diff --git a/renv.lock b/renv.lock
new file mode 100644
index 0000000000000000000000000000000000000000..3cfba30ad40b9241ba57b7bb18d953397a1d49b6
--- /dev/null
+++ b/renv.lock
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+ "Package": "permute",
+ "Version": "0.9-7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats"
+ ],
+ "Hash": "abf0ca85c1c752e0d04f46334e635046"
+ },
+ "pillar": {
+ "Package": "pillar",
+ "Version": "1.9.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "cli",
+ "fansi",
+ "glue",
+ "lifecycle",
+ "rlang",
+ "utf8",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "15da5a8412f317beeee6175fbc76f4bb"
+ },
+ "pkgconfig": {
+ "Package": "pkgconfig",
+ "Version": "2.0.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "utils"
+ ],
+ "Hash": "01f28d4278f15c76cddbea05899c5d6f"
+ },
+ "png": {
+ "Package": "png",
+ "Version": "0.1-8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "bd54ba8a0a5faded999a7aab6e46b374"
+ },
+ "prettyunits": {
+ "Package": "prettyunits",
+ "Version": "1.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
+ },
+ "progress": {
+ "Package": "progress",
+ "Version": "1.2.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "crayon",
+ "hms",
+ "prettyunits"
+ ],
+ "Hash": "f4625e061cb2865f111b47ff163a5ca6"
+ },
+ "proxy": {
+ "Package": "proxy",
+ "Version": "0.4-27",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "utils"
+ ],
+ "Hash": "e0ef355c12942cf7a6b91a6cfaea8b3e"
+ },
+ "purrr": {
+ "Package": "purrr",
+ "Version": "1.0.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "lifecycle",
+ "magrittr",
+ "rlang",
+ "vctrs"
+ ],
+ "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
+ },
+ "rappdirs": {
+ "Package": "rappdirs",
+ "Version": "0.3.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
+ },
+ "readbitmap": {
+ "Package": "readbitmap",
+ "Version": "0.1.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "bmp",
+ "jpeg",
+ "png",
+ "tiff"
+ ],
+ "Hash": "ec19e2be05f06df441857070a456dbe5"
+ },
+ "renv": {
+ "Package": "renv",
+ "Version": "1.0.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "utils"
+ ],
+ "Hash": "397b7b2a265bc5a7a06852524dabae20"
+ },
+ "rgl": {
+ "Package": "rgl",
+ "Version": "1.3.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "base64enc",
+ "grDevices",
+ "graphics",
+ "htmltools",
+ "htmlwidgets",
+ "jsonlite",
+ "knitr",
+ "magrittr",
+ "mime",
+ "stats",
+ "utils"
+ ],
+ "Hash": "54f8dcdef54a2c7737c0eec27d394dfd"
+ },
+ "rlang": {
+ "Package": "rlang",
+ "Version": "1.1.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "utils"
+ ],
+ "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
+ },
+ "rmarkdown": {
+ "Package": "rmarkdown",
+ "Version": "2.27",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "bslib",
+ "evaluate",
+ "fontawesome",
+ "htmltools",
+ "jquerylib",
+ "jsonlite",
+ "knitr",
+ "methods",
+ "tinytex",
+ "tools",
+ "utils",
+ "xfun",
+ "yaml"
+ ],
+ "Hash": "27f9502e1cdbfa195f94e03b0f517484"
+ },
+ "s2": {
+ "Package": "s2",
+ "Version": "1.1.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp",
+ "wk"
+ ],
+ "Hash": "32f7b1a15bb01ae809022960abad5363"
+ },
+ "sass": {
+ "Package": "sass",
+ "Version": "0.4.9",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R6",
+ "fs",
+ "htmltools",
+ "rappdirs",
+ "rlang"
+ ],
+ "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+ },
+ "scales": {
+ "Package": "scales",
+ "Version": "1.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "RColorBrewer",
+ "cli",
+ "farver",
+ "glue",
+ "labeling",
+ "lifecycle",
+ "munsell",
+ "rlang",
+ "viridisLite"
+ ],
+ "Hash": "c19df082ba346b0ffa6f833e92de34d1"
+ },
+ "sf": {
+ "Package": "sf",
+ "Version": "1.0-16",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "DBI",
+ "R",
+ "Rcpp",
+ "classInt",
+ "grDevices",
+ "graphics",
+ "grid",
+ "magrittr",
+ "methods",
+ "s2",
+ "stats",
+ "tools",
+ "units",
+ "utils"
+ ],
+ "Hash": "ad57b543f7c3fca05213ba78ff63df9b"
+ },
+ "sp": {
+ "Package": "sp",
+ "Version": "2.1-4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "grid",
+ "lattice",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "75940133cca2e339afce15a586f85b11"
+ },
+ "stringi": {
+ "Package": "stringi",
+ "Version": "1.8.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "tools",
+ "utils"
+ ],
+ "Hash": "39e1144fd75428983dc3f63aa53dfa91"
+ },
+ "stringr": {
+ "Package": "stringr",
+ "Version": "1.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "magrittr",
+ "rlang",
+ "stringi",
+ "vctrs"
+ ],
+ "Hash": "960e2ae9e09656611e0b8214ad543207"
+ },
+ "tibble": {
+ "Package": "tibble",
+ "Version": "3.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "fansi",
+ "lifecycle",
+ "magrittr",
+ "methods",
+ "pillar",
+ "pkgconfig",
+ "rlang",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
+ },
+ "tidyselect": {
+ "Package": "tidyselect",
+ "Version": "1.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang",
+ "vctrs",
+ "withr"
+ ],
+ "Hash": "829f27b9c4919c16b593794a6344d6c0"
+ },
+ "tiff": {
+ "Package": "tiff",
+ "Version": "0.1-12",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "74b5f7f00e466398fdc0af8889add582"
+ },
+ "tinytex": {
+ "Package": "tinytex",
+ "Version": "0.51",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "xfun"
+ ],
+ "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
+ },
+ "units": {
+ "Package": "units",
+ "Version": "0.8-5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp"
+ ],
+ "Hash": "119d19da480e873f72241ff6962ffd83"
+ },
+ "utf8": {
+ "Package": "utf8",
+ "Version": "1.2.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "62b65c52671e6665f803ff02954446e9"
+ },
+ "vctrs": {
+ "Package": "vctrs",
+ "Version": "0.6.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang"
+ ],
+ "Hash": "c03fa420630029418f7e6da3667aac4a"
+ },
+ "vegan": {
+ "Package": "vegan",
+ "Version": "2.6-6.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "MASS",
+ "R",
+ "cluster",
+ "lattice",
+ "mgcv",
+ "permute"
+ ],
+ "Hash": "46a520e3fd3286168c3e4dc5e6fbb5b1"
+ },
+ "viridis": {
+ "Package": "viridis",
+ "Version": "0.6.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "ggplot2",
+ "gridExtra",
+ "viridisLite"
+ ],
+ "Hash": "acd96d9fa70adeea4a5a1150609b9745"
+ },
+ "viridisLite": {
+ "Package": "viridisLite",
+ "Version": "0.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
+ },
+ "withr": {
+ "Package": "withr",
+ "Version": "3.0.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics"
+ ],
+ "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
+ },
+ "wk": {
+ "Package": "wk",
+ "Version": "0.9.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5d4545e140e36476f35f20d0ca87963e"
+ },
+ "xfun": {
+ "Package": "xfun",
+ "Version": "0.45",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "grDevices",
+ "stats",
+ "tools"
+ ],
+ "Hash": "ca59c87fe305b16a9141a5874c3a7889"
+ },
+ "yaml": {
+ "Package": "yaml",
+ "Version": "2.3.8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "29240487a071f535f5e5d5a323b7afbd"
+ }
+ }
+}
diff --git a/renv/.gitignore b/renv/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..0ec0cbba2d7755cbd91956afaa585449906a1e16
--- /dev/null
+++ b/renv/.gitignore
@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/
diff --git a/renv/activate.R b/renv/activate.R
new file mode 100644
index 0000000000000000000000000000000000000000..d13f9932a16a92986a514d8cb439662d85db3add
--- /dev/null
+++ b/renv/activate.R
@@ -0,0 +1,1220 @@
+
+local({
+
+ # the requested version of renv
+ version <- "1.0.7"
+ attr(version, "sha") <- NULL
+
+ # the project directory
