R/exCon.R
In bryanhanson/exCon: Interactive Exploration of Contour Data
##' Explore Contour Data Interactively
##'
##' These functions compute contour lines from matrix data and display them
##' in an interactive web page using the d3 javascript library. \code{exCon}
##' displays slices along the x and y directions. \code{exCon2} does not
##' display the slices and is faster.
##'
##' @param M A matrix.
##'
##' @param x A vector of numeric values giving the locations of the grid defining
##' the matrix. Must have length \code{nrow(M)}. These values become the scale
##' along the x axis.
##'
##' @param y A vector of numeric values giving the locations of the grid defining
##' the matrix. Must have length \code{ncol(M)}. These values become the scale
##' along the y axis.
##'
##' @param nlevels Integer. The number of contour levels desired. Ignored if \code{levels}
##' is given.
##'
##' @param levels Numeric. A vector of values (altitudes if you will) at which to
##' compute the contours.
##'
##' @param browser Character. Something that will make sense to your OS. Only
##' necessary if you want to overide your system specified browser as understood by
##' \code{R}. See below for further details.
##'
##' @param minify Logical. Shall the JavaScript be minified? This improves
##' performance. However, it requires package \code{js} which in turn requires
##' package \code{V8}. The latter is not available on all platforms. Details
##' may be available at \url{https://github.com/jeroenooms/v8}
##'
##' @return The path to the temporary directory containing the web page files.
##' is returned invisibly.
##' The side effect is an interactive web page. The temporary directory
##' is deleted when you quit R, but you can use the return value to
##' save the files to a different location.
##'
##' @section Details: The computation of the contour lines is handled by
##' \code{\link[grDevices]{contourLines}}. The result here, however, is transposed so that the
##' output has the same orientation as the original matrix. This is necessary because
##' \code{\link[graphics]{contour}} tranposes its output: "Notice that
##' \code{contour} interprets the \code{z} matrix as a table of
##' \code{f(x[i], y[j])} values, so that the x axis corresponds to row number
##' and the y axis to column number, with column 1 at the bottom, i.e. a 90 degree
##' counter-clockwise rotation of the conventional textual layout."
##'
##' @section Interpretation: The contour lines are an interpolation of the data
##' in the matrix. In \code{exCon}, the slices are the actual values in the matrix
##' row or column
##' connected point-to-point. Thus a maximum in a slice may not correspond to
##' a peak in the contour plot.
##'
##' @section Browser Choice: The browser is called by
##' \code{\link[utils]{browseURL}}, which
##' in turn uses \code{options("browser")}. Exactly how this is handled
##' is OS dependent.
##'
##' @section Firefox Browser:
##" With Firefox the mouse cursor is offset from the guides. However,
##' the slices chosen and the values displayed are correct.
##'
##' @section RStudio Viewer: If browser is \code{NULL}, you are using RStudio,
##' and a viewer is specified, this will be called. You can stop this by with
##' \code{options(viewer = NULL)}.
##'
##' @section Browser Choice (Mac): On a Mac, the default browser is called
##' by \code{/bin/sh/open}
##' which in turn looks at which browser you have set in the system settings. You can
##' override your default with
##' \code{browser = "/usr/bin/open -a 'Google Chrome'"} for example.
##'
## @section Browser Choice (Other Systems): \code{exCon} has been tested
## on a Windows 7
## professional instance running in VirtualBox using Firefox and Chrome, and
## runs correctly (Firefox has the same mouse position issue as mentioned above).
## It runs similarly on Window 8.
##'
##' @section Browser Choice & Performance: You can check the performance of
##' your browser at peacekeeper.futuremark.com The most relevant score for
##' exCon is the rendering category.
##'
##' @section Performance Limits (YMMV): On a early 2015 MacBook Pro, with 16 Gb
##' RAM and an 2.9 GHz Intel Core i5 chip, a
##' 1500 x 1500 matrix with 1 contour level
##' requires about 15 seconds for R to render the web page using Chrome, Safari
##' or Firefox. A 2K x 2K matrix appears to be too large to handle. R seems
##' to hang during the handoff to the browser.
