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output.R
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#' Read a MODFLOW cell-by-cell budget file
#'
#' \code{rmf_read_cbc} reads in a MODFLOW cell-by-cell budget file
#'
#' @param file filename; typically '*.cbc'
#' @param dis dis object.
#' @param huf huf object; optional. Provide only if huf heads are being read and \code{dis} is not NULL. See details.
#' @param oc oc object; optional. See details.
#' @param fluxes character; denotes which fluxes to read. Defaults to reading all fluxes. See details.
#' @param precision either \code{'single'} or \code{'double'}. Specifies the precision of the binary file.
#' @param timesteps optional integer vector specifying which time steps to read. If -1 is specified, only the last time step is read. Defaults to NULL. See details.
#' @return object of class \code{cbc} which is a list consisting of named rmf_arrays and/or data.frames. The names of the elements correspond to the fluxes.
#'
#' @details
#' Fluxes include \code{'constant_head'}, \code{'storage'}, \code{'flow_right_face'}, \code{'flow_front_face'}, \code{'flow_lower_face'}, \code{'wells'},
#' \code{'river_leakage'}, \code{'recharge'}, \code{'drains'}, \code{'head_dep_bounds'} or any other description as written by MODFLOW.
#'
#' If no \code{oc} object is supplied, for all array flow terms a rmf_array of dimensions NROW x NCOL x NLAY x sum(NSTP) is created and filled. Time steps for which no output is given are filled with \code{NA}.
#' If a \code{oc} object is supplied, rmf_arrays of dimensions NROW x NCOL x NLAY are read and binded at each time step for which output is written.
#' The resulting dimensions of the final arrays are NROW x NCOL x NLAY x STPS where STPS are timesteps for which output is saved.
#'
#' If the timesteps argument is supplied, it overwrites the use of the oc argument. For all array flow terms a rmf_array of dimensions NROW x NCOL x NLAY x length(timesteps) is created and filled.
#'
#' If flows are interpolated to huf units, a \code{huf} object is to be supplied as well to dimension the array. This will only affect the constant-head and cell flow terms.
#' The final array will have NHUF layers instead of NLAY.
#'
#' @export
rmf_read_cbc <- function(file = {cat('Please select cell-by-cell budget file ...\n'); file.choose()},
dis = {cat('Please select corresponding dis file ...\n'); rmf_read_dis(file.choose())},
huf = NULL,
oc = NULL,
precision = 'single',
fluxes = 'all',
timesteps = NULL) {
headers <- trimws(rmfd_cbc_headers)
nbytes <- ifelse(precision == 'single', 4, 8)
binary <- TRUE # MODFLOW cbc budget file is always binary
if(binary) {
con <- file(file,open='rb')
cbc <- list()
try({
kstp <- readBin(con,what='integer',n=1)
kper <- readBin(con,what='integer',n=1)
desc <- readChar(con,nchars=16)
trial <- 1
fail <- c(FALSE,FALSE)
# nsteps to dimension array
if(!is.null(timesteps)) {
oc <- NULL
if(length(timesteps) == 1 && timesteps < 0) timesteps <- sum(dis$nstp)
}
if(is.null(oc)) {
nsteps <- sum(dis$nstp)
} else {
if(is.null(oc$save_budget)) {
nsteps <- length(which(oc$icbcfl == T))
} else {
# problem: oc records might be in non-ascending order or have non-existing time steps but output is still writen for current timestep
# e.g. UZFtest2
m_oc<- cbind(oc$iperoc, oc$itsoc)[oc$save_budget,]
if(!is.matrix(m_oc)) m_oc <- matrix(m_oc, ncol = 2, byrow = TRUE)
nsteps <- apply(m_oc, 1, function(i) rmfi_ifelse0(i[1] == 1, ifelse(i[2] > dis$nstp[i[1]], NA, i[2]), cumsum(dis$nstp)[i[1]-1]+i[2]))
# check before going into nested for-loop
if(any(is.na(nsteps)) || !all(diff(nsteps) >= 0)) {
nsteps <- 0
i <- 0
for(k in 1:dis$nper) {
for(l in 1:dis$nstp[k]) {
if(m_oc[i+1,1] < k || (m_oc[i+1,1]==k && m_oc[i+1,2] < l)) {
i <- i + 1
m_oc[i,1] <- k
m_oc[i,2] <- l
nsteps <- nsteps + 1
} else if(m_oc[i+1,1]==k && m_oc[i+1,2]==l){
nsteps <- nsteps + 1
i <- i + 1
}
}
}
} else {
nsteps <- min(sum(dis$nstp), length(which(oc$save_budget == TRUE)))
}
}
}
# loop
while(length(desc!=0)) {
name <- gsub(' ', '_', tolower(trimws(desc)))
name_chck <- trimws(desc)
if(trial == 1) {
if(!(name_chck %in% headers)) {
fail[1] = TRUE
}
} else if(trial == 2) {
if(!(name_chck %in% headers)) {
fail[2] = TRUE
}
}
if(any(fail)) {
stop(paste('Header descriptions do not match. Are you sure the file is', precision,'precision?'), call. = FALSE)
}
read <- ifelse((fluxes[1] != 'all' && !(name %in% fluxes)), FALSE, TRUE)
ncol <- readBin(con,what='integer',n=1)
nrow <- readBin(con,what='integer',n=1)
nlay <- readBin(con,what='integer',n=1)
if(!read) {
if(nlay > 0) {
invisible(readBin(con,what='numeric',n=nrow*ncol*nlay,size = nbytes))
} else {
itype <- readBin(con,what='integer',n=1)
invisible(readBin(con,what='numeric',n=3,size = nbytes))
if(itype==5) {
nval <- readBin(con,what='integer',n=1)
} else {
nval <- 1
}
if(nval > 1) invisible(readChar(con,nchars=(nval-1)*16))
if(itype %in% c(2,5)) {
nlist <- readBin(con,what='integer',n=1)
if(nlist > 0) {
for(nr in 1:nlist) {
invisible(readBin(con,what='integer',n=1))
invisible(readBin(con,what='numeric',n=nval,size = nbytes))
}
}
}