+ project <- Sys.getenv("RENV_PROJECT")
+ if (!nzchar(project))
+ project <- getwd()
+
+ # use start-up diagnostics if enabled
+ diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+ if (diagnostics) {
+ start <- Sys.time()
+ profile <- tempfile("renv-startup-", fileext = ".Rprof")
+ utils::Rprof(profile)
+ on.exit({
+ utils::Rprof(NULL)
+ elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+ writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+ writeLines(sprintf("- Profile: %s", profile))
+ print(utils::summaryRprof(profile))
+ }, add = TRUE)
+ }
+
+ # figure out whether the autoloader is enabled
+ enabled <- local({
+
+ # first, check config option
+ override <- getOption("renv.config.autoloader.enabled")
+ if (!is.null(override))
+ return(override)
+
+ # if we're being run in a context where R_LIBS is already set,
+ # don't load -- presumably we're being run as a sub-process and
+ # the parent process has already set up library paths for us
+ rcmd <- Sys.getenv("R_CMD", unset = NA)
+ rlibs <- Sys.getenv("R_LIBS", unset = NA)
+ if (!is.na(rlibs) && !is.na(rcmd))
+ return(FALSE)
+
+ # next, check environment variables
+ # TODO: prefer using the configuration one in the future
+ envvars <- c(
+ "RENV_CONFIG_AUTOLOADER_ENABLED",
+ "RENV_AUTOLOADER_ENABLED",
+ "RENV_ACTIVATE_PROJECT"
+ )
+
+ for (envvar in envvars) {
+ envval <- Sys.getenv(envvar, unset = NA)
+ if (!is.na(envval))
+ return(tolower(envval) %in% c("true", "t", "1"))
+ }
+
+ # enable by default
+ TRUE
+
+ })
+
+ # bail if we're not enabled
+ if (!enabled) {
+
+ # if we're not enabled, we might still need to manually load
+ # the user profile here
+ profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+ if (file.exists(profile)) {
+ cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+ if (tolower(cfg) %in% c("true", "t", "1"))
+ sys.source(profile, envir = globalenv())
+ }
+
+ return(FALSE)
+
+ }
+
+ # avoid recursion
+ if (identical(getOption("renv.autoloader.running"), TRUE)) {
+ warning("ignoring recursive attempt to run renv autoloader")
+ return(invisible(TRUE))
+ }
+
+ # signal that we're loading renv during R startup
+ options(renv.autoloader.running = TRUE)
+ on.exit(options(renv.autoloader.running = NULL), add = TRUE)
+
+ # signal that we've consented to use renv
+ options(renv.consent = TRUE)
+
+ # load the 'utils' package eagerly -- this ensures that renv shims, which
+ # mask 'utils' packages, will come first on the search path
+ library(utils, lib.loc = .Library)
+
+ # unload renv if it's already been loaded
+ if ("renv" %in% loadedNamespaces())
+ unloadNamespace("renv")
+
+ # load bootstrap tools
+ `%||%` <- function(x, y) {
+ if (is.null(x)) y else x
+ }
+
+ catf <- function(fmt, ..., appendLF = TRUE) {
+
+ quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+ if (quiet)
+ return(invisible())
+
+ msg <- sprintf(fmt, ...)
+ cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
+
+ invisible(msg)
+
+ }
+
+ header <- function(label,
+ ...,
+ prefix = "#",
+ suffix = "-",
+ n = min(getOption("width"), 78))
+ {
+ label <- sprintf(label, ...)
+ n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
+ if (n <= 0)
+ return(paste(prefix, label))
+
+ tail <- paste(rep.int(suffix, n), collapse = "")
+ paste0(prefix, " ", label, " ", tail)
+
+ }
+
+ heredoc <- function(text, leave = 0) {
+
+ # remove leading, trailing whitespace
+ trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+
+ # split into lines
+ lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+
+ # compute common indent
+ indent <- regexpr("[^[:space:]]", lines)
+ common <- min(setdiff(indent, -1L)) - leave
+ paste(substring(lines, common), collapse = "\n")
+
+ }
+
+ startswith <- function(string, prefix) {
+ substring(string, 1, nchar(prefix)) == prefix
+ }
+
+ bootstrap <- function(version, library) {
+
+ friendly <- renv_bootstrap_version_friendly(version)
+ section <- header(sprintf("Bootstrapping renv %s", friendly))
+ catf(section)
+
+ # attempt to download renv
+ catf("- Downloading renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ tarball <- renv_bootstrap_download(version),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to download:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+ on.exit(unlink(tarball), add = TRUE)
+
+ # now attempt to install
+ catf("- Installing renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ status <- renv_bootstrap_install(version, tarball, library),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to install:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+
+ # add empty line to break up bootstrapping from normal output
+ catf("")
+
+ return(invisible())
+ }
+
+ renv_bootstrap_tests_running <- function() {
+ getOption("renv.tests.running", default = FALSE)
+ }
+
+ renv_bootstrap_repos <- function() {
+
+ # get CRAN repository
+ cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
+
+ # check for repos override
+ repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+ if (!is.na(repos)) {
+
+ # check for RSPM; if set, use a fallback repository for renv
+ rspm <- Sys.getenv("RSPM", unset = NA)
+ if (identical(rspm, repos))
+ repos <- c(RSPM = rspm, CRAN = cran)
+
+ return(repos)
+
+ }
+
+ # check for lockfile repositories
+ repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
+ if (!inherits(repos, "error") && length(repos))
+ return(repos)
+
+ # retrieve current repos
+ repos <- getOption("repos")
+
+ # ensure @CRAN@ entries are resolved
+ repos[repos == "@CRAN@"] <- cran
+
+ # add in renv.bootstrap.repos if set
+ default <- c(FALLBACK = "https://cloud.r-project.org")
+ extra <- getOption("renv.bootstrap.repos", default = default)
+ repos <- c(repos, extra)
+
+ # remove duplicates that might've snuck in
+ dupes <- duplicated(repos) | duplicated(names(repos))
+ repos[!dupes]
+
+ }
+
+ renv_bootstrap_repos_lockfile <- function() {
+
+ lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
+ if (!file.exists(lockpath))
+ return(NULL)
+
+ lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
+ if (inherits(lockfile, "error")) {
+ warning(lockfile)
+ return(NULL)
+ }
+
+ repos <- lockfile$R$Repositories
+ if (length(repos) == 0)
+ return(NULL)
+
+ keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
+ vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
+ names(vals) <- keys
+
+ return(vals)
+
+ }
+
+ renv_bootstrap_download <- function(version) {
+
+ sha <- attr(version, "sha", exact = TRUE)
+
+ methods <- if (!is.null(sha)) {
+
+ # attempting to bootstrap a development version of renv
+ c(
+ function() renv_bootstrap_download_tarball(sha),
+ function() renv_bootstrap_download_github(sha)
+ )
+
+ } else {
+
+ # attempting to bootstrap a release version of renv
+ c(
+ function() renv_bootstrap_download_tarball(version),
+ function() renv_bootstrap_download_cran_latest(version),
+ function() renv_bootstrap_download_cran_archive(version)
+ )
+
+ }
+
+ for (method in methods) {
+ path <- tryCatch(method(), error = identity)
+ if (is.character(path) && file.exists(path))
+ return(path)
+ }
+
+ stop("All download methods failed")
+
+ }
+
+ renv_bootstrap_download_impl <- function(url, destfile) {
+
+ mode <- "wb"
+
+ # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+ fixup <-
+ Sys.info()[["sysname"]] == "Windows" &&
+ substring(url, 1L, 5L) == "file:"
+
+ if (fixup)
+ mode <- "w+b"
+
+ args <- list(
+ url = url,
+ destfile = destfile,
+ mode = mode,
+ quiet = TRUE
+ )
+
+ if ("headers" %in% names(formals(utils::download.file)))
+ args$headers <- renv_bootstrap_download_custom_headers(url)
+
+ do.call(utils::download.file, args)
+
+ }
+
+ renv_bootstrap_download_custom_headers <- function(url) {
