Nothing
R/BatchProcess.r
In RiverSurvey: River Research and Modelling
#This code handles batch-processing in R
#Copyright (C) 2014 Claude Flener, University of Turku.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#Generic function for batch processing a certain file type. If a single file is given as path, that will be handled using FUN. If a directory is given as path, all files of type ext in that directory will be processed using FUN.
batchProcess <- function(FUN=NA, ext=NA, path=getwd(), verbose=TRUE, interact=FALSE){
if(class(ext)!="character") cat("Error: ext needs to be of format 'character'")
extPattern <- paste0("*[.]",ext,"$") # avoid repeating regex
# if path is a file name, start processing
if(grepl(extPattern ,path)){
# pathnames <- basename(path)
pathname <- path # required for for loop
pathnames <- path # required for for loop
path <- dirname(path) # required for writing the file later
}else{
# if path is a directory, get all .ext files and process them in sequence
ext.files <- list.files(path=path, pattern=extPattern)
pattern <- sprintf(extPattern, version)
pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)
# filenamesfull <- list.files(pattern=pattern)
# extract file names without extensions
# filenames <- sub(".mat$|$","",filenamesfull)
if(verbose==TRUE) cat("Loading all .",ext," files in ", path.expand(path), "...\n", sep="")
}
# read files
for (pathname in pathnames) {
cat("Processing .",ext," file: ", basename(pathname), "\n", sep="")
#filename <- sub(extPattern,"",basename(pathname))
x <- FUN(pathname)
#return( FUN(pathname) )
#optional interactive mode to interrupt processing before continuing to next file
#if (interact==TRUE){
#if (interactive()) {
#cat("Press ENTER to view data:")
#readline()
#}
#print(dat)
#}
}
return(x)
}
#batchProcess(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18/20130518190800.mat")
#x <- batchProcess(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18")
#Generic function for gathering batches of a certain file type. This is primarily intended to be called from inside another function to add automatic batching functionality. Returns a vector of Pathnames to be used in a loop outside this function. If a single file is given as path, that path will be returned as a result. If a directory is given as path, all paths of files of type ext in that directory will be returned.
#Returns a vector "pathnames" of type Character
#Use in conjunction with a loop like this:
#for (pathname in pathnames) {
#cat("Processing .",ext," file: ", basename(pathname), "\n", sep="")
#x <- FUN(pathname)
#}
batchFiles <- function(ext=NA, path=getwd(), verbose=TRUE, interact=FALSE){
if(class(ext)!="character") cat("Error: ext needs to be of format 'character'")
extPattern <- paste0("*[.]",ext,"$") # avoid repeating regex
# if path is a file name, start processing
if(grepl(extPattern ,path)){
# pathnames <- basename(path)
pathname <- path # required for for loop
pathnames <- path # required for for loop
path <- dirname(path) # required for writing the file later
}else{
# if path is a directory, get all .ext files and process them in sequence
ext.files <- list.files(path=path, pattern=extPattern)
pattern <- sprintf(extPattern, version)
pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)
# filenamesfull <- list.files(pattern=pattern)
# extract file names without extensions
# filenames <- sub(".mat$|$","",filenamesfull)
if(verbose==TRUE) cat("Loading all .",ext," files in ", path.expand(path), "...\n", sep="")
}
return(pathnames)
}
#Generic function for batch handling a certain file type. This is primarily intended for batch reading files of a specific type to be called from inside another function. If a single file is given as path, that will be handled using FUN and returned as a result. If a directory is given as path, all files of type ext in that directory will be handled using FUN and the results returned as a list.
