX);
x <- x[newRows,newCols,drop=FALSE];
} else if (ncol(x) > ratioThreshold * nrow(x)) {
if (verbose) {
printDebug("fix_matrix_ratio(): ",
"ncol(x) is more than ", ratioThreshold, "x nrow(x).");
}
dupRowX <- floor((ncol(x)-0)/(nrow(x)-0));
newRows <- rep(1:(nrow(x)-0), each=dupRowX);
x <- x[newRows,,drop=FALSE];
}
return(x);
}
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