if(itype %in% c(0,1)) invisible(readBin(con,what='numeric',n=ncol*nrow*abs(nlay),size = nbytes))
if(itype ==3) {
invisible(readBin(con,what='integer',n=ncol*nrow))
invisible(readBin(con,what='numeric',n=ncol*nrow,size = nbytes))
}
if(itype ==4) invisible(readBin(con,what='numeric',n=ncol*nrow,size = nbytes))
}
# read
} else {
# create arrays
nnlay <- dis$nlay
if(!is.null(huf) && !is.null(huf$iohufflows) && huf$iohufflows > 0 && name %in% c('constant_head','flow_right_face','flow_front_face','flow_lower_face')) nnlay <- huf$nhuf
if(is.null(cbc[[name]])) {
cbc[[name]] <- rmf_create_array(NA, dim = c(dis$nrow, dis$ncol, nnlay, nsteps))
attr(cbc[[name]], 'kstp') <- attr(cbc[[name]], 'kper') <- attr(cbc[[name]], 'pertim') <- attr(cbc[[name]], 'totim') <- attr(cbc[[name]], 'delt') <- attr(cbc[[name]], 'nstp') <- rep(NA, nsteps)
}
# set step number
if(is.null(oc)) {
stp_nr <- ifelse(kper==1,kstp,cumsum(dis$nstp)[kper-1]+kstp)
} else {
if(is.null(oc$save_budget)) {
stp_nr <- length(which(oc$icbcfl[1:ifelse(kper==1,kstp,cumsum(dis$nstp)[kper-1]+kstp)] == T))
} else {
stp_nr <- length(which(oc$save_budget[1:which(m_oc[,1] == kper)[m_oc[,2][m_oc[,1] == kper] == kstp]] == T))
}
}
# not compact
if(nlay > 0) {
cbc[[name]][,,,stp_nr] <- aperm(array(readBin(con,what='numeric',n=dis$nrow*dis$ncol*nnlay,size = nbytes),dim=c(dis$ncol,dis$nrow,nnlay)),c(2,1,3))
# compact
} else {
itype <- readBin(con,what='integer',n=1)
delt <- readBin(con,what='numeric',n=1,size = nbytes)
pertim <- readBin(con,what='numeric',n=1,size = nbytes)
totim <- readBin(con,what='numeric',n=1,size = nbytes)
if(itype==5) {
nval <- readBin(con,what='integer',n=1)
} else {
nval <- 1
}
if(nval > 1) {
if(is.null(attr(cbc[[name]], 'ctmp'))) attr(cbc[[name]], 'ctmp') <- as.list(rep(NA,nsteps))
ctmp <- rep(NA, (nval-1))
for(nr in 1:(nval-1)) {
ctmp[nr] <- tolower(trimws(readChar(con,nchars=16)))
}
}
# return a rmf_list
if(itype %in% c(2,5)) {
nlist <- readBin(con,what='integer',n=1)
if(nlist > 0) {
df <- matrix(NA,nrow=nlist,ncol=nval+1)
for(nr in 1:nlist) {
df[nr,] <- c(readBin(con,what='integer',n=1),readBin(con,what='numeric',n=nval,size = nbytes))
}
ijk <- rmf_convert_id_to_ijk(df[,1], dis = list(nrow=nrow,ncol=ncol,nlay=abs(nlay)),type='modflow')
if(is.null(cbc[[name]]) || is.array(cbc[[name]])) {
nstp <- ifelse(is.null(dis), 1, stp_nr)
cbc[[name]] <- as.data.frame(cbind(ijk$k,ijk$i,ijk$j,as.data.frame(df)[,-1], nstp, kper, kstp))
names(cbc[[name]]) <- tolower(c('k','i','j', 'value', if(nval > 1) {ctmp},'nstp', 'kper','kstp'))
cbc[[name]] <- rmf_create_list(cbc[[name]])
rm(df)
} else {
nstp <- ifelse(is.null(dis), cbc[[name]][nrow(cbc[[name]]),nstp]+1, stp_nr)
df <- as.data.frame(cbind(ijk$k,ijk$i,ijk$j, as.data.frame(df)[,-1], nstp, kper, kstp))
names(df) <- tolower(c('k','i','j', 'value', if(nval > 1) {ctmp},'nstp', 'kper', 'kstp'))
cbc[[name]] <- rbind(cbc[[name]], df)
}
} else {
if(is.array(cbc[[name]])) cbc[[name]] = NULL
}
}
if(itype %in% c(0,1)) {
cbc[[name]][,,,stp_nr] <- aperm(array(readBin(con,what='numeric',n=dis$ncol*dis$nrow*nnlay,size = nbytes),dim=c(dis$ncol,dis$nrow,nnlay)),c(2,1,3))
}
if(itype == 3) {
layer <- matrix(readBin(con,what='integer',n=ncol*nrow),ncol=ncol,nrow=nrow,byrow=TRUE)
data <- matrix(readBin(con,what='numeric',n=ncol*nrow,size = nbytes),ncol=ncol,nrow=nrow,byrow=TRUE)
cbc[[name]][,,,stp_nr] <- 0
cbc[[name]][,,c(layer),stp_nr] <- c(data)
rm(layer, data)
}
if(itype ==4) {
cbc[[name]][,,1,stp_nr] <- matrix(readBin(con,what='numeric',n=dis$ncol*dis$nrow,size = nbytes),ncol=dis$ncol,nrow=dis$nrow,byrow=TRUE)
}
}
# set attributes
if(!is.null(cbc[[name]])) {
if(nlay > 0 || itype %in% c(2,5)) {
# cbc[[name]] <- rmf_create_list(cbc[[name]], kper = attr(cbc[[name]], 'kper'))
} else {
cbc[[name]] <- rmf_create_array(cbc[[name]], kper = attr(cbc[[name]], 'kper'))
}
attr(cbc[[name]], 'kstp')[stp_nr] <- kstp
attr(cbc[[name]], 'kper')[stp_nr] <- kper
attr(cbc[[name]], 'nstp')[stp_nr] <- ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1]+kstp)
if(nlay < 0) {
attr(cbc[[name]], 'pertim')[stp_nr] <- pertim
attr(cbc[[name]], 'totim')[stp_nr] <- totim
attr(cbc[[name]], 'delt')[stp_nr] <- delt
if(nval > 1) attr(cbc[[name]], 'ctmp')[[stp_nr]] <- ctmp
} else {
stp <- ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1]+kstp)
attr(cbc[[name]], 'pertim')[stp_nr] <- rmf_time_steps(perlen = dis$perlen[kper], tsmult = dis$tsmult[kper], nstp = dis$nstp[kper])[[2]][kstp]
attr(cbc[[name]], 'totim')[stp_nr] <- rmf_time_steps(dis=dis)[[2]][stp]
attr(cbc[[name]], 'delt')[stp_nr] <- rmf_time_steps(dis=dis)[[1]][stp]
}
}
}
kstp <- readBin(con,what='integer',n=1)
kper <- readBin(con,what='integer',n=1)
desc <- readChar(con,nchars=16)
trial <- ifelse(trial == 1, 2, 0)
}
})
close(con)
if(!is.null(timesteps)) {
timestp <- function(list_obj) {
if(inherits(list_obj, 'data.frame')) {
subset(list_obj, nstp %in% timesteps)
} else if(inherits(list_obj, 'rmf_4d_array')) {
rmf_create_array(list_obj[,,,timesteps], dim = c(dim(list_obj)[1:3], length(timesteps)))
}
}
cbc <- lapply(cbc, timestp)
}
class(cbc) <- 'cbc'
return(cbc)
} else {
stop('Code not up to date', call. = FALSE)