batchProcess2List <- function(FUN=NA, ext=NA, path=getwd(), merge=FALSE, verbose=TRUE, interact=FALSE){
if(class(ext)!="character") cat("Error: ext needs to be of format 'character'")
extPattern <- paste0("*[.]",ext,"$") # avoid repeating regex
# if path is a file name, start processing
if(grepl(extPattern ,path)){
# pathnames <- basename(path)
pathname <- path # required for for loop
pathnames <- path # required for for loop
path <- dirname(path) # required for writing the file later
}else{
# if path is a directory, get all .ext files and process them in sequence
ext.files <- list.files(path=path, pattern=extPattern)
pattern <- sprintf(extPattern, version)
pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)
# filenamesfull <- list.files(pattern=pattern)
# extract file names without extensions
# filenames <- sub(".mat$|$","",filenamesfull)
if(verbose==TRUE) cat("Loading all .",ext," files in ", path.expand(path), "...\n", sep="")
}
# read files
data <- list()
if(merge==FALSE){
for (pathname in pathnames) {
cat("Processing .",ext," file: ", basename(pathname), "\n", sep="")
filename <- sub(extPattern,"",basename(pathname))
#data[basename(pathname)] <- FUN(pathname)
x <- FUN(pathname)
#print(x)
#data[[basename(pathname)]] <- x
data[[filename]] <- x
}
}else{
cat(pathnames[1], "\n\n")
print(pathnames[2:length(pathnames)])
data <- FUN(pathnames[1])
for (pathname in pathnames[2:length(pathnames)]) {
x <- FUN(pathname)
data <- mapply(c, data, x, SIMPLIFY=FALSE)
}
}
#return( FUN(pathname) )
#optional interactive mode to interrupt processing before continuing to next file
#if (interact==TRUE){
#if (interactive()) {
#cat("Press ENTER to view data:")
#readline()
#}
#print(dat)
#}
return(data)
}
#x <- batchProcess2List(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18/20130518190800.mat")
#x <- batchProcess2List(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18")
#y <- x[[ 1 ]]
#length(x)
#names(x)[1]
#basename(names(x)[1])
readRivMat <- function(x){
riv <- readMat(x)
#extract structure names from Matlab format to use in R
names(riv$Setup) <- dimnames( riv$Setup)[[1]]
names(riv$Processing) <- dimnames( riv$Processing)[[1]]
# Mat file contains two $System structures
# Rename first one to Specs
names(riv)[3] <- "Specs"
names(riv$Specs) <- dimnames( riv$Specs)[[1]]
names(riv$Transformation.Matrices) <- dimnames( riv$Transformation.Matrices)[[1]]
names(riv$System) <- dimnames( riv$System)[[1]]
names(riv$Summary) <- dimnames( riv$Summary)[[1]]
names(riv$BottomTrack) <- dimnames( riv$BottomTrack)[[1]]
names(riv$GPS) <- dimnames( riv$GPS)[[1]]
names(riv$WaterTrack) <- dimnames( riv$WaterTrack)[[1]]
names(riv$Compas) <- dimnames( riv$Compas)[[1]]
names(riv$RawGPSData) <- dimnames( riv$RawGPSData)[[1]]
return(riv)
}
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RiverSurvey documentation built on May 2, 2019, 5:46 p.m.
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#This code handles batch-processing in R
#Copyright (C) 2014 Claude Flener, University of Turku.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#Generic function for batch processing a certain file type. If a single file is given as path, that will be handled using FUN. If a directory is given as path, all files of type ext in that directory will be processed using FUN.
batchProcess <- function(FUN=NA, ext=NA, path=getwd(), verbose=TRUE, interact=FALSE){
if(class(ext)!="character") cat("Error: ext needs to be of format 'character'")
extPattern <- paste0("*[.]",ext,"$") # avoid repeating regex
# if path is a file name, start processing
if(grepl(extPattern ,path)){
# pathnames <- basename(path)
pathname <- path # required for for loop
pathnames <- path # required for for loop
path <- dirname(path) # required for writing the file later
}else{
# if path is a directory, get all .ext files and process them in sequence
ext.files <- list.files(path=path, pattern=extPattern)
pattern <- sprintf(extPattern, version)
pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)
# filenamesfull <- list.files(pattern=pattern)
# extract file names without extensions
# filenames <- sub(".mat$|$","",filenamesfull)
if(verbose==TRUE) cat("Loading all .",ext," files in ", path.expand(path), "...\n", sep="")
}
# read files
for (pathname in pathnames) {
cat("Processing .",ext," file: ", basename(pathname), "\n", sep="")
#filename <- sub(extPattern,"",basename(pathname))
x <- FUN(pathname)
#return( FUN(pathname) )
#optional interactive mode to interrupt processing before continuing to next file
#if (interact==TRUE){
#if (interactive()) {
#cat("Press ENTER to view data:")
#readline()
#}
#print(dat)
#}
}
return(x)
}
#batchProcess(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18/20130518190800.mat")
#x <- batchProcess(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18")
#Generic function for gathering batches of a certain file type. This is primarily intended to be called from inside another function to add automatic batching functionality. Returns a vector of Pathnames to be used in a loop outside this function. If a single file is given as path, that path will be returned as a result. If a directory is given as path, all paths of files of type ext in that directory will be returned.
