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## Utilities for the Harwell-Boeing and MatrixMarket formats
readone <- function(ln, iwd, nper, conv)
{
ln <- gsub("D", "E", ln)
inds <- seq(0, by = iwd, length = nper + 1)
(conv)(substring(ln, 1 + inds[-length(inds)], inds[-1]))
}
readmany <- function(conn, nlines, nvals, fmt, conv)
{
if (!grep("[[:digit:]]+[DEFGI][[:digit:]]+", fmt))
stop("Not a valid format")
Iind <- regexpr('[DEFGI]', fmt)
nper <- as.integer(substr(fmt, regexpr('[[:digit:]]+[DEFGI]', fmt), Iind - 1))
iwd <- as.integer(substr(fmt, Iind + 1, regexpr('[\\.\\)]', fmt) - 1))
rem <- nvals %% nper
full <- nvals %/% nper
ans <- vector("list", nvals %/% nper)
for (i in seq_len(full))
ans[[i]] <- readone(readLines(conn, 1, ok = FALSE),
iwd, nper, conv)
if (!rem) return(unlist(ans))
c(unlist(ans),
readone(readLines(conn, 1, ok = FALSE), iwd, rem, conv))
}
readHB <- function(file)
{
if (is.character(file))
file <- if (file == "") stdin() else file(file)
if (!inherits(file, "connection"))
stop("'file' must be a character string or connection")
if (!isOpen(file)) {
open(file)
on.exit(close(file))
}
hdr <- readLines(file, 4, ok = FALSE)
## Title <- sub('[[:space:]]+$', '', substr(hdr[1], 1, 72))
## Key <- sub('[[:space:]]+$', '', substr(hdr[1], 73, 80))
## totln <- as.integer(substr(hdr[2], 1, 14))
ptrln <- as.integer(substr(hdr[2], 15, 28))
indln <- as.integer(substr(hdr[2], 29, 42))
valln <- as.integer(substr(hdr[2], 43, 56))
rhsln <- as.integer(substr(hdr[2], 57, 70))
if (!(t1 <- substr(hdr[3], 1, 1)) %in% c('C', 'R', 'P'))
stop(gettextf("Invalid storage type: %s", t1), domain=NA)
if (t1 != 'R') stop("Only numeric sparse matrices allowed")
## _FIXME: Patterns should also be allowed
if (!(t2 <- substr(hdr[3], 2, 2)) %in% c('H', 'R', 'S', 'U', 'Z'))
stop(gettextf("Invalid storage format: %s", t2), domain=NA)
if (!(t3 <- substr(hdr[3], 3, 3)) %in% c('A', 'E'))
stop(gettextf("Invalid assembled indicator: %s", t3), domain=NA)
nr <- as.integer(substr(hdr[3], 15, 28))
nc <- as.integer(substr(hdr[3], 29, 42))
nz <- as.integer(substr(hdr[3], 43, 56))
## nel <- as.integer(substr(hdr[3], 57, 70))
ptrfmt <- toupper(sub('[[:space:]]+$', '', substr(hdr[4], 1, 16)))
indfmt <- toupper(sub('[[:space:]]+$', '', substr(hdr[4], 17, 32)))
valfmt <- toupper(sub('[[:space:]]+$', '', substr(hdr[4], 33, 52)))
## rhsfmt <- toupper(sub('[[:space:]]+$', '', substr(hdr[4], 53, 72)))
if (!is.na(rhsln) && rhsln > 0) readLines(file, 1, ok = FALSE) # h5
ptr <- readmany(file, ptrln, nc + 1, ptrfmt, as.integer)
ind <- readmany(file, indln, nz, indfmt, as.integer)
vals <- readmany(file, valln, nz, valfmt, as.numeric)
if (t2 == 'S')
new("dsCMatrix", uplo = "L", p = ptr - 1L,
i = ind - 1L, x = vals, Dim = c(nr, nc))
else
new("dgCMatrix", p = ptr - 1L,
i = ind - 1L, x = vals, Dim = c(nr, nc))
}
readMM <- function(file)
{
if (is.character(file))
file <- if(file == "") stdin() else file(file)
if (!inherits(file, "connection"))
stop("'file' must be a character string or connection")
if (!isOpen(file)) {
open(file)
on.exit(close(file))
}
scan1 <- function(what, ...)