+
+ headers <- getOption("renv.download.headers")
+ if (is.null(headers))
+ return(character())
+
+ if (!is.function(headers))
+ stopf("'renv.download.headers' is not a function")
+
+ headers <- headers(url)
+ if (length(headers) == 0L)
+ return(character())
+
+ if (is.list(headers))
+ headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
+
+ ok <-
+ is.character(headers) &&
+ is.character(names(headers)) &&
+ all(nzchar(names(headers)))
+
+ if (!ok)
+ stop("invocation of 'renv.download.headers' did not return a named character vector")
+
+ headers
+
+ }
+
+ renv_bootstrap_download_cran_latest <- function(version) {
+
+ spec <- renv_bootstrap_download_cran_latest_find(version)
+ type <- spec$type
+ repos <- spec$repos
+
+ baseurl <- utils::contrib.url(repos = repos, type = type)
+ ext <- if (identical(type, "source"))
+ ".tar.gz"
+ else if (Sys.info()[["sysname"]] == "Windows")
+ ".zip"
+ else
+ ".tgz"
+ name <- sprintf("renv_%s%s", version, ext)
+ url <- paste(baseurl, name, sep = "/")
+
+ destfile <- file.path(tempdir(), name)
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (inherits(status, "condition"))
+ return(FALSE)
+
+ # report success and return
+ destfile
+
+ }
+
+ renv_bootstrap_download_cran_latest_find <- function(version) {
+
+ # check whether binaries are supported on this system
+ binary <-
+ getOption("renv.bootstrap.binary", default = TRUE) &&
+ !identical(.Platform$pkgType, "source") &&
+ !identical(getOption("pkgType"), "source") &&
+ Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
+
+ types <- c(if (binary) "binary", "source")
+
+ # iterate over types + repositories
+ for (type in types) {
+ for (repos in renv_bootstrap_repos()) {
+
+ # retrieve package database
+ db <- tryCatch(
+ as.data.frame(
+ utils::available.packages(type = type, repos = repos),
+ stringsAsFactors = FALSE
+ ),
+ error = identity
+ )
+
+ if (inherits(db, "error"))
+ next
+
+ # check for compatible entry
+ entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+ if (nrow(entry) == 0)
+ next
+
+ # found it; return spec to caller
+ spec <- list(entry = entry, type = type, repos = repos)
+ return(spec)
+
+ }
+ }
+
+ # if we got here, we failed to find renv
+ fmt <- "renv %s is not available from your declared package repositories"
+ stop(sprintf(fmt, version))
+
+ }
+
+ renv_bootstrap_download_cran_archive <- function(version) {
+
+ name <- sprintf("renv_%s.tar.gz", version)
+ repos <- renv_bootstrap_repos()
+ urls <- file.path(repos, "src/contrib/Archive/renv", name)
+ destfile <- file.path(tempdir(), name)
+
+ for (url in urls) {
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (identical(status, 0L))
+ return(destfile)
+
+ }
+
+ return(FALSE)
+
+ }
+
+ renv_bootstrap_download_tarball <- function(version) {
+
+ # if the user has provided the path to a tarball via
+ # an environment variable, then use it
+ tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
+ if (is.na(tarball))
+ return()
+
+ # allow directories
+ if (dir.exists(tarball)) {
+ name <- sprintf("renv_%s.tar.gz", version)
+ tarball <- file.path(tarball, name)
+ }
+
+ # bail if it doesn't exist
+ if (!file.exists(tarball)) {
+
+ # let the user know we weren't able to honour their request
+ fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
+ msg <- sprintf(fmt, tarball)
+ warning(msg)
+
+ # bail
+ return()
+
+ }
+
+ catf("- Using local tarball '%s'.", tarball)
+ tarball
+
+ }
+
+ renv_bootstrap_download_github <- function(version) {
+
+ enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+ if (!identical(enabled, "TRUE"))
+ return(FALSE)
+
+ # prepare download options
+ pat <- Sys.getenv("GITHUB_PAT")
+ if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+ fmt <- "--location --fail --header \"Authorization: token %s\""
+ extra <- sprintf(fmt, pat)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "curl", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
+ fmt <- "--header=\"Authorization: token %s\""
+ extra <- sprintf(fmt, pat)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "wget", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ }
+
+ url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+ name <- sprintf("renv_%s.tar.gz", version)
+ destfile <- file.path(tempdir(), name)
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (!identical(status, 0L))
+ return(FALSE)
+
+ renv_bootstrap_download_augment(destfile)
+
+ return(destfile)
+
+ }
+
+ # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
+ # can use renv::install() to fully capture metadata.
+ renv_bootstrap_download_augment <- function(destfile) {
+ sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
+ if (is.null(sha)) {
+ return()
+ }
+
+ # Untar
+ tempdir <- tempfile("renv-github-")
+ on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
+ untar(destfile, exdir = tempdir)
+ pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
+
+ # Modify description
+ desc_path <- file.path(pkgdir, "DESCRIPTION")
+ desc_lines <- readLines(desc_path)
+ remotes_fields <- c(
+ "RemoteType: github",
+ "RemoteHost: api.github.com",
+ "RemoteRepo: renv",
+ "RemoteUsername: rstudio",
+ "RemotePkgRef: rstudio/renv",
+ paste("RemoteRef: ", sha),
+ paste("RemoteSha: ", sha)
+ )
+ writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
+
+ # Re-tar
+ local({
+ old <- setwd(tempdir)
+ on.exit(setwd(old), add = TRUE)
+
+ tar(destfile, compression = "gzip")
+ })
+ invisible()
+ }
+
+ # Extract the commit hash from a git archive. Git archives include the SHA1
+ # hash as the comment field of the tarball pax extended header
+ # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
+ # For GitHub archives this should be the first header after the default one
+ # (512 byte) header.
+ renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
+
+ # open the bundle for reading
+ # We use gzcon for everything because (from ?gzcon)
+ # > Reading from a connection which does not supply a 'gzip' magic
+ # > header is equivalent to reading from the original connection
+ conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
+ on.exit(close(conn))
+
+ # The default pax header is 512 bytes long and the first pax extended header
+ # with the comment should be 51 bytes long
+ # `52 comment=` (11 chars) + 40 byte SHA1 hash
+ len <- 0x200 + 0x33
+ res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
+
+ if (grepl("^52 comment=", res)) {
+ sub("52 comment=", "", res)
+ } else {
+ NULL
+ }
+ }
+
+ renv_bootstrap_install <- function(version, tarball, library) {
+
+ # attempt to install it into project library
+ dir.create(library, showWarnings = FALSE, recursive = TRUE)
+ output <- renv_bootstrap_install_impl(library, tarball)
+
+ # check for successful install
+ status <- attr(output, "status")
+ if (is.null(status) || identical(status, 0L))
+ return(status)
+
+ # an error occurred; report it
+ header <- "installation of renv failed"
+ lines <- paste(rep.int("=", nchar(header)), collapse = "")
+ text <- paste(c(header, lines, output), collapse = "\n")
+ stop(text)
+
+ }
+
+ renv_bootstrap_install_impl <- function(library, tarball) {
+
+ # invoke using system2 so we can capture and report output
+ bin <- R.home("bin")
+ exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+ R <- file.path(bin, exe)
+
+ args <- c(
+ "--vanilla", "CMD", "INSTALL", "--no-multiarch",
+ "-l", shQuote(path.expand(library)),
+ shQuote(path.expand(tarball))
+ )
+
+ system2(R, args, stdout = TRUE, stderr = TRUE)
+
+ }
+
+ renv_bootstrap_platform_prefix <- function() {
+
+ # construct version prefix
+ version <- paste(R.version$major, R.version$minor, sep = ".")
+ prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
+
+ # include SVN revision for development versions of R
+ # (to avoid sharing platform-specific artefacts with released versions of R)
+ devel <-
+ identical(R.version[["status"]], "Under development (unstable)") ||
+ identical(R.version[["nickname"]], "Unsuffered Consequences")
+
+ if (devel)
+ prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
+
+ # build list of path components
+ components <- c(prefix, R.version$platform)
+
+ # include prefix if provided by user
+ prefix <- renv_bootstrap_platform_prefix_impl()
+ if (!is.na(prefix) && nzchar(prefix))
+ components <- c(prefix, components)
+
+ # build prefix
+ paste(components, collapse = "/")
+
+ }
+
+ renv_bootstrap_platform_prefix_impl <- function() {
+
+ # if an explicit prefix has been supplied, use it
+ prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
+ if (!is.na(prefix))
+ return(prefix)
+
+ # if the user has requested an automatic prefix, generate it
+ auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+ if (is.na(auto) && getRversion() >= "4.4.0")
+ auto <- "TRUE"
+
+ if (auto %in% c("TRUE", "True", "true", "1"))
+ return(renv_bootstrap_platform_prefix_auto())
+
+ # empty string on failure
+ ""
+
+ }
+
+ renv_bootstrap_platform_prefix_auto <- function() {
+
+ prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
+ if (inherits(prefix, "error") || prefix %in% "unknown") {
+
+ msg <- paste(
+ "failed to infer current operating system",
+ "please file a bug report at https://github.com/rstudio/renv/issues",
+ sep = "; "
+ )
+
+ warning(msg)
+
+ }
+
+ prefix
+
+ }
+
+ renv_bootstrap_platform_os <- function() {
+
+ sysinfo <- Sys.info()
+ sysname <- sysinfo[["sysname"]]
+
+ # handle Windows + macOS up front
+ if (sysname == "Windows")
+ return("windows")
+ else if (sysname == "Darwin")
+ return("macos")
+
+ # check for os-release files
+ for (file in c("/etc/os-release", "/usr/lib/os-release"))
+ if (file.exists(file))
+ return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
+
+ # check for redhat-release files
+ if (file.exists("/etc/redhat-release"))
+ return(renv_bootstrap_platform_os_via_redhat_release())
+
+ "unknown"
+
+ }
+
+ renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
+
+ # read /etc/os-release
+ release <- utils::read.table(
+ file = file,
+ sep = "=",
+ quote = c("\"", "'"),
+ col.names = c("Key", "Value"),
+ comment.char = "#",
+ stringsAsFactors = FALSE
+ )
+
+ vars <- as.list(release$Value)
+ names(vars) <- release$Key
+
+ # get os name
+ os <- tolower(sysinfo[["sysname"]])
+
+ # read id
+ id <- "unknown"
+ for (field in c("ID", "ID_LIKE")) {
+ if (field %in% names(vars) && nzchar(vars[[field]])) {
+ id <- vars[[field]]
+ break
+ }
+ }
+
+ # read version
+ version <- "unknown"
+ for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
+ if (field %in% names(vars) && nzchar(vars[[field]])) {
+ version <- vars[[field]]
+ break
+ }
+ }
+
+ # join together
+ paste(c(os, id, version), collapse = "-")
+
+ }
+
+ renv_bootstrap_platform_os_via_redhat_release <- function() {
+
+ # read /etc/redhat-release
+ contents <- readLines("/etc/redhat-release", warn = FALSE)
+
+ # infer id
+ id <- if (grepl("centos", contents, ignore.case = TRUE))
+ "centos"
+ else if (grepl("redhat", contents, ignore.case = TRUE))
+ "redhat"
+ else
+ "unknown"
+
+ # try to find a version component (very hacky)
+ version <- "unknown"
+
+ parts <- strsplit(contents, "[[:space:]]")[[1L]]
+ for (part in parts) {
+
+ nv <- tryCatch(numeric_version(part), error = identity)
+ if (inherits(nv, "error"))
+ next
+
+ version <- nv[1, 1]
+ break
+
+ }
+
+ paste(c("linux", id, version), collapse = "-")
+
+ }
+
+ renv_bootstrap_library_root_name <- function(project) {
+
+ # use project name as-is if requested
+ asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
+ if (asis)
+ return(basename(project))
+
+ # otherwise, disambiguate based on project's path
+ id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+ paste(basename(project), id, sep = "-")
+
+ }
+
+ renv_bootstrap_library_root <- function(project) {
+
+ prefix <- renv_bootstrap_profile_prefix()
+
+ path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+ if (!is.na(path))
+ return(paste(c(path, prefix), collapse = "/"))
+
+ path <- renv_bootstrap_library_root_impl(project)
+ if (!is.null(path)) {
+ name <- renv_bootstrap_library_root_name(project)
+ return(paste(c(path, prefix, name), collapse = "/"))
+ }
+
+ renv_bootstrap_paths_renv("library", project = project)
+
+ }
+
+ renv_bootstrap_library_root_impl <- function(project) {
+
+ root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+ if (!is.na(root))
+ return(root)
+
+ type <- renv_bootstrap_project_type(project)
+ if (identical(type, "package")) {
+ userdir <- renv_bootstrap_user_dir()
+ return(file.path(userdir, "library"))
+ }
+
+ }
+
+ renv_bootstrap_validate_version <- function(version, description = NULL) {
+
+ # resolve description file
+ #
+ # avoid passing lib.loc to `packageDescription()` below, since R will
+ # use the loaded version of the package by default anyhow. note that
+ # this function should only be called after 'renv' is loaded
+ # https://github.com/rstudio/renv/issues/1625
+ description <- description %||% packageDescription("renv")
+
+ # check whether requested version 'version' matches loaded version of renv
+ sha <- attr(version, "sha", exact = TRUE)
+ valid <- if (!is.null(sha))
+ renv_bootstrap_validate_version_dev(sha, description)
+ else
+ renv_bootstrap_validate_version_release(version, description)
+
+ if (valid)
+ return(TRUE)
+
+ # the loaded version of renv doesn't match the requested version;
+ # give the user instructions on how to proceed
+ dev <- identical(description[["RemoteType"]], "github")
+ remote <- if (dev)
+ paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
+ else
+ paste("renv", description[["Version"]], sep = "@")
+
+ # display both loaded version + sha if available
+ friendly <- renv_bootstrap_version_friendly(
+ version = description[["Version"]],
+ sha = if (dev) description[["RemoteSha"]]
+ )
+
+ fmt <- heredoc("
+ renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+ - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+ - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+ ")
+ catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
+
+ FALSE
+
+ }
+
+ renv_bootstrap_validate_version_dev <- function(version, description) {
+ expected <- description[["RemoteSha"]]
+ is.character(expected) && startswith(expected, version)
+ }
+
+ renv_bootstrap_validate_version_release <- function(version, description) {
+ expected <- description[["Version"]]
+ is.character(expected) && identical(expected, version)
+ }
+
+ renv_bootstrap_hash_text <- function(text) {
+
+ hashfile <- tempfile("renv-hash-")
+ on.exit(unlink(hashfile), add = TRUE)
+
+ writeLines(text, con = hashfile)
+ tools::md5sum(hashfile)
+
+ }
+
+ renv_bootstrap_load <- function(project, libpath, version) {
+
+ # try to load renv from the project library
+ if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+ return(FALSE)
+
+ # warn if the version of renv loaded does not match
+ renv_bootstrap_validate_version(version)
+
+ # execute renv load hooks, if any
+ hooks <- getHook("renv::autoload")
+ for (hook in hooks)
+ if (is.function(hook))
+ tryCatch(hook(), error = warnify)
+
+ # load the project
+ renv::load(project)
+
+ TRUE
+
+ }
+
+ renv_bootstrap_profile_load <- function(project) {
+
+ # if RENV_PROFILE is already set, just use that
+ profile <- Sys.getenv("RENV_PROFILE", unset = NA)
+ if (!is.na(profile) && nzchar(profile))
+ return(profile)
+
+ # check for a profile file (nothing to do if it doesn't exist)
+ path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
+ if (!file.exists(path))
+ return(NULL)
+
+ # read the profile, and set it if it exists
+ contents <- readLines(path, warn = FALSE)
+ if (length(contents) == 0L)
+ return(NULL)
+
+ # set RENV_PROFILE
+ profile <- contents[[1L]]
+ if (!profile %in% c("", "default"))
+ Sys.setenv(RENV_PROFILE = profile)
+
+ profile
+
+ }
+
+ renv_bootstrap_profile_prefix <- function() {
+ profile <- renv_bootstrap_profile_get()
+ if (!is.null(profile))
+ return(file.path("profiles", profile, "renv"))
+ }
+
+ renv_bootstrap_profile_get <- function() {
+ profile <- Sys.getenv("RENV_PROFILE", unset = "")
+ renv_bootstrap_profile_normalize(profile)
+ }
+
+ renv_bootstrap_profile_set <- function(profile) {
+ profile <- renv_bootstrap_profile_normalize(profile)
+ if (is.null(profile))
+ Sys.unsetenv("RENV_PROFILE")
+ else
+ Sys.setenv(RENV_PROFILE = profile)
+ }
+
+ renv_bootstrap_profile_normalize <- function(profile) {
+
+ if (is.null(profile) || profile %in% c("", "default"))
+ return(NULL)
+
+ profile
+
+ }
+
+ renv_bootstrap_path_absolute <- function(path) {
+
+ substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
+ substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
+ substr(path, 2L, 3L) %in% c(":/", ":\\")
+ )
+
+ }
+
+ renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
+ renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
+ root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
+ prefix <- if (profile) renv_bootstrap_profile_prefix()
+ components <- c(root, renv, prefix, ...)