# # update this to match the above structure!
# cbc <- list()
# cbc.lines <- readr::read_lines(file, lazy = FALSE)
# while(length(cbc.lines)!=0) {
# name <- substr(cbc.lines[1],25,40)
# cat('Processing',name,'...\n')
# cbc[[name]] <- list()
# cbc[[name]]$sp <- as.numeric(substr(cbc.lines[1],1,12))
# cbc[[name]]$ts <- as.numeric(substr(cbc.lines[1],13,24))
# cbc[[name]]$ncols <- as.numeric(substr(cbc.lines[1],41,52))
# cbc[[name]]$nrows <- as.numeric(substr(cbc.lines[1],53,64))
# cbc[[name]]$nlays <- as.numeric(substr(cbc.lines[1],65,76))
# cbc.lines <- cbc.lines[-1]
#
# cbc[[name]]$code <- as.numeric(substr(cbc.lines[1],1,12))
# cbc[[name]]$delt <- as.numeric(substr(cbc.lines[1],13,27))
# cbc[[name]]$pertim <- as.numeric(substr(cbc.lines[1],28,42))
# cbc[[name]]$totim <- as.numeric(substr(cbc.lines[1],43,57))
# cbc.lines <- cbc.lines[-1]
#
# if(cbc[[name]]$code==1) {
# nrecords <- cbc[[name]]$ncols * cbc[[name]]$nrows * cbc[[name]]$nlays
# nlines <- ceiling(nrecords/5)
# # use rmfi_parse_array or rmfi_parse_variables instead!!
# dataVector <- NULL
# dataVector <- as.numeric(split_line_numbers(paste(cbc.lines[1:nlines],collapse=' ')))
# cbc[[name]]$data <- array(dataVector,dim=c(cbc[[name]]$ncols,cbc[[name]]$nrows,cbc[[name]]$nlays))
# cbc[[name]]$data <- aperm(cbc[[name]]$data,c(2,1,3))
# names(cbc[[name]]$data) <- c('ID','FLUX')
# cbc.lines <- cbc.lines[-c(1:nlines)]
# cbc.lines <- cbc.lines[-1]
# }
# if(cbc[[name]]$code==2) {
# nrecords <- as.numeric(rmfi_remove_empty_strings(strsplit(cbc.lines[1],' ')[[1]]))
# cbc.lines <- cbc.lines[-1]
# # use rmfi_parse_array or rmfi_parse_variables instead!!
# dataVector <- as.numeric(split_line_numbers(paste(cbc.lines[1:nrecords],collapse=' ')))
# cbc[[name]]$data <- as.data.frame(matrix(dataVector,nrow=nrecords,ncol=2,byrow=T))
# names(cbc[[name]]$data) <- c('ID','FLUX')
# cbc.lines <- cbc.lines[-c(1:nrecords)]
# cbc.lines <- cbc.lines[-1]
# }
# if(cbc[[name]]$code==3 | cbc[[name]]$code==4) {
# nrecords <- cbc[[name]]$ncols * cbc[[name]]$nrows
# nlines <- ceiling(nrecords/5)
# dataVector <- NULL
# # use rmfi_parse_array or rmfi_parse_variables instead!!
# dataVector <- as.numeric(split_line_numbers(paste(cbc.lines[1:nlines],collapse=' ')))
# cbc[[name]]$data <- matrix(dataVector,ncol=cbc[[name]]$ncols,nrow=cbc[[name]]$nrows,byrow=T)
# cbc.lines <- cbc.lines[-c(1:nlines)]
# cbc.lines <- cbc.lines[-1]
# }
# if(cbc[[name]]$code==5) {
# nvalues <- as.numeric(rmfi_remove_empty_strings(strsplit(cbc.lines[1],' ')[[1]]))
# cbc.lines <- cbc.lines[-1]
# if(nvalues > 1) {
# additionalColumns <- rep(NA,nvalues-1)
# for(i in 1:(nvalues-1)) {
# additionalColumns[i] <- rmfi_remove_empty_strings(strsplit(cbc.lines[1],' ')[[1]])
# cbc.lines <- cbc.lines[-1]
# }
# #cbc.lines <- cbc.lines[-1] #IFACE
# #cbc.lines <- cbc.lines[-1] #CONDFACT
# #cbc.lines <- cbc.lines[-1] #CELLGRP
# }
# nrecords <- as.numeric(rmfi_remove_empty_strings(strsplit(cbc.lines[1],' ')[[1]]))
# cbc.lines <- cbc.lines[-1]
# # use rmfi_parse_array or rmfi_parse_variables instead!!
# dataVector <- as.numeric(split_line_numbers(paste(cbc.lines[1:nrecords],collapse=' ')))
# cbc[[name]]$data <- as.data.frame(matrix(dataVector,nrow=nrecords,ncol=nvalues+1,byrow=T))
# if(nvalues > 1) names(cbc[[name]]$data) <- c('ID','FLUX',additionalColumns)
# if(nvalues == 1)names(cbc[[name]]$data) <- c('ID','FLUX')
# cbc.lines <- cbc.lines[-c(1:nrecords)]
# cbc.lines <- cbc.lines[-1]
# }
# }
# class(cbc) <- 'cbc'
# return(cbc)
}
}
#' Read a MODFLOW head file
#'
#' \code{rmf_read_hed} reads in a MODFLOW head file and returns it as an \code{RMODFLOW} hed object.
#'
#' @param file filename; typically '*.hed'
#' @param dis dis object
#' @param huf huf object; optional. Provide only if huf heads are being read. See details.
#' @param oc oc object; optional. See details.
#' @param bas bas object; optional. If supplied, is used to set the hnoflo values to NA.