scan(file, nmax = 1, what = what, quiet = TRUE, ...)
if (scan1(character()) != "%%MatrixMarket")# hdr
stop("file is not a MatrixMarket file")
if (!(typ <- tolower(scan1(character()))) %in% "matrix")
stop(gettextf("type '%s' not recognized", typ), domain = NA)
if (!(repr <- tolower(scan1(character()))) %in% c("coordinate", "array"))
stop(gettextf("representation '%s' not recognized", repr), domain = NA)
elt <- tolower(scan1(character()))
if (!elt %in% c("real", "complex", "integer", "pattern"))
stop(gettextf("element type '%s' not recognized", elt), domain = NA)
sym <- tolower(scan1(character()))
if (!sym %in% c("general", "symmetric", "skew-symmetric", "hermitian"))
stop(gettextf("symmetry form '%s' not recognized", sym), domain = NA)
nr <- scan1(integer(), comment.char = "%")
nc <- scan1(integer())
nz <- scan1(integer())
checkIJ <- function(els) {
if(any(els$i < 1 | els$i > nr))
stop("readMM(): row values 'i' are not in 1:nr", call.=FALSE)
if(any(els$j < 1 | els$j > nc))
stop("readMM(): column values 'j' are not in 1:nc", call.=FALSE)
}
if (repr == "coordinate") {
switch(elt,
"real" = ,
"integer" = {
## TODO: the "integer" element type should be returned as
## an object of an "iMatrix" subclass--once there are
els <- scan(file, nmax = nz, quiet = TRUE,
what= list(i= integer(), j= integer(), x= numeric()))
checkIJ(els)
switch(sym,
"general" = {
new("dgTMatrix", Dim = c(nr, nc), i = els$i - 1L,
j = els$j - 1L, x = els$x)
},
"symmetric" = {
new("dsTMatrix", uplo = "L", Dim = c(nr, nc),
i = els$i - 1L, j = els$j - 1L, x = els$x)
},
"skew-symmetric" = {
stop("symmetry form 'skew-symmetric' not yet implemented for reading")
## FIXME: use dgT... but must expand the (i,j,x) slots!
new("dgTMatrix", uplo = "L", Dim = c(nr, nc),
i = els$i - 1L, j = els$j - 1L, x = els$x)
},
"hermitian" = {
stop("symmetry form 'hermitian' not yet implemented for reading")
},
## otherwise (not possible; just defensive programming):
stop(gettextf("symmetry form '%s' is not yet implemented",
sym), domain = NA)
)
},
"pattern" = {
els <- scan(file, nmax = nz, quiet = TRUE,
what = list(i = integer(), j = integer()))
checkIJ(els)
switch(sym,
"general" = {
new("ngTMatrix", Dim = c(nr, nc),
i = els$i - 1L, j = els$j - 1L)
},
"symmetric" = {
new("nsTMatrix", uplo = "L", Dim = c(nr, nc),
i = els$i - 1L, j = els$j - 1L)
},
"skew-symmetric" = {
stop("symmetry form 'skew-symmetric' not yet implemented for reading")
## FIXME: use dgT... but must expand the (i,j,x) slots!
new("ngTMatrix", uplo = "L", Dim = c(nr, nc),
i = els$i - 1L, j = els$j - 1L)
},
"hermitian" = {
stop("symmetry form 'hermitian' not yet implemented for reading")
},
## otherwise (not possible; just defensive programming):
stop(gettextf("symmetry form '%s' is not yet implemented",
sym), domain = NA)
)
},
"complex" = {
stop("element type 'complex' not yet implemented")
},
## otherwise (not possible currently):
stop(gettextf("'%s()' is not yet implemented for element type '%s'",
"readMM", elt), domain = NA))
}
else
stop(gettextf("'%s()' is not yet implemented for representation '%s'",
"readMM", repr), domain = NA)
}
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