+ paste(components, collapse = "/")
+ }
+
+ renv_bootstrap_project_type <- function(path) {
+
+ descpath <- file.path(path, "DESCRIPTION")
+ if (!file.exists(descpath))
+ return("unknown")
+
+ desc <- tryCatch(
+ read.dcf(descpath, all = TRUE),
+ error = identity
+ )
+
+ if (inherits(desc, "error"))
+ return("unknown")
+
+ type <- desc$Type
+ if (!is.null(type))
+ return(tolower(type))
+
+ package <- desc$Package
+ if (!is.null(package))
+ return("package")
+
+ "unknown"
+
+ }
+
+ renv_bootstrap_user_dir <- function() {
+ dir <- renv_bootstrap_user_dir_impl()
+ path.expand(chartr("\\", "/", dir))
+ }
+
+ renv_bootstrap_user_dir_impl <- function() {
+
+ # use local override if set
+ override <- getOption("renv.userdir.override")
+ if (!is.null(override))
+ return(override)
+
+ # use R_user_dir if available
+ tools <- asNamespace("tools")
+ if (is.function(tools$R_user_dir))
+ return(tools$R_user_dir("renv", "cache"))
+
+ # try using our own backfill for older versions of R
+ envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
+ for (envvar in envvars) {
+ root <- Sys.getenv(envvar, unset = NA)
+ if (!is.na(root))
+ return(file.path(root, "R/renv"))
+ }
+
+ # use platform-specific default fallbacks
+ if (Sys.info()[["sysname"]] == "Windows")
+ file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
+ else if (Sys.info()[["sysname"]] == "Darwin")
+ "~/Library/Caches/org.R-project.R/R/renv"
+ else
+ "~/.cache/R/renv"
+
+ }
+
+ renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
+ sha <- sha %||% attr(version, "sha", exact = TRUE)
+ parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+ paste(parts, collapse = "")
+ }
+
+ renv_bootstrap_exec <- function(project, libpath, version) {
+ if (!renv_bootstrap_load(project, libpath, version))
+ renv_bootstrap_run(version, libpath)
+ }
+
+ renv_bootstrap_run <- function(version, libpath) {
+
+ # perform bootstrap
+ bootstrap(version, libpath)
+
+ # exit early if we're just testing bootstrap
+ if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+ return(TRUE)
+
+ # try again to load
+ if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+ return(renv::load(project = getwd()))
+ }
+
+ # failed to download or load renv; warn the user
+ msg <- c(
+ "Failed to find an renv installation: the project will not be loaded.",
+ "Use `renv::activate()` to re-initialize the project."
+ )
+
+ warning(paste(msg, collapse = "\n"), call. = FALSE)
+
+ }
+
+ renv_json_read <- function(file = NULL, text = NULL) {
+
+ jlerr <- NULL
+
+ # if jsonlite is loaded, use that instead
+ if ("jsonlite" %in% loadedNamespaces()) {
+
+ json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
+ if (!inherits(json, "error"))
+ return(json)
+
+ jlerr <- json
+
+ }
+
+ # otherwise, fall back to the default JSON reader
+ json <- tryCatch(renv_json_read_default(file, text), error = identity)
+ if (!inherits(json, "error"))
+ return(json)
+
+ # report an error
+ if (!is.null(jlerr))
+ stop(jlerr)
+ else
+ stop(json)
+
+ }
+
+ renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+ jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
+ }
+
+ renv_json_read_default <- function(file = NULL, text = NULL) {
+
+ # find strings in the JSON
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+ pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
+ locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
+
+ # if any are found, replace them with placeholders
+ replaced <- text
+ strings <- character()
+ replacements <- character()
+
+ if (!identical(c(locs), -1L)) {
+
+ # get the string values
+ starts <- locs
+ ends <- locs + attr(locs, "match.length") - 1L
+ strings <- substring(text, starts, ends)
+
+ # only keep those requiring escaping
+ strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
+
+ # compute replacements
+ replacements <- sprintf('"\032%i\032"', seq_along(strings))
+
+ # replace the strings
+ mapply(function(string, replacement) {
+ replaced <<- sub(string, replacement, replaced, fixed = TRUE)
+ }, strings, replacements)
+
+ }
+
+ # transform the JSON into something the R parser understands
+ transformed <- replaced
+ transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
+ transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
+ transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
+ transformed <- gsub(":", "=", transformed, fixed = TRUE)
+ text <- paste(transformed, collapse = "\n")
+
+ # parse it
+ json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
+
+ # construct map between source strings, replaced strings
+ map <- as.character(parse(text = strings))
+ names(map) <- as.character(parse(text = replacements))
+
+ # convert to list
+ map <- as.list(map)
+
+ # remap strings in object
+ remapped <- renv_json_read_remap(json, map)
+
+ # evaluate
+ eval(remapped, envir = baseenv())
+
+ }
+
+ renv_json_read_remap <- function(json, map) {
+
+ # fix names
+ if (!is.null(names(json))) {
+ lhs <- match(names(json), names(map), nomatch = 0L)
+ rhs <- match(names(map), names(json), nomatch = 0L)
+ names(json)[rhs] <- map[lhs]
+ }
+
+ # fix values
+ if (is.character(json))
+ return(map[[json]] %||% json)
+
+ # handle true, false, null
+ if (is.name(json)) {
+ text <- as.character(json)
+ if (text == "true")
+ return(TRUE)
+ else if (text == "false")
+ return(FALSE)
+ else if (text == "null")
+ return(NULL)
+ }
+
+ # recurse
+ if (is.recursive(json)) {
+ for (i in seq_along(json)) {
+ json[i] <- list(renv_json_read_remap(json[[i]], map))
+ }
+ }
+
+ json
+
+ }
+
+ # load the renv profile, if any
+ renv_bootstrap_profile_load(project)
+
+ # construct path to library root
+ root <- renv_bootstrap_library_root(project)
+
+ # construct library prefix for platform
+ prefix <- renv_bootstrap_platform_prefix()
+
+ # construct full libpath
+ libpath <- file.path(root, prefix)
+
+ # run bootstrap code
+ renv_bootstrap_exec(project, libpath, version)
+
+ invisible()
+
+})
diff --git a/renv/settings.json b/renv/settings.json
new file mode 100644
index 0000000000000000000000000000000000000000..ffdbb3200f779343ad1aa1a2fb6c74a02fd9b365
--- /dev/null
+++ b/renv/settings.json
@@ -0,0 +1,19 @@
+{
+ "bioconductor.version": null,
+ "external.libraries": [],
+ "ignored.packages": [],
+ "package.dependency.fields": [
+ "Imports",
+ "Depends",
+ "LinkingTo"
+ ],
+ "ppm.enabled": null,
+ "ppm.ignored.urls": [],
+ "r.version": null,
+ "snapshot.type": "implicit",
+ "use.cache": true,
+ "vcs.ignore.cellar": true,
+ "vcs.ignore.library": true,
+ "vcs.ignore.local": true,
+ "vcs.manage.ignores": true
+}
diff --git a/scripts/draw.R b/scripts/draw.R
new file mode 100644
index 0000000000000000000000000000000000000000..78e48360ef468128f8e0abe2aeaf954366150c1e
--- /dev/null
+++ b/scripts/draw.R
@@ -0,0 +1,67 @@
+####
+# Plotting functions.
+####
+
+# global imports
+import::here("dplyr", "filter", .character_only = TRUE)
+import::here(
+ "ggplot2",
+ c(
+ "aes", "facet_wrap", "geom_histogram", "geom_raster", "ggplot",
+ "scale_x_continuous", "scale_y_continuous", "scale_fill_viridis_c"
+ ),
+ .character_only = TRUE
+)
+import::here("magrittr", "%>%", .character_only = TRUE)
+
+# local import
+import::here("image.R", "img_to_df", .character_only = TRUE)
+
+
+#' Channel histogram
+#'
+#' Histogram ggplot of each color channel of an image.
+#'
+#' @param img an imager::cimg
+#' @param cc a character vector, subset of ("R", "G", "B").