##'
##' @aliases exCon2 exCon
##' @export exCon exCon2
##' @import jsonlite
##' @importFrom utils browseURL
##' @importFrom grDevices contourLines
##' @keywords plot interactive
##'
##' @examples
##' if (interactive()) {
##' require(jsonlite)
##'
##' # minify is FALSE in the examples as not all platforms support the required pkgs (see above)
##'
##' exCon(M = volcano, minify = FALSE)
##'
##' exCon2(M = volcano, minify = FALSE) # no slices
##'
##' # This next example will label the axes with the actual values, relative to the
##' # lower left corner (original data collected on 10 meter grid). Giving
##' # x and y affects only the scale, and the native values displayed at the top.
##'
##' exCon(M = volcano, minify = FALSE,
##' x = seq(from = 0, by = 10, length.out = nrow(volcano)),
##' y = seq(from = 0, by = 10, length.out = ncol(volcano)))
##' }
##'
##' @describeIn exCon Interactive contour display with slices
exCon <- function(M = NULL,
x = seq(0, 1, length.out = nrow(M)),
y = seq(0, 1, length.out = ncol(M)),
nlevels = 5,
levels = pretty(range(M, na.rm = TRUE), nlevels),
browser = NULL, minify = TRUE) {
# Bryan A. Hanson, DePauw University, April 2014
# This is the R front end controlling everything
# The html and js files called indirectly written by
# Kristina Mulry and Bryan A. Hanson
if (is.null(M)) stop("You must provide a matrix M")
if (!is.matrix(M)) stop("M must be a matrix")
# M is the raw, topographic data matrix:
# think of it as altitudes on an x,y grid
# Major steps
# 1. Convert M to contour lines (CL)
# 2. Read in the existing js, then pre-pend
# M and CL to to it and write it back out
# 3. Call a browser on the html to open it automatically
# Compute contour lines
# (Eventually need to supply nlevels & levels,
# Also a name for the data set)
dimnames(M) <- list(rep("x", nrow(M)), rep("y", ncol(M)))
CL <- contourLines(z = M, nlevels = nlevels, levels = levels,
x = x, y = y)
# Get the contour lines into JSON format
CL <- toJSON(CL)
# Get M into JSON format
# [ [row1...], [row2...], [lastRow...] ]
M <- toJSON(t(M))
# We need the first and last values of x and y
# to be the xD and yD (the domains)
# These are in the units of whatever is supplied (native)
DX <- toJSON(c(x[1], x[length(x)]))
DY <- toJSON(c(y[1], y[length(y)]))
# Prepare the data
data1 <- paste("var CL = ", CL, sep = "")
data2 <- paste("var M = ", M, sep = "")
data3 <- paste("var Dx = ", DX, sep = "")
data4 <- paste("var Dy = ", DY, sep = "")
# Get the JavaScript modules & related files
td <- tempdir()
fd <- system.file("extdata", package = "exCon")
eCfiles <- c("eC.css", "eC_globals.js", "eC_controls.js", "eC_contours.js",
"eC_brushNguides.js", "eC_slices.js", "eC_main.js", "exCon.html")
chk2 <- file.copy(from=file.path(fd, eCfiles), to=file.path(td, eCfiles),
overwrite = TRUE)
if (!all(chk2)) stop("Copying to temporary directory failed")
js1 <- readLines(con = file.path(td,"eC_globals.js"))
js2 <- readLines(con = file.path(td,"eC_controls.js"))
js3 <- readLines(con = file.path(td,"eC_contours.js"))
js4 <- readLines(con = file.path(td,"eC_brushNguides.js"))
js5 <- readLines(con = file.path(td,"eC_slices.js"))
js6 <- readLines(con = file.path(td,"eC_main.js"))
scopeFunHeader <- "(function() {"
scopeFunTail <- "})();"
# Now write
text = c(scopeFunHeader, data1, data2, data3, data4,
js1, js2, js3, js4, js5, js6, scopeFunTail)
# text = c(data1, data2, data3, data4,
# js1, js2, js3, js4, js5, js6)
if (minify) {
if (requireNamespace("js", quietly = TRUE)) {
text <- js::uglify_optimize(text, unused = FALSE)
}
if (!requireNamespace("js", quietly = TRUE)) {
stop("You need to install package js to minify the JavaScript code. See ?exCon for details.")
