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Updated mincPlotSliceSeries to be able to specify alternative colours #311

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597b17a
Updated mincPlotSliceSeries to be able to specify alternative colours…
vfonov Jun 16, 2022
1314d63
Merge branch 'master' of https://github.com/Mouse-Imaging-Centre/RMIN…
vfonov Dec 12, 2022
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101 changes: 75 additions & 26 deletions R/minc_vis2D.R
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Original file line number Diff line number Diff line change
Expand Up @@ -75,22 +75,24 @@ getSlice <- function(volume, slice, dimension) {
return(list(slice=outs, asp=outa))
}

plotLocator <- function(dimension, anatomy, indicatorLevels, slices){
plotLocator <- function(dimension, anatomy,
indicatorLevels, slices, locatorCol = "white", sliceCol="yellow",
anatomyMask=NULL){
d <- dim(anatomy)
if(length(d) != 3) stop("anatomy must be 3 dimensional, you may be missing a call to mincArray")

locatorDimension <- ifelse(dimension %in% 2:3, 1, 2)
locatorSlice <- ceiling(d[locatorDimension] / 2)

mincContour(anatomy, dimension=locatorDimension,
slice=locatorSlice, col="white", levels=indicatorLevels,
axes=F, drawlabels=F)
slice=locatorSlice, col=locatorCol, levels=indicatorLevels,
axes=F, drawlabels=F,volumeMask=anatomyMask)

if (dimension %in% 1:2) {
abline(v=slices, col="yellow")
abline(v=slices, col=sliceCol)
}
else {
abline(h=slices, col="yellow")
abline(h=slices, col=sliceCol)
}

invisible(NULL)
Expand All @@ -99,7 +101,7 @@ plotLocator <- function(dimension, anatomy, indicatorLevels, slices){
sliceSeriesLayout <-
function(anatomy, dimension, mfrow, begin, end, plottitle, legend, locator){
nslices <- prod(mfrow)
par(bg = "black")
#par(bg = "transparent") # TO allow using user-specified color
if (locator || !is.null(legend)) { # use the layout function
# create a layout matrix - sets up a matrix that is the same as par(mfrow=) would be,
# and then adds on an extra column for the slice locator and the legend
Expand Down Expand Up @@ -193,7 +195,13 @@ mincPlotSliceSeries <-
plottitle = NULL,
indicatorLevels = NULL,
discreteStats = FALSE,
legendHeight = .5){
legendHeight = .5,
legendCol = "white",
titleCol = legendCol,
locatorCol="white",
sliceCol="yellow",
anatomyMask = NULL
){

if(length(dim(anatomy)) != 3)
stop("anatomy must be 3 dimensional, you may be missing a call to mincArray")
Expand Down Expand Up @@ -226,11 +234,16 @@ mincPlotSimpleSliceSeries <-
plottitle = NULL,
legend = NULL,
locator = !is.null(legend),
indicatorLevels = NULL){
indicatorLevels = NULL,
locatorCol="white",
sliceCol="yellow",
anatomyMask = NULL){

opar <- par(no.readonly = TRUE)
on.exit(par(opar))


#

slices <- sliceSeriesLayout(anatomy, dimension, mfrow,
begin, end, plottitle, legend, locator)

Expand All @@ -241,11 +254,14 @@ mincPlotSimpleSliceSeries <-
lapply(slices, function(current_slice) {
mincImage(anatomy, dimension, slice=current_slice,
low=anatRange[1], high=anatRange[2],
axes = FALSE, underTransparent = TRUE, col = anatCol)
axes = FALSE, underTransparent = TRUE, col = anatCol,
volumeMask = anatomyMask
)
})

if(locator) plotLocator(dimension, anatomy,
indicatorLevels, slices)
indicatorLevels, slices, locatorCol, sliceCol,
anatomyMask=anatomyMask)

if (!is.null(plottitle))
mtext(plottitle, outer=T, side=3, line=-1, col="white", cex=2)
Expand All @@ -266,9 +282,14 @@ mincPlotStatsSliceSeries <-
legend = NULL,
locator = !is.null(legend),
plottitle = NULL,
indicatorLevels = c(900, 1200),
indicatorLevels = NULL,
discreteStats = FALSE,
legendHeight = .5) {
legendHeight = .5,
legendCol="white",
titleCol=legendCol,
locatorCol="white",
sliceCol="yellow",
anatomyMask = NULL ) {

opar <- par(no.readonly = TRUE)
on.exit(par(opar))
Expand Down Expand Up @@ -296,12 +317,15 @@ mincPlotStatsSliceSeries <-
mincPlotAnatAndStatsSlice(anatomy, statistics, dimension, slice=slices[i],
low=statRange[1], high=statRange[2], anatLow=anatRange[1],
anatHigh=anatRange[2], col=col, legend=NULL,
symmetric=symmetric, acol = anatCol)
symmetric=symmetric, acol = anatCol,
anatomyMask=anatomyMask)
}

#Add the plot locator if desired
if(locator) plotLocator(dimension, anatomy,
indicatorLevels, slices)
indicatorLevels, slices,
locatorCol, sliceCol,
anatomyMask=anatomyMask)