+#'
+#' @returns a ggplot2 graph
+channel_hist <- function(img, cc = c("R", "G", "B")) {
+ if (all(cc %in% c("R", "G", "B"))) {
+ gg <- img %>%
+ img_to_df() %>%
+ filter(channel %in% cc) %>%
+ ggplot(aes(value, col = channel)) +
+ geom_histogram(bins = 30L) +
+ facet_wrap(~channel)
+ } else {
+ stop("Invalid 'cc' argument.")
+ }
+ return(gg)
+}
+
+
+#' Raster channel
+#'
+#' Raster ggplot of an image channel.
+#'
+#' @param img an imager::cimg
+#' @param cc character, specify the image channel, one of "R", "G", "B".
+#'
+#' @returns a ggplot2 graph
+raster_channel <- function(img, cc = NULL) {
+ if (cc %in% c("R", "G", "B")) {
+ gg <- img %>%
+ img_to_df() %>%
+ filter(channel == cc) %>%
+ ggplot(aes(x, y, fill = value)) +
+ geom_raster() +
+ scale_x_continuous(expand = c(0L, 0L)) +
+ scale_y_continuous(expand = c(0L, 0L), trans = scales::reverse_trans()) +
+ scale_fill_viridis_c(direction = 1L, option = "plasma")
+ } else {
+ stop("Invalid 'cc' argument.")
+ }
+
+ return(gg)
+}
diff --git a/scripts/image.R b/scripts/image.R
new file mode 100644
index 0000000000000000000000000000000000000000..60cd445ad928de5b55c7a5a2d2a0283660efe175
--- /dev/null
+++ b/scripts/image.R
@@ -0,0 +1,147 @@
+####
+# Utility functions for imager::cimg objects.
+####
+
+# global imports
+import::here("dplyr", c("mutate", "sample_n"), .character_only = TRUE)
+import::here(
+ "imager",
+ c("grayscale", "HSVtoRGB", "imappend", "imsplit", "map_il", "RGBtoHSV"),
+ .character_only = TRUE
+)
+import::here("magrittr", "%>%", .character_only = TRUE)
+import::here("mclust", "densityMclust", .character_only = TRUE)
+import::here("purrr", "modify_at", .character_only = TRUE)
+
+# local imports
+import::here("utils.R", "sample_histogram", .character_only = TRUE)
+
+
+#' DataFrame conversion
+#'
+#' Convert image to dataframe and expose color channel.
+#'
+#' @param img an imager::cimg
+#'
+#' @returns a data.frame
+img_to_df <- function(img) {
+ out <- img %>%
+ as.data.frame() %>%
+ mutate(channel = factor(cc, labels = c("R", "G", "B")))
+ return(out)
+}
+
+
+#' Histogram equalization
+#'
+#' Flatten histogram by replacing the pixel value of an image by their rank.
+#'
+#' @param img an imager::cimg
+#'
+#' @returns an imager::cimg
+hist_eq <- function(img) {
+ return(as.cimg(ecdf(img)(img), dim = dim(img)))
+}
+
+
+#' Enhance contrast
+#'
+#' Enhance the contrasts of an image by running an histogram equalization
+#' separately on each channel and combining the results.
+#'
+#' @param img an imager::cimg
+#'
+#' @returns an imager::cimg
+enhance_contrast <- function(img) {
+ out <- img %>%
+ imsplit("cc") %>%
+ map_il(hist_eq) %>%
+ imappend("cc")
+ return(out)
+}
+
+
+#' Reduce saturation
+#'
+#' Reduce the saturation of an image through HSV conversion.
+#'
+#' @param img an imager::cimg
+#' @param ratio an integer, how much to divide the saturation by.
+#'
+#' @returns an imager::cimg
+desaturation <- function(img, ratio = 2L) {
+ out <- img %>%
+ RGBtoHSV() %>%
+ imsplit("cc") %>%
+ modify_at(2L, ~ . / ratio) %>%
+ imappend("cc") %>%
+ HSVtoRGB()
+ return(out)
+}
+
+
+#' Correct illumination
+#'
+#' Correct a gray-scaled image illumination by fitting a linear model and
+#' removing the spatial trend.
+#'
+#' @param img an imager::cimg
+#' @param nsamples an integer, pixel subsampling value.
+#'
+#' @returns an imager::cimg object
+correct_illumination <- function(img, nsamples = 1e4L) {
+ # convert to grayscale if needed
+ if (rev(dim(img))[1L] > 1L) {
+ img <- grayscale(img)
+ }
+ # linear regression trend
+ trend <- img %>%
+ as.data.frame() %>%
+ sample_n(nsamples) %>%
+ lm(value ~ x * y, data = .) %>%
+ predict(img)
+ out <- img - trend
+ return(out)
+}
+
+
+#' Invert grayscale image
+#'
+#' @param img an imager::cimg
+#'
+#' @returns an imager::cimg
+invert_grayscale <- function(img) {
+ # convert to grayscale if needed
+ if (rev(dim(img))[1L] > 1L) {
+ img <- grayscale(img)
+ }
+ out <- max(img) - img
+ return(out)
+}
+
+
+#' Binarize
+#'
+#' Binarize a grayscale image.
+#'
+#' @param img an imager::cimg
+#' @param quantile a real, the quantile level used for thresholding.
+#' @param ... mclust::densityMclust parameters
+#'
+#' @returns an imager::cimg
+binarize <- function(img, quantile = 0.95, ...) {
+ # convert to grayscale if needed and invert
+ if (rev(dim(img))[1L] > 1L) {
+ stop("A grayscale image is expected.")
+ }
+ # sample
+ sample <- sample_histogram(img)
+ # fit Gaussian mixture
+ gm <- densityMclust(sample, G = 1L, plot = FALSE, ...)
+ # threshold based on 95% quantile
+ threshold <- qnorm(
+ quantile, gm$parameters$mean[1L], sqrt(gm$parameters$variance$sigmasq[1L])
+ )
+ out <- img > threshold
+ return(out)
+}
diff --git a/scripts/main.R b/scripts/main.R
new file mode 100644
index 0000000000000000000000000000000000000000..e76dc1c8fcb31b33fc87a4dc529da1e288df08e6
--- /dev/null
+++ b/scripts/main.R
@@ -0,0 +1,241 @@
+####
+# Test steps on single image
+####
+
+# global imports
+import::from("cluster", "ellipsoidhull", .character_only = TRUE)
+import::from(
+ "imager",
+ c("grabRect", "grayscale", "grow", "load.image", "shrink",
+ "split_connected", "%inr%"),
+ .character_only = TRUE
+)
+import::from("magrittr", c("%>%", "%$%"), .character_only = TRUE)
+import::from("mclust", "densityMclust", .character_only = TRUE)
+import::from("Momocs", c("import_jpg", "Out"), .character_only = TRUE)
+import::from("purrr", c("discard", "keep", "map"), .character_only = TRUE)
+
+# local imports
+import::from(
+ file.path("scripts", "image.R"),
+ c("binarize", "correct_illumination", "invert_grayscale"),
+ .character_only = TRUE
+)
+import::from(
+ file.path("scripts", "pixset.R"),
+ c("combine", "intersect_borders", "combine_bis", "rotation_angle"),
+ .character_only = TRUE
+)
+import::from(
+ file.path("scripts", "utils.R"),
+ c("ehull", "cm_to_pixel"),
+ .character_only = TRUE
+)
+
+
+# Load image -------------------------------------------------------------------
+
+fpath <- file.path("data", "Example", "DSC_6177.JPG")
+img <- load.image(fpath)
+
+
+# Remove tray edges manually ---------------------------------------------------
+
+# try to isolate tray edges
+img_reduc <- grabRect(img, output = "im")
+
+
+# Binarize ---------------------------------------------------------------------
+
+# convert to grayscale
+img_gr <- grayscale(img_reduc)
+plot(img_gr, main = "grayscale")
+
+# correct illumination and invert grayscale
+img_gr_inv <- img_gr %>%
+ correct_illumination() %>%
+ invert_grayscale()
+plot(img_gr_inv, main = "grayscale inverted")
+
+# binarize (alternative is to use the imager::threshold function)
+img_pix <- binarize(img_gr_inv, quantile = 0.95)
+plot(img_pix, main = "binarized")
+
+
+# Extract connected components and ruler ---------------------------------------
+
+set_pix <- img_pix %>%
+ # small dilatation to improve components detection