}
}
writeLines(text, sep = "\n", con = file.path(td,"exCon.js"))
# Open the file in a browser
pg <- file.path(td,"exCon.html")
if (!is.null(browser)) {
browseURL(pg, browser = browser)
} else {
# open in RStudio if viewer is not null
# similar to htmltools::html_print
viewer <- getOption("viewer")
if (is.null(browser) && !is.null(viewer)) {
viewer(pg)
} else {
browseURL(pg)
}
}
# message("The exCon web page is in the following temp directory which is deleted when you quit R: ")
# message(td)
invisible(td)
}
##' @describeIn exCon Interactive contour display without slices
exCon2 <- function(M = NULL,
x = seq(0, 1, length.out = nrow(M)),
y = seq(0, 1, length.out = ncol(M)),
nlevels = 5,
levels = pretty(range(M, na.rm = TRUE), nlevels),
browser = NULL, minify = TRUE) {
# Bryan A. Hanson, DePauw University, June 2014
# This is the R front end controlling everything
# The html and js files called indirectly written by
# Kristina Mulry and Bryan A. Hanson
if (is.null(M)) stop("You must provide a matrix M")
if (!is.matrix(M)) stop("M must be a matrix")
# M is the raw, topographic data matrix:
# think of it as altitudes on an x,y grid
# Major steps
# 1. Convert M to contour lines (CL)
# 2. Read in the existing js, then pre-pend
# M and CL to to it and write it back out
# 3. Call a browser on the html to open it automatically
# Compute contour lines
# (Eventually need to supply nlevels & levels,
# Also a name for the data set)
dimnames(M) <- list(rep("x", nrow(M)), rep("y", ncol(M)))
CL <- contourLines(z = M, nlevels = nlevels, levels = levels,
x = x, y = y)
# Get the contour lines into JSON format
CL <- toJSON(CL)
# Get M into JSON format
# [ [row1...], [row2...], [lastRow...] ]
M <- toJSON(t(M))
# We need the first and last values of x and y
# to be the xD and yD (the domains)
# These are in the units of whatever is supplied (native)
DX <- toJSON(c(x[1], x[length(x)]))
DY <- toJSON(c(y[1], y[length(y)]))
# Prepare the data
data1 <- paste("var CL = ", CL, sep = "")
data2 <- paste("var M = ", M, sep = "")
data3 <- paste("var Dx = ", DX, sep = "")
data4 <- paste("var Dy = ", DY, sep = "")
# Get the JavaScript modules & related files
td <- tempdir()
fd <- system.file("extdata", package = "exCon")
eCfiles <- c("eC.css", "eC2_globals.js", "eC2_contours.js",
"eC2_brushNguides.js", "eC2_main.js", "exCon2.html")
chk2 <- file.copy(from=file.path(fd, eCfiles), to=file.path(td, eCfiles),
overwrite = TRUE)
if (!all(chk2)) stop("Copying to temporary directory failed")
js1 <- readLines(con = file.path(td,"eC2_globals.js"))
js2 <- readLines(con = file.path(td,"eC2_contours.js"))
js3 <- readLines(con = file.path(td,"eC2_brushNguides.js"))
js4 <- readLines(con = file.path(td,"eC2_main.js"))
scopeFunHeader <- "(function() {"
scopeFunTail <- "})();"
# Now write
text = c(scopeFunHeader, data1, data2, data3, data4,
js1, js2, js3, js4, scopeFunTail)
# text = c(data1, data2, data3, data4,
# js1, js2, js3, js4)
if (minify) {
if (requireNamespace("js", quietly = TRUE)) {
text <- js::uglify_optimize(text, unused = FALSE)
}
if (!requireNamespace("js", quietly = TRUE)) {
stop("You need to install package js to minify the JavaScript code. See ?exCon for details.")
}
}
writeLines(text, sep = "\n", con = file.path(td,"exCon2.js"))
# Open the file in a browser
pg <- file.path(td,"exCon2.html")
if (!is.null(browser)) {
browseURL(pg, browser = browser)
} else {
# open in RStudio if viewer is not null
# similar to htmltools::html_print
viewer <- getOption("viewer")
if (is.null(browser) && !is.null(viewer)) {
viewer(pg)
} else {
browseURL(pg)
}
}
# message("The exCon2 web page is in the following temp directory which is deleted when you quit R: ")
# message(td)
invisible(td)
}
bryanhanson/exCon documentation built on May 13, 2019, 8:10 a.m.