#Returns a vector "pathnames" of type Character
#Use in conjunction with a loop like this:
#for (pathname in pathnames) {
#cat("Processing .",ext," file: ", basename(pathname), "\n", sep="")
#x <- FUN(pathname)
#}
batchFiles <- function(ext=NA, path=getwd(), verbose=TRUE, interact=FALSE){
if(class(ext)!="character") cat("Error: ext needs to be of format 'character'")
extPattern <- paste0("*[.]",ext,"$") # avoid repeating regex
# if path is a file name, start processing
if(grepl(extPattern ,path)){
# pathnames <- basename(path)
pathname <- path # required for for loop
pathnames <- path # required for for loop
path <- dirname(path) # required for writing the file later
}else{
# if path is a directory, get all .ext files and process them in sequence
ext.files <- list.files(path=path, pattern=extPattern)
pattern <- sprintf(extPattern, version)
pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)
# filenamesfull <- list.files(pattern=pattern)
# extract file names without extensions
# filenames <- sub(".mat$|$","",filenamesfull)
if(verbose==TRUE) cat("Loading all .",ext," files in ", path.expand(path), "...\n", sep="")
}
return(pathnames)
}
#Generic function for batch handling a certain file type. This is primarily intended for batch reading files of a specific type to be called from inside another function. If a single file is given as path, that will be handled using FUN and returned as a result. If a directory is given as path, all files of type ext in that directory will be handled using FUN and the results returned as a list.
batchProcess2List <- function(FUN=NA, ext=NA, path=getwd(), merge=FALSE, verbose=TRUE, interact=FALSE){
if(class(ext)!="character") cat("Error: ext needs to be of format 'character'")
extPattern <- paste0("*[.]",ext,"$") # avoid repeating regex
# if path is a file name, start processing
if(grepl(extPattern ,path)){
# pathnames <- basename(path)
pathname <- path # required for for loop
pathnames <- path # required for for loop
path <- dirname(path) # required for writing the file later
}else{
# if path is a directory, get all .ext files and process them in sequence
ext.files <- list.files(path=path, pattern=extPattern)
pattern <- sprintf(extPattern, version)
pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)
# filenamesfull <- list.files(pattern=pattern)
# extract file names without extensions
# filenames <- sub(".mat$|$","",filenamesfull)
if(verbose==TRUE) cat("Loading all .",ext," files in ", path.expand(path), "...\n", sep="")
}
# read files
data <- list()
if(merge==FALSE){
for (pathname in pathnames) {
cat("Processing .",ext," file: ", basename(pathname), "\n", sep="")
filename <- sub(extPattern,"",basename(pathname))
#data[basename(pathname)] <- FUN(pathname)
x <- FUN(pathname)
#print(x)
#data[[basename(pathname)]] <- x
data[[filename]] <- x
}
}else{
cat(pathnames[1], "\n\n")
print(pathnames[2:length(pathnames)])
data <- FUN(pathnames[1])
for (pathname in pathnames[2:length(pathnames)]) {
x <- FUN(pathname)
data <- mapply(c, data, x, SIMPLIFY=FALSE)
}
}
#return( FUN(pathname) )
#optional interactive mode to interrupt processing before continuing to next file
#if (interact==TRUE){
#if (interactive()) {
#cat("Press ENTER to view data:")
#readline()
#}
#print(dat)
#}
return(data)
}
#x <- batchProcess2List(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18/20130518190800.mat")
#x <- batchProcess2List(readMat, "mat", path="/Users/claude/GIS/Pulmanki/River_Surveyor_raw_data/2013_kevat/2013_05_18")
#y <- x[[ 1 ]]
#length(x)
#names(x)[1]
#basename(names(x)[1])
readRivMat <- function(x){
riv <- readMat(x)
#extract structure names from Matlab format to use in R
names(riv$Setup) <- dimnames( riv$Setup)[[1]]
names(riv$Processing) <- dimnames( riv$Processing)[[1]]
# Mat file contains two $System structures
# Rename first one to Specs
names(riv)[3] <- "Specs"
names(riv$Specs) <- dimnames( riv$Specs)[[1]]
names(riv$Transformation.Matrices) <- dimnames( riv$Transformation.Matrices)[[1]]
names(riv$System) <- dimnames( riv$System)[[1]]
names(riv$Summary) <- dimnames( riv$Summary)[[1]]
names(riv$BottomTrack) <- dimnames( riv$BottomTrack)[[1]]
names(riv$GPS) <- dimnames( riv$GPS)[[1]]
names(riv$WaterTrack) <- dimnames( riv$WaterTrack)[[1]]
names(riv$Compas) <- dimnames( riv$Compas)[[1]]
names(riv$RawGPSData) <- dimnames( riv$RawGPSData)[[1]]
return(riv)
}
Try the RiverSurvey package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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