#' @param hdry numeric value as set by the flow package (bcf, lpf, huf or upw). If supplied, cells with this value are dry and their values are set to NA. Defaults to NULL (unless huf is supplied)
#' @param binary logical; is the file binary?
#' @param precision either \code{'single'} or \code{'double'}. Specifies the precision of the binary file.
#' @param timesteps optional integer vector specifying which time steps to read. If -1 is specified, only the last time step is read. Defaults to NULL. See details.
#' @return object of class hed and rmf_4d_array.
#' @details
#' When huf heads are to be read, a \code{huf} object should also be supplied. The final array will have NHUF layers instead of NLAY.
#'
#' If no \code{oc} object is supplied, a rmf_array of dimensions NROW x NCOL x NLAY x sum(NSTP) is created and filled. Time steps for which no output is given are filled with \code{NA}.
#' If a \code{oc} object is supplied, the dimensions of the returned array are NROW x NCOL x NLAY x STPS where STPS are timesteps for which output is saved.
#' If the array is in ASCII format and no headers are present, a \code{OC} object must be supplied. In that case, it is assumed that the file being read only contains head values and the keyword XSECTION in the bas file is not present.
#'
#' If the timesteps argument is supplied, it overwrites the use of the oc argument. For all array flow terms a rmf_array of dimensions NROW x NCOL x NLAY x length(timesteps) is created and filled.
#'
#' The only use of the bas argument is to replace the hnoflo values in the final array with NA's.
#'
#' @export
rmf_read_hed <- function(file = {cat('Please select head file ...\n'); file.choose()},
dis = {cat('Please select corresponding dis file ...\n'); rmf_read_dis(file.choose())},
huf = NULL,
oc = NULL,
bas = NULL,
hdry = huf$hdry,
binary = TRUE,
precision = 'single',
timesteps = NULL) {
headers <- trimws(rmfd_state_headers)
other_desc <- NULL
xsection <- FALSE
if(binary) { # Binary
hed <- NULL
real_number_bytes <- ifelse(precision == 'single', 4, 8)
con <- file(file,open='rb')
try({
if(!is.null(huf) && huf$iohufheads > 0) {
dis$nlay <- huf$nhuf
}
if(!is.null(timesteps)) {
oc <- NULL
if(length(timesteps) == 1 && timesteps < 0) timesteps <- sum(dis$nstp)
}
# check time steps if oc is specified
if(!is.null(oc)) {
# oc using words
if(!is.null(oc$save_head)) {
# problem: oc records might be in non-ascending order or have non-existing time steps but output is still writen for current timestep
# e.g. UZFtest2
m_oc<- cbind(oc$iperoc, oc$itsoc)[rmfi_ifelse0(is.matrix(oc$save_head), apply(oc$save_head, 2, any), oc$save_head),]
if(!is.matrix(m_oc)) m_oc <- matrix(m_oc, ncol = 2, byrow = TRUE)
nsteps <- apply(m_oc, 1, function(i) rmfi_ifelse0(i[1] == 1, ifelse(i[2] > dis$nstp[i[1]], NA, i[2]), cumsum(dis$nstp)[i[1]-1]+i[2]))
# check before going into nested for-loop
if(any(is.na(nsteps)) || !all(diff(nsteps) >= 0)) {
nsteps <- 0
i <- 0
for(k in 1:dis$nper) {
for(l in 1:dis$nstp[k]) {
if(m_oc[i+1,1] < k || (m_oc[i+1,1]==k && m_oc[i+1,2] < l)) {
i <- i + 1
m_oc[i,1] <- k
m_oc[i,2] <- l
nsteps <- nsteps + 1
} else if(m_oc[i+1,1]==k && m_oc[i+1,2]==l){
nsteps <- nsteps + 1
i <- i + 1
}
}
}
} else {
nsteps <- min(sum(dis$nstp), length(which(oc$save_head == TRUE)))
}
# oc using codes
} else {
nsteps <- length(which(apply(oc$hdsv,1,function(i) any(i==TRUE))==TRUE))
}
} else {
nsteps <- sum(dis$nstp)
}
first <- TRUE
kstp <- readBin(con,what='integer',n=1)
kper <- readBin(con,what='integer',n=1)
pertim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
totim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
desc <- trimws(readChar(con,nchars=16))
if(! desc %in% headers) {
stop('Array description not recognized. Is the file really binary? If so, you could try double precision. If not, set the binary argument to FALSE.', call. = FALSE)
}
while(length(desc != 0)) {
name <- gsub(' ', '_', tolower(desc))