+ grow(2L) %>%
+ # extract components
+ split_connected(., high_connectivity = TRUE)
+
+# there are 3 kind of components: small disconnected bits (antenna, legs),
+# medium (geriss), one large (ruler)
+# fit mixture of gaussian distribution with 2 comps
+set_size <- set_pix %>% lapply(sum) %>% unlist()
+gm <- densityMclust(log10(set_size), G = 2L, plot = FALSE)
+thresholds <- qnorm(
+ c(5e-3, 1L - 5e-3),
+ gm$parameters$mean[2L],
+ sqrt(rev(gm$parameters$variance$sigmasq)[1L])
+)
+plot(gm, what = "density", data = log10(set_size), breaks = 200L)
+abline(v = thresholds, col = "purple", lty = 2L)
+
+# split components then shrink back
+set_pix_small <- set_pix %>%
+ keep(~ sum(.) %inr% c(2L, 10L**thresholds[1L])) %>%
+ map(shrink, 2L)
+set_pix_med <- set_pix %>%
+ keep(~ (sum(.) %inr% 10L**thresholds)) %>%
+ map(shrink, 2L)
+ruler <- set_pix %>%
+ keep((~ sum(.) > 10L**thresholds[2L])) %>%
+ map(shrink, 2L)
+rm(set_pix)
+
+# remove pixsets that intersect the image borders
+set_pix_med <- set_pix_med %>%
+ discard(~ intersect_borders(., img_gr))
+
+# plot first medium component
+set_pix_med[[1L]] %>%
+ imager::autocrop() %>%
+ imager::pad(50L, "xy") %>%
+ plot(main = "first medium component")
+
+
+# Re-attach small component to medium ones -------------------------------------
+
+set_pix_med <- set_pix_med %>%
+ map(~ combine(., set_pix_small))
+rm(set_pix_small)
+
+set_pix_med[[1L]] %>%
+ imager::autocrop() %>%
+ imager::pad(50L, "xy") %>%
+ plot(main = "re-attached first component")
+
+
+# Get conversion factor from ruler --------------------------------------------
+
+# get the conversion factor cm to pixel
+conv_factor <- cm_to_pixel(ruler[[1L]])
+
+ruler_ct <- ruler[[1L]] %>%
+ imager::contours(nlevels = 1L)
+plot(
+ ruler[[1L]], main = "ruler", xlim = c(1200L, 1800L), ylim = c(1500L, 1000L)
+)
+ruler_ct[[1L]] %$% {points(x, y, col = "red")}
+ruler_ct[[3L]] %$% {points(x, y, col = "green")}
+
+
+# Split superimposed components -----------------------------------------------
+
+# TODO create function that split connected pixset using morphological opening
+# illustration with two elements
+
+# morphological opening (erosion o dilation) to isolate abdomen
+pixset_l <- set_pix_med[[4L]] %>%
+ imager::mopening_square(6L) %>%
+ imager::split_connected(high_connectivity = TRUE) %>%
+ keep(~ (sum(.) > 1e2L))
+plot(
+ pixset_l %>% imager::parany() %>%
+ imager::autocrop() %>% imager::pad(50L, "xy")
+)
+
+# further split apart the remaining parts
+pixset_part <- (set_pix_med[[4L]] - pixset_l %>% imager::parany()) %>%
+ imager::split_connected(high_connectivity = TRUE)
+plot(
+ (set_pix_med[[4L]] - pixset_l %>% imager::parany()) %>%
+ imager::autocrop() %>% imager::pad(50L, "xy")
+)
+
+# try to re-attach parts to each component
+pixset_l <- pixset_l %>%
+ map(~ combine_bis(., pixset_part, padding = 25L))
+rm(pixset_part)
+plot(pixset_l[[1L]] %>% imager::autocrop() %>% imager::pad(50L, "xy"))
+plot(pixset_l[[2L]] %>% imager::autocrop() %>% imager::pad(50L, "xy"))
+
+# TODO better alternative: fit an ellipsoid hull around each abdomen (also
+# increase both semi-axis length) then check which part satisfy the ellipsoid
+# equation -> re-attach back if so
+
+
+# Rotate along x-axis ----------------------------------------------------------
+
+# get the rotation angle along x-axis
+theta <- rotation_angle(set_pix_med[[1L]], size = 6L)
+eh <- ehull(set_pix_med[[1L]], 6L)
+
+set_pix_med[[1L]] %>%
+ plot(main = "ellipsoid hull", xlim = c(800L, 950L), ylim = c(150L, 1L))
+set_pix_med[[1L]] %>%
+ imager::mopening_square(6L) %>% imager::as.pixset() %>% imager::where() %$%
+ {points(x, y, cex = 0.25, col = "green")}
+lines(predict(eh), col = "red")
+
+# rotated pixset
+pixset %>%
+ imager::imrotate(theta * 180L / pi, ehull$loc[1L], ehull$loc[2L], 1L) %>%
+ plot(main = "rotated", xlim = c(800L, 950L), ylim = c(150L, 1L))
+
+
+# TODO: Need to further orientate the head towards the y-axis (±pi/2).
+
+
+# Export component and ruler to JPG (for Momocs) -------------------------------
+
+# create temp directory
+tmp_dir <- file.path("data", "tmp")
+dir.create(tmp_dir, showWarnings = FALSE)
+# export component
+for (idx in seq_along(set_pix_med)) {
+ set_pix_med[[idx]] %>%
+ imager::autocrop(.) %>%
+ imager::pad(50L, "xy") %>%
+ {max(.) - .} %>%
+ imager::as.cimg(.) %>%
+ imager::save.image(
+ file.path(tmp_dir, paste0("comp", "_", idx, ".jpg")),
+ quality = 1.0
+ )
+}
+# export ruler
+ruler %>%
+ .[[1L]] %>%
+ imager::autocrop(.) %>%
+ imager::pad(20L, "xy") %>%
+ {max(.) - .} %>%
+ imager::as.cimg(.) %>%
+ imager::save.image(file.path(tmp_dir, "ruler.jpg"), quality = 1.0)
+
+
+# Measurements through Momocs --------------------------------------------------
+
+# import jpg file
+coo <- import_jpg(jpg.paths = file.path(tmp_dir, "comp_1.jpg"))
+# find contour
+ct_bis <- Out(coo)
+# plot contour
+ct_bis[1L] %>% Momocs::coo_plot()
+
+# TODO: some useful functions to investigate:
+# * Momocs::coo_oscillo : shape analysis (Fourier elliptic and the likes)
+#
+# * Momocs::coo_intersect_segment, Momocs::coo_intersect_angle : find points of
+# a contour that intersect with a line defined by a segment (or an angle)
+#
+# * Momocs::coo_right, Momocs::coo_left, Momocs::coo_top, Momocs::coo_down :
+# to keep only the right (left, top or down) part of the contour
+#
+# * Momocs::coo_untiltx : correct rotational biases appearing after applying
+# sliding methods.
+#
+# There are more interesting functions, see the doc:
+# https://cran.r-project.org/web/packages/Momocs/Momocs.pdf
diff --git a/scripts/pixset.R b/scripts/pixset.R
new file mode 100644
index 0000000000000000000000000000000000000000..46a2e84a6f74849760b8dd140b77e4cf002cef82
--- /dev/null
+++ b/scripts/pixset.R
@@ -0,0 +1,160 @@
+####
+# Utility functions for imager::pixset objects.
+####
+
+import::here("dplyr", "inner_join", .character_only = TRUE)
+import::here(
+ "imager",
+ c(
+ "as.cimg", "as.pixset", "get.stencil", "imshift", "is.pixset", "parany",
+ "px.borders", "where"
+ ),
+ .character_only = TRUE
+)
+import::here("magrittr", "%>%", .character_only = TRUE)
+
+# local imports
+import::here("utils.R", c("ehull", "square_stencil"), .character_only = TRUE)
+
+
+#' Get centroid of a pixset.
+#'
+#' @param pixset an imager::pixset
+#'
+#' @returns an integer vector
+get_centroid <- function(pixset) {
+ centroid <- pixset %>%
+ where() %>%
+ colMeans() %>%
+ as.integer()
+ return(centroid)
+}
+
+
+#' Center a pixset.
+#'
+#' @param pixset an imager::pixset
+#'
+#' @returns an imager::pixset
+px_center <- function(pixset) {
+ centroid <- get_centroid(pixset)
+ delta <- dim(pixset)[1L:2L] / 2L - centroid
+ out <- pixset %>%
+ as.cimg() %>%
+ imshift(delta_x = delta[1L], delta_y = delta[2L]) %>%
+ as.pixset()
+ return(out)
+}
+
+
+#' Intersect borders
+#'
+#' Test whether a pixset intersect an image borders.