R Package Documentation
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##' Explore Contour Data Interactively
##'
##' These functions compute contour lines from matrix data and display them
##' in an interactive web page using the d3 javascript library. \code{exCon}
##' displays slices along the x and y directions. \code{exCon2} does not
##' display the slices and is faster.
##'
##' @param M A matrix.
##'
##' @param x A vector of numeric values giving the locations of the grid defining
##' the matrix. Must have length \code{nrow(M)}. These values become the scale
##' along the x axis.
##'
##' @param y A vector of numeric values giving the locations of the grid defining
##' the matrix. Must have length \code{ncol(M)}. These values become the scale
##' along the y axis.
##'
##' @param nlevels Integer. The number of contour levels desired. Ignored if \code{levels}
##' is given.
##'
##' @param levels Numeric. A vector of values (altitudes if you will) at which to
##' compute the contours.
##'
##' @param browser Character. Something that will make sense to your OS. Only
##' necessary if you want to overide your system specified browser as understood by
##' \code{R}. See below for further details.
##'
##' @param minify Logical. Shall the JavaScript be minified? This improves
##' performance. However, it requires package \code{js} which in turn requires
##' package \code{V8}. The latter is not available on all platforms. Details
##' may be available at \url{https://github.com/jeroenooms/v8}
##'
##' @return The path to the temporary directory containing the web page files.
##' is returned invisibly.
##' The side effect is an interactive web page. The temporary directory
##' is deleted when you quit R, but you can use the return value to
##' save the files to a different location.
##'
##' @section Details: The computation of the contour lines is handled by
##' \code{\link[grDevices]{contourLines}}. The result here, however, is transposed so that the
##' output has the same orientation as the original matrix. This is necessary because
##' \code{\link[graphics]{contour}} tranposes its output: "Notice that
##' \code{contour} interprets the \code{z} matrix as a table of
##' \code{f(x[i], y[j])} values, so that the x axis corresponds to row number
##' and the y axis to column number, with column 1 at the bottom, i.e. a 90 degree
##' counter-clockwise rotation of the conventional textual layout."
##'
##' @section Interpretation: The contour lines are an interpolation of the data
##' in the matrix. In \code{exCon}, the slices are the actual values in the matrix
##' row or column
##' connected point-to-point. Thus a maximum in a slice may not correspond to
##' a peak in the contour plot.
##'
##' @section Browser Choice: The browser is called by
##' \code{\link[utils]{browseURL}}, which
##' in turn uses \code{options("browser")}. Exactly how this is handled
##' is OS dependent.
##'
##' @section Firefox Browser:
##" With Firefox the mouse cursor is offset from the guides. However,
##' the slices chosen and the values displayed are correct.
##'
##' @section RStudio Viewer: If browser is \code{NULL}, you are using RStudio,
##' and a viewer is specified, this will be called. You can stop this by with
##' \code{options(viewer = NULL)}.
##'
##' @section Browser Choice (Mac): On a Mac, the default browser is called
##' by \code{/bin/sh/open}
##' which in turn looks at which browser you have set in the system settings. You can
##' override your default with
##' \code{browser = "/usr/bin/open -a 'Google Chrome'"} for example.
##'
## @section Browser Choice (Other Systems): \code{exCon} has been tested
## on a Windows 7
## professional instance running in VirtualBox using Firefox and Chrome, and
## runs correctly (Firefox has the same mouse position issue as mentioned above).
## It runs similarly on Window 8.
##'
##' @section Browser Choice & Performance: You can check the performance of
##' your browser at peacekeeper.futuremark.com The most relevant score for
##' exCon is the rendering category.
##'
##' @section Performance Limits (YMMV): On a early 2015 MacBook Pro, with 16 Gb
##' RAM and an 2.9 GHz Intel Core i5 chip, a
##' 1500 x 1500 matrix with 1 contour level
##' requires about 15 seconds for R to render the web page using Chrome, Safari
##' or Firefox. A 2K x 2K matrix appears to be too large to handle. R seems
##' to hang during the handoff to the browser.