# if IOHUFHEADS > 0, there will also be normal head per layer arrays. Do not return those.
if(!is.null(huf) && huf$iohufheads > 0 && desc != 'HEAD IN HGU'){
other_desc <- append(other_desc, desc)
invisible(readBin(con, what='integer', n=3))
invisible(readBin(con,what='numeric',n = dis$ncol * dis$nrow, size = real_number_bytes))
invisible(readBin(con, what='integer', n=2))
invisible(readBin(con,what='numeric',n = 2, size = real_number_bytes))
desc <- trimws(readChar(con,nchars=16))
} else if(is.null(huf) && name != 'head') {
other_desc <- append(other_desc, name)
invisible(readBin(con, what='integer', n=3))
invisible(readBin(con,what='numeric',n = dis$ncol * dis$nrow, size = real_number_bytes))
invisible(readBin(con, what='integer', n=2))
invisible(readBin(con,what='numeric',n = 2, size = real_number_bytes))
desc <- trimws(readChar(con,nchars=16))
} else {
ncol <- readBin(con, what = 'integer', n = 1)
nrow <- readBin(con, what = 'integer', n = 1)
ilay <- readBin(con, what = 'integer', n = 1)
# xsection - ilay never negative with huf. Only do this once.
xsection <- FALSE
if(ilay < 0 && first) {
xsection <- TRUE
dis$nrow <- dis$nlay
dis$nlay <- 1
}
ilay <- abs(ilay)
if(first) {
hed <- array(NA, dim = c(dis$nrow, dis$ncol, dis$nlay, nsteps))
attr(hed, 'kstp') <- attr(hed, 'kper') <- attr(hed, 'pertim') <- attr(hed, 'totim') <- attr(hed, 'nstp') <- rep(NA, nsteps)
}
if(is.null(oc)) {
stp_nr <- ifelse(kper==1,kstp,cumsum(dis$nstp)[kper-1]+kstp)
} else {
if(first) {
stp_nr <- 1
} else {
stp_nr <- ifelse(ilay == 1, stp_nr+1, stp_nr)
}
}
hed[,,ilay,stp_nr] <- aperm(array(readBin(con,what='numeric',n = ncol * nrow, size = real_number_bytes),dim=c(ncol, nrow)), c(2, 1))
attr(hed,'kstp')[stp_nr] <- kstp
attr(hed,'kper')[stp_nr] <- kper
attr(hed,'pertim')[stp_nr] <- pertim
attr(hed,'totim')[stp_nr] <- totim
attr(hed, 'nstp')[stp_nr] <- ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1]+kstp)
first <- FALSE
kstp <- readBin(con,what='integer',n=1)
kper <- readBin(con,what='integer',n=1)
pertim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
totim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
desc <- trimws(readChar(con,nchars=16))
}
}
if(!is.null(bas)) hed[which(hed == bas$hnoflo)] <- NA
if(!is.null(hdry)) hed[which(hed == hdry)] <- NA
if(!is.null(other_desc) && length(other_desc) != 0) {
warning(paste('HEAD or HEAD IN HGU not found in file. Found ', length(other_desc), 'other descriptions:','\n',paste(other_desc, '\n'),'\n','Returning NULL'), call. = FALSE)
hed <- NULL
} else {
hed <- rmf_create_array(hed, dimlabels = rmfi_ifelse0(xsection, c('k', 'j', 'i', 'l'), c('i', 'j', 'k', 'l')))
if(!is.null(timesteps)) {
hed <- rmf_create_array(hed[,,,timesteps], dim = c(dim(hed)[1:3], length(timesteps)))
}
class(hed) <- c('hed', class(hed))
}
})
close(con)
if(is.null(hed)) {
stop('Error in reading binary head file.', call. = FALSE)
} else {
return(hed)
}
} else { # ASCII
hed.lines <- readr::read_lines(file, lazy = FALSE)
label <- TRUE
header_fmt <- '(1X,2I5,2E15.6,A17,3I6,A17)'
header_fmt <- rmfi_fortran_format(header_fmt)
variables <- trimws(substring(hed.lines[1], cumsum(header_fmt)[-length(header_fmt)] + 1, cumsum(header_fmt)[-1]))
# variables <- rmfi_remove_empty_strings(strsplit(variables,' ')[[1]])
desc <- paste(variables[5:(length(variables)-4)], collapse=' ')
if(! desc %in% headers) { # weak test to check if there's a label
# if(variables[2] != dis$ncol) {
# stop('Array description not recognized. Are you sure the file is not binary ?', call. = FALSE)
# }
label <- FALSE
if(is.null(oc)) {
stop('No label line detected in ASCII head file. Please specify an OC object.', call. = FALSE)
} else {
warning('No label line detected in ASCII head file. Assuming file only contains head values.', call. = FALSE)
}
}
# skip non-head arrays
if(label) {
if(!is.null(huf) && huf$iohufheads > 0){
if(any(grepl('HEAD IN HGU', hed.lines))) {
hed.lines <- hed.lines[grep('HEAD IN HGU', hed.lines)[1]:length(hed.lines)]
dis$nlay <- huf$nhuf
} else {
other_desc <- headers[vapply(seq_along(headers), function(i) any(grepl(headers[i], hed.lines)), FUN.VALUE = FALSE)]
hed.lines <- NULL
}
} else {
if(any(grepl('HEAD', hed.lines))) {
hed.lines <- hed.lines[grep('HEAD', hed.lines)[1]:length(hed.lines)]
} else {
other_desc <- headers[vapply(seq_along(headers), function(i) any(grepl(headers[i], hed.lines)), FUN.VALUE = FALSE)]
hed.lines <- NULL
}
}
}
if(!is.null(timesteps)) {
oc <- NULL
if(length(timesteps) == 1 && timesteps < 0) timesteps <- sum(dis$nstp)
}
# check time steps if oc is specified
if(!is.null(oc)) {
# oc using words
if(!is.null(oc$save_head) ) {
if(is.matrix(oc$save_head)) {
nsteps <- length(which(apply(oc$save_head,2,function(i) any(i==TRUE))==TRUE))
} else {
nsteps <- length(which(oc$save_head == TRUE))
}
# oc using codes
} else {