#Add a legend for the statistics if desired
if(!is.null(legend)){
Expand All @@ -317,21 +341,21 @@ mincPlotStatsSliceSeries <-
col <- colorRampPalette(c("red", "yellow"))(255)
rcol <- colorRampPalette(c("blue", "turquoise1"))(255)
plotrix::color.legend(0.3, 0.05, 0.5, 0.45, c(high*-1, low*-1),
rev(rcol), gradient="y", align="rb", col="white")
rev(rcol), gradient="y", align="rb", col=legendCol)
plotrix::color.legend(0.3, 0.55, 0.5, 0.95, c(low, high),
col, gradient="y", align="rb", col="white")
col, gradient="y", align="rb", col=legendCol)
}
else {
plotrix::color.legend(.3, (1 - legendHeight) / 2, .5, 1 - (1 - legendHeight) / 2, labs,
col, gradient="y", align="rb", col="white")
col, gradient="y", align="rb", col=legendCol)
}

text(0.85, 0.5, labels=legend, srt=90, col="white", cex=2)
text(0.85, 0.5, labels=legend, srt=90, col=legendCol, cex=2)
}

#Add a title if desired
if (!is.null(plottitle)) {
mtext(plottitle, outer=T, side=3, line=-1, col="white", cex=2)
mtext(plottitle, outer=T, side=3, line=-1, col=titleCol, cex=2)
}

return(invisible(NULL))
Expand Down Expand Up @@ -445,6 +469,7 @@ mincTriplanarSlicePlot <- function(anatomy, statistics, slice=NULL,
#' @param acol colours to use for the anatomy
#' @param legend an optional string to name the legend, indicating desire for a legend
#' @param legendTextColour an optional description of the text colour for the legend
#' @param anatomyMask optional mask for anatomy
#' (or not)
#' @return invisible NULL
#' @export
Expand All @@ -457,7 +482,8 @@ mincPlotAnatAndStatsSlice <- function(anatomy, statistics, slice=NULL,
symmetric=FALSE,
col=NULL, rcol=NULL, legend=NULL,
acol = gray.colors(255, start=0.0),
legendTextColour="black") {
legendTextColour="black",
anatomyMask=NULL) {

if(length(dim(anatomy)) != 3)
stop("anatomy must be 3 dimensional, you may be missing a call to mincArray")
Expand All @@ -479,8 +505,8 @@ mincPlotAnatAndStatsSlice <- function(anatomy, statistics, slice=NULL,

anatCols = acol

mincImage(anatomy, dimension, slice, axes = FALSE, col=anatCols,
low=anatLow, high=anatHigh)
mincImage(anatomy, dimension, slice, axes = FALSE, col=anatCols, underTransparent = TRUE,
low=anatLow, high=anatHigh, volumeMask=anatomyMask)

mincImage(statistics, dimension, slice, axes = FALSE, add = TRUE, col=col, underTransparent = TRUE,
low = low, high = high)
Expand Down Expand Up @@ -563,11 +589,20 @@ mincImage <- function(volume, dimension=2, slice=NULL,
reverse=FALSE, underTransparent=FALSE,
col = gray.colors(255),
add = FALSE,
volumeMask = NULL,
...) {
if(length(dim(volume)) != 3)
stop("volume must be 3 dimensional, you may be missing a call to mincArray")
if(!is.null(volumeMask) && length(dim(volumeMask)) != 3)
stop("volumeMask must be 3 dimensional, you may be missing a call to mincArray")
if(!is.null(volumeMask) && dim(volumeMask) != dim(volume))
stop("volumeMask and volume size mismatch")


s <- getSlice(volume, slice, dimension)
if(!is.null(volumeMask))
sm <- getSlice(volumeMask, slice, dimension)

# reverse means multiply scaling by -1
if (reverse) { m <- -1 } else { m <- 1 }

Expand Down Expand Up @@ -596,7 +631,11 @@ mincImage <- function(volume, dimension=2, slice=NULL,
colourDepth <- length(col)

paletteScaledSlice <- scaleSliceToPalette(s$slice, low, high, col)


# set masked out values to the lowest value (1) if mask is present
if(!is.null(volumeMask))
paletteScaledSlice[sm$slice<1]=NA

colourizedSlice <- col[paletteScaledSlice]
dim(colourizedSlice) <- sliceDims

Expand Down Expand Up @@ -663,6 +702,7 @@ scaleSliceToPalette <-
#' @param volume the output of mincArray
#' @param dimension the dimension (from 1 to 3)
#' @param slice the slice number
#' @param volumeMask the output of mincArray , for the mask
#' @param ... other parameters to pass on to \code{\link{contour}}
#'
#' @export
Expand All @@ -672,12 +712,21 @@ scaleSliceToPalette <-
#' mincImage(mincArray(anatVol), slice=100, col=gray.colors(255))
#' mincContour(mincArray(anatVol), slice=100, add=T, col=rainbow(2), levels=c(1000, 1400))
#' }
mincContour <- function(volume, dimension=2, slice=NULL, ...) {
mincContour <- function(volume, dimension=2, slice=NULL,volumeMask=NULL, ...) {

if(length(dim(volume)) != 3)
stop("volume must be 3 dimensional, you may be missing a call to mincArray")

if(!is.null(volumeMask) && length(dim(volumeMask)) != 3)
stop("volumeMask must be 3 dimensional, you may be missing a call to mincArray")
if(!is.null(volumeMask) && dim(volumeMask) != dim(volumeMask))
stop("volume and volumeMask size mismatch")

s <- getSlice(volume, slice, dimension)
if(!is.null(volumeMask))
{
sm <- getSlice(volumeMask, slice, dimension)
s$slice[sm$slice<1] <- min(s$slice, na.rm = TRUE) # TODO: should use some special value here?
}
sliceDims <- dim(s$slice)
contour(1:sliceDims[1], 1:sliceDims[2], s$slice, asp=1, ...)
}
Expand Down