##'
##' @aliases exCon2 exCon
##' @export exCon exCon2
##' @import jsonlite
##' @importFrom utils browseURL
##' @importFrom grDevices contourLines
##' @keywords plot interactive
##'
##' @examples
##' if (interactive()) {
##' require(jsonlite)
##'
##' # minify is FALSE in the examples as not all platforms support the required pkgs (see above)
##'
##' exCon(M = volcano, minify = FALSE)
##'
##' exCon2(M = volcano, minify = FALSE) # no slices
##'
##' # This next example will label the axes with the actual values, relative to the
##' # lower left corner (original data collected on 10 meter grid). Giving
##' # x and y affects only the scale, and the native values displayed at the top.
##'
##' exCon(M = volcano, minify = FALSE,
##' x = seq(from = 0, by = 10, length.out = nrow(volcano)),
##' y = seq(from = 0, by = 10, length.out = ncol(volcano)))
##' }
##'
##' @describeIn exCon Interactive contour display with slices
exCon <- function(M = NULL,
x = seq(0, 1, length.out = nrow(M)),
y = seq(0, 1, length.out = ncol(M)),
nlevels = 5,
levels = pretty(range(M, na.rm = TRUE), nlevels),
browser = NULL, minify = TRUE) {
# Bryan A. Hanson, DePauw University, April 2014
# This is the R front end controlling everything
# The html and js files called indirectly written by
# Kristina Mulry and Bryan A. Hanson
if (is.null(M)) stop("You must provide a matrix M")
if (!is.matrix(M)) stop("M must be a matrix")
# M is the raw, topographic data matrix:
# think of it as altitudes on an x,y grid
# Major steps
# 1. Convert M to contour lines (CL)
# 2. Read in the existing js, then pre-pend
# M and CL to to it and write it back out
# 3. Call a browser on the html to open it automatically
# Compute contour lines
# (Eventually need to supply nlevels & levels,
# Also a name for the data set)
dimnames(M) <- list(rep("x", nrow(M)), rep("y", ncol(M)))
CL <- contourLines(z = M, nlevels = nlevels, levels = levels,
x = x, y = y)
# Get the contour lines into JSON format
CL <- toJSON(CL)
# Get M into JSON format
# [ [row1...], [row2...], [lastRow...] ]
M <- toJSON(t(M))
# We need the first and last values of x and y
# to be the xD and yD (the domains)
# These are in the units of whatever is supplied (native)
DX <- toJSON(c(x[1], x[length(x)]))
DY <- toJSON(c(y[1], y[length(y)]))
# Prepare the data
data1 <- paste("var CL = ", CL, sep = "")
data2 <- paste("var M = ", M, sep = "")
data3 <- paste("var Dx = ", DX, sep = "")
data4 <- paste("var Dy = ", DY, sep = "")
# Get the JavaScript modules & related files
td <- tempdir()
fd <- system.file("extdata", package = "exCon")
eCfiles <- c("eC.css", "eC_globals.js", "eC_controls.js", "eC_contours.js",
"eC_brushNguides.js", "eC_slices.js", "eC_main.js", "exCon.html")
chk2 <- file.copy(from=file.path(fd, eCfiles), to=file.path(td, eCfiles),
overwrite = TRUE)
if (!all(chk2)) stop("Copying to temporary directory failed")
js1 <- readLines(con = file.path(td,"eC_globals.js"))
js2 <- readLines(con = file.path(td,"eC_controls.js"))
js3 <- readLines(con = file.path(td,"eC_contours.js"))
js4 <- readLines(con = file.path(td,"eC_brushNguides.js"))
js5 <- readLines(con = file.path(td,"eC_slices.js"))
js6 <- readLines(con = file.path(td,"eC_main.js"))
scopeFunHeader <- "(function() {"
scopeFunTail <- "})();"
# Now write
text = c(scopeFunHeader, data1, data2, data3, data4,
js1, js2, js3, js4, js5, js6, scopeFunTail)
# text = c(data1, data2, data3, data4,
# js1, js2, js3, js4, js5, js6)
if (minify) {
if (requireNamespace("js", quietly = TRUE)) {
text <- js::uglify_optimize(text, unused = FALSE)
}
if (!requireNamespace("js", quietly = TRUE)) {
stop("You need to install package js to minify the JavaScript code. See ?exCon for details.")