nsteps <- length(which(apply(oc$hdsv,2,function(i) any(i==TRUE))==TRUE))
}
} else {
nsteps <- sum(dis$nstp)
}
first <- TRUE
while(length(hed.lines) != 0) {
if(label) {
# variables <- rmfi_remove_empty_strings(strsplit(hed.lines[1],' ')[[1]])
variables <- trimws(substring(hed.lines[1], cumsum(header_fmt)[-length(header_fmt)] + 1, cumsum(header_fmt)[-1]))
kstp <- as.numeric(variables[1])
kper <- as.numeric(variables[2])
pertim <- as.numeric(variables[3])
totim <- as.numeric(variables[4])
desc <- paste(variables[5:(length(variables)-4)], collapse=' ')
fmt <- variables[length(variables)]
if(! desc %in% headers) {
stop('Array description not recognized. Are you sure the file is not binary ?', call. = FALSE)
}
name <- gsub(' ', '_', tolower(trimws(desc)))
ncol <- as.numeric(variables[length(variables)-3])
nrow <- as.numeric(variables[length(variables)-2])
ilay <- abs(as.numeric(variables[length(variables)-1]))
hed.lines <- hed.lines[-1]
# xsection - ilay never negative with huf. Only do this once.
xsection <- FALSE
if(ilay < 0 && !is.null(dis) && first) {
xsection <- TRUE
dis$nrow <- dis$nlay
dis$nlay <- 1
}
ilay <- abs(ilay)
# no label
} else {
# oc words
if(!is.null(oc$save_head)) {
fmt <- oc$chedfm
if(is.matrix(oc$save_head)) {
ind <- ifelse(first, 1, ind + 1)
read <- oc$save_head[ind]
ilay <- arrayInd(ind, dim(oc$save_head))[1]
kstp <- oc$itsoc[arrayInd(ind, dim(oc$save_head))[2]]
kper <- oc$iperoc[arrayInd(ind, dim(oc$save_head))[2]]
tsl <- rmf_time_steps(dis = dis)$tsl
totim <- sum(tsl[1:ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1] + kstp)])
pertim <- totim - ifelse(kper == 1, 0, sum(tsl[1:cumsum(dis$nstp)[kper-1]]))
} else {
ind <- ifelse(first, 1, ifelse(ilay == dis$nlay, ind, ind + 1))
read <- oc$save_head[ind]
if(read) {
if(first) {
ilay <- 1
} else {
ilay <- ifelse(ilay != dis$nlay, ilay + 1, 1)
}
kstp <- oc$itsoc[ind]
kper <- oc$iperoc[ind]
tsl <- rmf_time_steps(dis = dis)$tsl
totim <- sum(tsl[1:ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1] + kstp)])
pertim <- totim - ifelse(kper == 1, 0, sum(tsl[1:cumsum(dis$nstp)[kper-1]]))
}
}
# oc codes; not possible if output file is ASCII
} else if(!is.null(oc$hdsv)) {
ind <- ifelse(first, 1, ind + 1)
read <- oc$hdsv[ind]
ilay <- arrayInd(ind, dim(oc$hdsv))[1]
nstp <- arrayInd(ind, dim(oc$hdsv))[2]
kper <- findInterval(nstp, cumsum(dis$nstp), left.open = T) + 1
kstp <- rmfi_ifelse0(kper == 1, nstp, nstp - cumsum(dis$nstp)[kper - 1])
tsl <- rmf_time_steps(dis = dis)$tsl
totim <- sum(tsl[1:ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1] + kstp)])
pertim <- totim - ifelse(kper == 1, 0, sum(tsl[1:cumsum(dis$nstp)[kper-1]]))
}
}
# read array
data_set <- rmfi_parse_array(hed.lines,dis$nrow,dis$ncol,1, ndim = 2, skip_header = TRUE, fmt = fmt)
if(first) {
hed <- array(NA, dim = c(dis$nrow, dis$ncol, dis$nlay, nsteps))
attr(hed, 'kstp') <- attr(hed, 'kper') <- attr(hed, 'pertim') <- attr(hed, 'totim') <- attr(hed, 'nstp') <- rep(NA, nsteps)
}
if(is.null(oc)) {
stp_nr <- ifelse(kper==1,kstp,cumsum(dis$nstp)[kper-1]+kstp)
} else {
if(first) {
stp_nr <- 1
} else {
stp_nr <- ifelse(ilay == 1, stp_nr+1, stp_nr)
}
}
hed[,,ilay,stp_nr] <- data_set$array
attr(hed,'kstp')[stp_nr] <- kstp
attr(hed,'kper')[stp_nr] <- kper
attr(hed,'pertim')[stp_nr] <- pertim
attr(hed,'totim')[stp_nr] <- totim
attr(hed, 'nstp')[stp_nr] <- ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1]+kstp)
first <- FALSE
hed.lines <- data_set$remaining_lines
# skip non-head arrays
if(label) {
if(!is.null(huf) && huf$iohufheads > 0){
if(any(grepl('HEAD IN HGU', hed.lines))) {
hed.lines <- hed.lines[grep('HEAD IN HGU', hed.lines)[1]:length(hed.lines)]
dis$nlay <- huf$nhuf
} else {
other_desc <- headers[vapply(seq_along(headers), function(i) any(grepl(headers[i], hed.lines)), FUN.VALUE = FALSE)]
hed.lines <- NULL
}
} else {
if(any(grepl('HEAD', hed.lines))) {
hed.lines <- hed.lines[grep('HEAD', hed.lines)[1]:length(hed.lines)]
} else {
other_desc <- headers[vapply(seq_along(headers), function(i) any(grepl(headers[i], hed.lines)), FUN.VALUE = FALSE)]
hed.lines <- NULL
}
}
}
}
if(!is.null(bas)) hed[which(hed == bas$hnoflo)] <- NA
if(!is.null(hdry)) hed[which(hed == hdry)] <- NA
if(!is.null(other_desc) && length(other_desc) != 0) {
warning(paste('HEAD or HEAD IN HGU not found in file. Found ', length(other_desc), 'other descriptions:','\n',paste(other_desc, '\n'),'\n','Returning NULL'), call. = FALSE)
return(NULL)
} else {
hed <- rmf_create_array(hed, dimlabels = rmfi_ifelse0(xsection, c('k', 'j', 'i', 'l'), c('i', 'j', 'k', 'l')))
if(!is.null(timesteps)) {
hed <- rmf_create_array(hed[,,,timesteps], dim = c(dim(hed)[1:3], length(timesteps)))
}
class(hed) <- c('hed', class(hed))
return(hed)
}
}
}
#' @describeIn rmf_read_hed
#' @export
rmf_read_head <- function(...) {
rmf_read_hed(...)
