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account for differently ordered birth and death columns from tda #52

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account for differently ordered birth and death columns from tda #52

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9 changes: 8 additions & 1 deletion R/persistence-class.R
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,13 @@ as_persistence.matrix <- function(x, warn = TRUE, ...) {
#' @export
as_persistence.diagram <- function(x, warn = TRUE, ...) {
info <- attributes(x)
# check column names
stopifnot(
info$dimnames[[2L]][1L] == "dimension",
all(c("Birth", "Death") %in% info$dimnames[[2L]][c(2L, 3L)])
)
bd_cols <- match(c("Birth", "Death"), info$dimnames[[2L]])

filt_nm <- gsub("*Diag", "", rlang::call_name(info$call))
if (filt_nm == "rips") {
filt_nm <- "Vietoris-Rips"
Expand All @@ -281,7 +288,7 @@ as_persistence.diagram <- function(x, warn = TRUE, ...) {
}

dims <- dim(x)
x <- as.matrix(x)[1:dims[1], 1:dims[2]]
x <- as.matrix(x)[1:dim(x)[1], c(1L, bd_cols)]
colnames(x) <- base::tolower(colnames(x))
as_persistence.matrix(x, warn = warn, rlang::splice(params))
}
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8 changes: 8 additions & 0 deletions inst/tinytest/test-persistence-class.R
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Expand Up @@ -121,6 +121,14 @@ expect_message(
pattern = "Negative, infinite, and missing dimensions will be omitted."
)

# Test that as_persistence() locates births and deaths in columns 2 and 3
x <- TDA::gridDiag(FUNvalues = volcano, sublevel = FALSE)
expect_message(p <- as_persistence(x), pattern = "[Bb]irth")
expect_equal(p$pairs[[1]][, 1], x$diagram[x$diagram[, 1] == 0, 3])
expect_equal(p$pairs[[1]][, 2], x$diagram[x$diagram[, 1] == 0, 2])
expect_equal(p$pairs[[2]][, 1], unname(x$diagram[x$diagram[, 1] == 1, 3]))
expect_equal(p$pairs[[2]][, 2], unname(x$diagram[x$diagram[, 1] == 1, 2]))

# Test that as_persistence() errors out if provided with a matrix with
# less than 2 columns
x <- matrix(1:6, ncol = 1)
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