}
}
writeLines(text, sep = "\n", con = file.path(td,"exCon.js"))
# Open the file in a browser
pg <- file.path(td,"exCon.html")
if (!is.null(browser)) {
browseURL(pg, browser = browser)
} else {
# open in RStudio if viewer is not null
# similar to htmltools::html_print
viewer <- getOption("viewer")
if (is.null(browser) && !is.null(viewer)) {
viewer(pg)
} else {
browseURL(pg)
}
}
# message("The exCon web page is in the following temp directory which is deleted when you quit R: ")
# message(td)
invisible(td)
}
##' @describeIn exCon Interactive contour display without slices
exCon2 <- function(M = NULL,
x = seq(0, 1, length.out = nrow(M)),
y = seq(0, 1, length.out = ncol(M)),
nlevels = 5,
levels = pretty(range(M, na.rm = TRUE), nlevels),
browser = NULL, minify = TRUE) {
# Bryan A. Hanson, DePauw University, June 2014
# This is the R front end controlling everything
# The html and js files called indirectly written by
# Kristina Mulry and Bryan A. Hanson
if (is.null(M)) stop("You must provide a matrix M")
if (!is.matrix(M)) stop("M must be a matrix")
# M is the raw, topographic data matrix:
# think of it as altitudes on an x,y grid
# Major steps
# 1. Convert M to contour lines (CL)
# 2. Read in the existing js, then pre-pend
# M and CL to to it and write it back out
# 3. Call a browser on the html to open it automatically
# Compute contour lines
# (Eventually need to supply nlevels & levels,
# Also a name for the data set)
dimnames(M) <- list(rep("x", nrow(M)), rep("y", ncol(M)))
CL <- contourLines(z = M, nlevels = nlevels, levels = levels,
x = x, y = y)
# Get the contour lines into JSON format
CL <- toJSON(CL)
# Get M into JSON format
# [ [row1...], [row2...], [lastRow...] ]
M <- toJSON(t(M))
# We need the first and last values of x and y
# to be the xD and yD (the domains)
# These are in the units of whatever is supplied (native)
DX <- toJSON(c(x[1], x[length(x)]))
DY <- toJSON(c(y[1], y[length(y)]))
# Prepare the data
data1 <- paste("var CL = ", CL, sep = "")
data2 <- paste("var M = ", M, sep = "")
data3 <- paste("var Dx = ", DX, sep = "")
data4 <- paste("var Dy = ", DY, sep = "")
# Get the JavaScript modules & related files
td <- tempdir()
fd <- system.file("extdata", package = "exCon")
eCfiles <- c("eC.css", "eC2_globals.js", "eC2_contours.js",
"eC2_brushNguides.js", "eC2_main.js", "exCon2.html")
chk2 <- file.copy(from=file.path(fd, eCfiles), to=file.path(td, eCfiles),
overwrite = TRUE)
if (!all(chk2)) stop("Copying to temporary directory failed")
js1 <- readLines(con = file.path(td,"eC2_globals.js"))
js2 <- readLines(con = file.path(td,"eC2_contours.js"))
js3 <- readLines(con = file.path(td,"eC2_brushNguides.js"))
js4 <- readLines(con = file.path(td,"eC2_main.js"))
scopeFunHeader <- "(function() {"
scopeFunTail <- "})();"
# Now write
text = c(scopeFunHeader, data1, data2, data3, data4,
js1, js2, js3, js4, scopeFunTail)
# text = c(data1, data2, data3, data4,
# js1, js2, js3, js4)
if (minify) {
if (requireNamespace("js", quietly = TRUE)) {
text <- js::uglify_optimize(text, unused = FALSE)
}
if (!requireNamespace("js", quietly = TRUE)) {
stop("You need to install package js to minify the JavaScript code. See ?exCon for details.")
}
}
writeLines(text, sep = "\n", con = file.path(td,"exCon2.js"))
# Open the file in a browser
pg <- file.path(td,"exCon2.html")
if (!is.null(browser)) {
browseURL(pg, browser = browser)
} else {
# open in RStudio if viewer is not null
# similar to htmltools::html_print
viewer <- getOption("viewer")
if (is.null(browser) && !is.null(viewer)) {
viewer(pg)
} else {
browseURL(pg)
}
}
# message("The exCon2 web page is in the following temp directory which is deleted when you quit R: ")
# message(td)
invisible(td)
}
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