}
#' @describeIn rmf_read_hed Compatible with default ModelMuse file extension
#' @export
rmf_read_fhd <- function(...) {
rmf_read_hed(..., binary = FALSE)
}
#' @describeIn rmf_read_hed Compatible with default ModelMuse file extension
#' @export
rmf_read_bhd <- function(...) {
rmf_read_hed(..., binary = TRUE)
}
#' Read a MODFLOW drawdown file
#'
#' \code{rmf_read_ddn} reads in a MODFLOW drawdown file and returns it as an \code{RMODFLOW} ddn object.
#'
#' @param file filename; typically '*.ddn'
#' @param dis dis object
#' @param oc oc object; optional. See details.
#' @param bas bas object; optional. If supplied, is used to set the hnoflo values to NA.
#' @param hdry numeric value as set by the flow package (bcf, lpf, huf or upw). If supplied, cells with this value are dry and their values are set to NA. Defaults to NULL
#' @param binary logical; is the file binary?
#' @param precision either \code{'single'} or \code{'double'}. Specifies the precision of the binary file.
#' @param timesteps optional integer vector specifying which time steps to read. If -1 is specified, only the last time step is read. Defaults to NULL. See details.
#' @return object of class ddn and rmf_4d_array
#' @details
#'
#' If no \code{oc} object is supplied, a rmf_array of dimensions NROW x NCOL x NLAY x sum(NSTP) is created and filled. Time steps for which no output is given are filled with \code{NA}.
#' If a \code{oc} object is supplied, the dimensions of the returned array are NROW x NCOL x NLAY x STPS where STPS are timesteps for which output is saved.
#' If the array is in ASCII format and no headers are present, a \code{OC} object must be supplied. In that case, it is assumed that the file being read only contains head values and the keyword XSECTION in the bas file is not present.
#'
#' If the timesteps argument is supplied, it overwrites the use of the oc argument. For all array flow terms a rmf_array of dimensions NROW x NCOL x NLAY x length(timesteps) is created and filled.
#'
#' The only use of the bas argument is to replace the hnoflo values in the final array with NA's.
#'
#' @export
rmf_read_ddn <- function(file = {cat('Please select ddn file ...\n'); file.choose()},
dis = {cat('Please select corresponding dis file ...\n'); rmf_read_dis(file.choose())},
oc = NULL,
bas = NULL,
hdry = NULL,
binary = TRUE,
precision = 'single',
timesteps = NULL) {
headers <- rmfd_state_headers
other_desc <- NULL
xsection <- FALSE
if(binary) { # Binary
hed <- NULL
real_number_bytes <- ifelse(precision == 'single', 4, 8)
con <- file(file,open='rb')
try({
# if(!is.null(huf) && huf$iohufheads > 0) {
# dis$nlay <- huf$nhuf
# }
if(!is.null(timesteps)) {
oc <- NULL
if(length(timesteps) == 1 && timesteps < 0) timesteps <- sum(dis$nstp)
}
# check time steps if oc is specified
if(!is.null(oc)) {
# oc using words
if(!is.null(oc$save_drawdown) ) {
# problem: oc records might be in non-ascending order or have non-existing time steps but output is still writen for current timestep
# e.g. UZFtest2
m_oc<- cbind(oc$iperoc, oc$itsoc)[rmfi_ifelse0(is.matrix(oc$save_drawdown), apply(oc$save_drawdown, 2, any), oc$save_drawdown),]
if(!is.matrix(m_oc)) m_oc <- matrix(m_oc, ncol = 2, byrow = TRUE)
nsteps <- apply(m_oc, 1, function(i) rmfi_ifelse0(i[1] == 1, ifelse(i[2] > dis$nstp[i[1]], NA, i[2]), cumsum(dis$nstp)[i[1]-1]+i[2]))
# check before going into nested for-loop
if(any(is.na(nsteps)) || !all(diff(nsteps) >= 0)) {
nsteps <- 0
i <- 0
for(k in 1:dis$nper) {
for(l in 1:dis$nstp[k]) {
if(m_oc[i+1,1] < k || (m_oc[i+1,1]==k && m_oc[i+1,2] < l)) {
i <- i + 1
m_oc[i,1] <- k
m_oc[i,2] <- l
nsteps <- nsteps + 1
} else if(m_oc[i+1,1]==k && m_oc[i+1,2]==l){
nsteps <- nsteps + 1
i <- i + 1
}
}
}
} else {
nsteps <- min(sum(dis$nstp), length(which(oc$save_drawdown == TRUE)))
}
# oc using codes
} else {
nsteps <- length(which(apply(oc$ddsv,1,function(i) any(i==TRUE))==TRUE))
}
} else {
nsteps <- sum(dis$nstp)
}
first <- TRUE
kstp <- readBin(con,what='integer',n=1)
kper <- readBin(con,what='integer',n=1)
pertim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
totim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
desc <- trimws(readChar(con,nchars=16))
if(! desc %in% headers) {
stop('Array description not recognized. Is the file really binary? If so, you could try double precision. If not, set the binary argument to FALSE.', call. = FALSE)
}
while(length(desc != 0)) {
name <- gsub(' ', '_', tolower(desc))