+#'
+#' @param pixset an imager::pixset
+#' @param img an imager::cimg
+#'
+#' @returns a vector of boolean
+intersect_borders <- function(pixset, img) {
+ # extract the image borders (as pixels coordinates)
+ borders <- img %>%
+ px.borders() %>%
+ where()
+ # count the number of pixels intersecting the borders
+ pix_on_borders <- suppressMessages(
+ pixset %>%
+ where() %>%
+ inner_join(borders) %>%
+ nrow()
+ )
+ return(pix_on_borders > 0L)
+}
+
+
+#' Combine pixset
+#'
+#' Combine pixsets into a reference pixset according to a shared neighbourhood.
+#' The neighbourhood is defined as a squared stencil centered around each
+#' candidate pixset.
+#'
+#' @param pixset_ref an imager::pixset, the reference.
+#' @param pixset_list a list of imager::pixset, the list of pixsets to combine
+#' with the reference.
+#' @param padding an integer, the stencil length
+#'
+#' @returns a vector of boolean
+combine <- function(pixset_ref, pixset_list, padding = 50L) {
+ # convert candidat to list if there is only one
+ if (!is.list(pixset_list) & is.pixset(pixset_list)) {
+ pixset_list <- list(pixset_list)
+ }
+ # iterate over parts
+ for (idx in seq_along(pixset_list)) {
+ # get centroid
+ centroid <- get_centroid(pixset_list[[idx]])
+ # define stencil for neighborhood
+ stencil <- square_stencil(centroid, padding, pixset_ref)
+ # check overlap
+ overlap <- pixset_ref %>%
+ get.stencil(stencil, x = centroid[1L], y = centroid[2L]) %>%
+ sum()
+ # merge if overlap
+ if (overlap > 0L) {
+ pixset_ref <- parany(list(pixset_ref, pixset_list[[idx]]))
+ }
+ }
+ return(pixset_ref)
+}
+
+combine_bis <- function(pixset_ref, pixset_list, padding = 25L) {
+ # convert candidat to list if there is only one
+ if (!is.list(pixset_list) & is.pixset(pixset_list)) {
+ pixset_list <- list(pixset_list)
+ }
+ # get centroid
+ centroid <- get_centroid(pixset_ref)
+ # define stencil for neighborhood
+ stencil <- square_stencil(centroid, padding, pixset_ref)
+ # iterate over parts
+ for (idx in seq_along(pixset_list)) {
+ # check overlap
+ overlap <- pixset_list[[idx]] %>%
+ get.stencil(stencil, x = centroid[1L], y = centroid[2L]) %>%
+ sum()
+ # merge if overlap
+ if (overlap > 0L) {
+ pixset_ref <- parany(list(pixset_ref, pixset_list[[idx]]))
+ }
+ }
+ return(pixset_ref)
+}
+
+
+#' Rotation angle
+#'
+#' Get the rotation angle to align the abdomen along the x-axis. The function
+#' fits an ellipsoid hull around the pixset to derive the rotation angle.
+#'
+#' @param pixset an imager::pixset
+#' @param size an integer, the morphological opening factor (optional)
+#'
+#' @returns a real
+rotation_angle <- function(pixset, size = 6L) {
+ # compute ellipsoid hull
+ eh <- ehull(pixset, size)
+ # get semi-axis lengths
+ l_term <- (eh$cov[1L, 1L] + eh$cov[2L, 2L]) / 2L
+ r_term <- sum(
+ c((eh$cov[1L, 1L] - eh$cov[2L, 2L]) / 2L, eh$cov[1L, 2L]) ** 2L
+ )
+ lambda_1 <- l_term + sqrt(r_term)
+ lambda_2 <- l_term - sqrt(r_term)
+ axis_l <- c(sqrt(lambda_1), sqrt(lambda_2))
+ # get rotation angle (from x-axis)
+ if (eh$cov[1L, 2L] != 0L) {
+ theta <- pi - atan2(lambda_1 - eh$cov[1L, 1L], eh$cov[1L, 2L])
+ } else {
+ theta <- ifelse(eh$cov[1L, 1L] >= eh$cov[2L, 2L], 0L, pi / 2L)
+ }
+ return(theta)
+}
diff --git a/scripts/utils.R b/scripts/utils.R
new file mode 100644
index 0000000000000000000000000000000000000000..6a025ba6d50c3a8e4a1aa302b95bcf9458bb89de
--- /dev/null
+++ b/scripts/utils.R
@@ -0,0 +1,120 @@
+####
+# Additional utility functions.
+####
+
+# global imports
+import::here("cluster", "ellipsoidhull", .character_only = TRUE)
+import::here(
+ "imager",
+ c(
+ "as.pixset", "contours", "is.cimg", "is.pixset", "%inr%",
+ "mopening_square", "where"
+ ),
+ .character_only = TRUE
+)
+import::here("mclust", "densityMclust", .character_only = TRUE)
+import::here("purrr", c("keep", "map"), .character_only = TRUE)
+
+
+#' Sample pixel values from histogram
+#'
+#' @param obj an array-like object (img, pixset)
+#' @param ratio a real, the sampling ratio.
+#'
+#' @returns an integer vector
+sample_histogram <- function(obj, ratio = 0.02) {
+ n_samples <- min(1e4L, prod(dim(obj)[1L:2L]))
+ n_breaks <- as.integer(n_samples * ratio)
+ hist <- hist(obj, breaks = n_breaks, plot = FALSE)
+ bins <- with(
+ hist, sample(length(mids), n_samples, p = density, replace = TRUE)
+ )
+ sample <- runif(
+ length(bins), hist$breaks[bins], hist$breaks[bins + 1L]
+ )
+ return(sample)
+}
+
+
+#' Square stencil
+#'
+#' Define a square stencil within the boundaries of an image cropping points
+#' that are out of bounds.
+#'
+#' @param centroid an integer vector, the stencil centroid.
+#' @param pad an integer, the padding around the stencil centroid.
+#' @param obj an imager::cimg or an imager::pixset
+#'
+#' @returns a data.frame
+square_stencil <- function(centroid, pad, obj) {
+
+ # get image dimensions
+ if (is.cimg(obj) | is.pixset(obj)) {
+ dims <- as.integer(dim(obj)[1L:2L])
+ } else {
+ stop("Invalid 'obj' argument.")
+ }
+ # check bounds
+ bounds <- c(
+ ifelse(centroid - pad < 1L, -centroid + 1L, -pad),
+ ifelse(pad + centroid > dims, dims - centroid, pad)
+ )
+ # define stencil
+ stencil <- expand.grid(
+ dx = seq(bounds[1L], bounds[3L]),
+ dy = seq(bounds[2L], bounds[4L])
+ )
+ return(stencil)
+}
+
+
+#' Centimeter to pixel
+#'
+#' Get the centimeter to pixel conversion factor from a ruler defined as
+#' a pixset.
+#'
+#' @param ruler an imager::pixset
+#' @param quantile a real, the quantile level used for thresholding.
+#'
+#' @returns a data.frame
+cm_to_pixel <- function(ruler, quantile = 5e-3) {
+
+ # get ruler contours size
+ ct_size <- ruler %>%
+ contours(nlevels = 1L) %>%
+ map(~ length(.$x)) %>%
+ unlist()
+ # estimate the distribution by a Gaussian
+ gm <- densityMclust(log10(ct_size), G = 1L, plot = FALSE)
+ # threshold to discriminate square contours
+ thresholds <- qnorm(
+ c(quantile, 1L - quantile),
+ gm$parameters$mean[1L],
+ sqrt(gm$parameters$variance$sigmasq[1L])
+ )
+ # get the conversion factor cm to pixel
+ conv_factor <- ct_size %>%
+ keep(~ (. %inr% 10L ** thresholds)) %>%
+ {. / 4L} %>%
+ mean()
+ return(conv_factor)
+}
+
+
+#' Ellipsoid hull
+#'
+#' Fit an ellipsoid hull for a pixset with optional morphological opening.
+#'
+#' @param pixset an imager::pixset
+#' @param size an integer, the morphological opening factor.
+#'
+#' @returns a data.frame
+ehull <- function(pixset, size = 6L) {
+ out <- pixset %>%
+ mopening_square(size) %>%
+ as.pixset() %>%
+ where() %>%
+ as.matrix() %>%
+ ellipsoidhull()
+ return(out)
+}