# # if IOHUFHEADS > 0, there will also be normal head per layer arrays. Do not return those.
# if(!is.null(huf) && huf$iohufheads > 0 && desc != ' HEAD IN HGU'){
# other_desc <- append(other_desc, desc)
# invisible(readBin(con, what='integer', n=3))
# invisible(readBin(con,what='numeric',n = dis$ncol * dis$nrow, size = real_number_bytes))
# invisible(readBin(con, what='integer', n=2))
# invisible(readBin(con,what='numeric',n = 2, size = real_number_bytes))
# desc = readChar(con,nchars=16)
#
# } else
if(name != 'drawdown') {
other_desc <- append(other_desc, name)
invisible(readBin(con, what='integer', n=3))
invisible(readBin(con,what='numeric',n = dis$ncol * dis$nrow, size = real_number_bytes))
invisible(readBin(con, what='integer', n=2))
invisible(readBin(con,what='numeric',n = 2, size = real_number_bytes))
desc <- trimws(readChar(con,nchars=16))
} else {
ncol <- readBin(con, what = 'integer', n = 1)
nrow <- readBin(con, what = 'integer', n = 1)
ilay <- readBin(con, what = 'integer', n = 1)
# xsection - ilay never negative with huf. Only do this once.
xsection <- FALSE
if(ilay < 0 && first) {
xsection <- TRUE
dis$nrow <- dis$nlay
dis$nlay <- 1
}
ilay <- abs(ilay)
if(first) {
hed <- array(NA, dim = c(dis$nrow, dis$ncol, dis$nlay, nsteps))
attr(hed, 'kstp') <- attr(hed, 'kper') <- attr(hed, 'pertim') <- attr(hed, 'totim') <- attr(hed, 'nstp') <- rep(NA, nsteps)
}
if(is.null(oc)) {
stp_nr <- ifelse(kper==1,kstp,cumsum(dis$nstp)[kper-1]+kstp)
} else {
if(first) {
stp_nr <- 1
} else {
stp_nr <- ifelse(ilay == 1, stp_nr+1, stp_nr)
}
}
hed[,,ilay,stp_nr] <- aperm(array(readBin(con,what='numeric',n = ncol * nrow, size = real_number_bytes),dim=c(ncol, nrow)), c(2, 1))
attr(hed,'kstp')[stp_nr] <- kstp
attr(hed,'kper')[stp_nr] <- kper
attr(hed,'pertim')[stp_nr] <- pertim
attr(hed,'totim')[stp_nr] <- totim
attr(hed,'nstp')[stp_nr] <- ifelse(kper == 1, kstp, cumsum(dis$nstp)[kper-1]+kstp)
first <- FALSE
kstp <- readBin(con,what='integer',n=1)
kper <- readBin(con,what='integer',n=1)
pertim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
totim <- readBin(con,what='numeric',n = 1, size = real_number_bytes)
desc <- trimws(readChar(con,nchars=16))
}
}
if(!is.null(other_desc) && length(other_desc) != 0) {
warning(paste('DRAWDOWN not found in file. Found ', length(other_desc), 'other descriptions:','\n',paste(other_desc, '\n'),'\n','Returning NULL'), call. = FALSE)
hed <- NULL
} else {
if(!is.null(bas)) hed[which(hed == bas$hnoflo)] <- NA
if(!is.null(hdry)) hed[which(hed == hdry)] <- NA
hed <- rmf_create_array(hed, dimlabels = rmfi_ifelse0(xsection, c('k', 'j', 'i', 'l'), c('i', 'j', 'k', 'l')))
if(!is.null(timesteps)) {
hed <- rmf_create_array(hed[,,,timesteps], dim = c(dim(hed)[1:3], length(timesteps)))
}
class(hed) <- c('ddn', class(hed))
}
})
close(con)
if(is.null(hed)) {
stop('Error in reading binary drawdown file.', call. = FALSE)
} else {
return(hed)
}
} else { # ASCII
hed.lines <- readr::read_lines(file, lazy = FALSE)
label <- TRUE
header_fmt <- '(1X,2I5,2E15.6,A17,3I6,A17)'
header_fmt <- rmfi_fortran_format(header_fmt)
variables <- trimws(substring(hed.lines[1], cumsum(header_fmt)[-length(header_fmt)] + 1, cumsum(header_fmt)[-1]))
# variables <- rmfi_remove_empty_strings(strsplit(hed.lines[1],' ')[[1]])
desc <- paste(variables[5:(length(variables)-4)], collapse=' ')
if(! desc %in% headers) { # weak test to check if there's a label
# if(variables[2] != dis$ncol) {
# stop('Array description not recognized. Are you sure the file is not binary ?', call. = FALSE)
# }
label <- FALSE
if(is.null(oc)) {
stop('No label line detected in ASCII drawdown file. Please specify an OC object.', call. = FALSE)
} else {
warning('No label line detected in ASCII drawdown file. Assuming file only contains drawdown values.', call. = FALSE)
}
}