Fixed NAMESPACE Bug on fieldRotate() and documentation improvements.

.Rbuildignore

@@ -0,0 +1,4 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^Dockerfile$
+^\.dockerignore$

.dockerignore

@@ -0,0 +1,7 @@
+.RData
+.Rhistory
+.git
+.gitignore
+manifest.json
+rsconnect/
+Rproj.user

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -1,15 +1,45 @@
 Package: FIELDimageR
-Type: Package
-Title: FIELDimageR: A R Package to Analyze Orthomosaic Images from Agricultural Field Trials
-Version: 0.2.9
-Author: Filipe Inacio Matias
-Maintainer: Filipe Inacio Matias <fmatias@wisc.edu>
-Description: This package is a compilation of function to analyze pos-mosaicking images from research experimental fields, and allows to: reduce the mosaic dimension by cropping it in small sections; remove the soil effect; build vegetation indices; rotate the field and build the plot shape file; extract information for each plot; and evaluate stand count, plant height and canopy (greenness).
-License: GPL-2
-Imports: sp, raster, plyr, EBImage, doParallel, foreach, parallel, maptools
-Sugested:rgdal, rgeos, igraph
+Title: A Tool to Analyze Orthomosaic Images From Agricultural Field Trials
+Version: 0.1.0
+Authors@R: 
+    c(person(given = "Filipe",
+             family = "Matias",
+             role = c("cre", "aut"),
+             email = "filipematias23@gmail.com"))
+Description: A compilation of functions to analyze orthomosaic images 
+  from research fields. To prepare the image it first allows to crop the image, remove soil 
+  and weeds and rotate the image. The package also builds a plot shapefile in order to extract 
+  information for each plot to evaluate different wavelengths, vegetation indices, stand count, 
+  canopy percentage, and plant height.
+License: GPL-3 + file LICENSE
+biocViews:
+Imports: 
+    EBImage,
+    attempt,
+    config (>= 0.3.1),
+    DT,
+    fftwtools,
+    git2r,
+    glue,
+    maptools,
+    methods,
+    raster,
+    rgdal,
+    scales,
+    sp,
+    xml2,
+    foreach,
+    doParallel,
+    plyr,
+    processx,
+    grDevices
 Encoding: UTF-8
 LazyData: true
-URL: https://github.com/OpenDroneMap/FIELDimageR
-RoxygenNote: 6.1.1
-biocViews: EBImage
+RoxygenNote: 7.1.1
+Author: Filipe Matias [cre, aut]
+Maintainer: Filipe Matias <filipematias23@gmail.com>
+Suggests: 
+    spelling,
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+Language: en-US

FIELDimageR.Rproj

@@ -0,0 +1,19 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

NAMESPACE

@@ -1,12 +1,68 @@
-export(fieldRotate,fieldCrop,fieldShape,fieldPolygon,fieldObject,fieldIndex,fieldMask,fieldMap,fieldInfo,fieldPlot,fieldCount,fieldArea,fieldDraw)
-importFrom("sp", "Polygons","Polygon","SpatialPolygonsDataFrame","SpatialPolygons","spsample","SpatialPointsDataFrame","over", "proj4string")
-importFrom("raster", "stack", "projection","plotRGB","res","projectRaster","crs","extent","atan2","crop","rasterToPolygons","mask","extract","clump","drawLine","drawPoly","xyFromCell")
-importFrom("maptools", "elide")
-importFrom("parallel", "makeCluster", "detectCores")
-importFrom("foreach", "foreach", "%dopar%")
-importFrom("doParallel", "registerDoParallel")
-importFrom("graphics", "abline", "axis", "lines", "par", "plot","points","locator","legend")
-importFrom("utils", "read.csv")
-importFrom("grDevices", "rgb", "col2rgb")
-importFrom("plyr", "join")
-importFrom("EBImage","watershed","distmap")
+# Generated by roxygen2: do not edit by hand
+
+export(fieldArea)
+export(fieldCount)
+export(fieldCrop)
+export(fieldDraw)
+export(fieldIndex)
+export(fieldInfo)
+export(fieldMap)
+export(fieldMask)
+export(fieldObject)
+export(fieldPlot)
+export(fieldPolygon)
+export(fieldRotate)
+export(fieldShape)
+importFrom(EBImage,distmap)
+importFrom(EBImage,watershed)
+importFrom(doParallel,registerDoParallel)
+importFrom(foreach,"%dopar%")
+importFrom(foreach,foreach)
+importFrom(grDevices,col2rgb)
+importFrom(grDevices,colorRamp)
+importFrom(grDevices,grey)
+importFrom(grDevices,rgb)
+importFrom(graphics,abline)
+importFrom(graphics,axis)
+importFrom(graphics,legend)
+importFrom(graphics,lines)
+importFrom(graphics,locator)
+importFrom(graphics,par)
+importFrom(graphics,plot)
+importFrom(graphics,points)
+importFrom(maptools,elide)
+importFrom(methods,as)
+importFrom(methods,slot)
+importFrom(parallel,detectCores)
+importFrom(raster,as.data.frame)
+importFrom(raster,as.list)
+importFrom(raster,as.matrix)
+importFrom(raster,atan2)
+importFrom(raster,clump)
+importFrom(raster,crop)
+importFrom(raster,crs)
+importFrom(raster,drawLine)
+importFrom(raster,drawPoly)
+importFrom(raster,extent)
+importFrom(raster,extract)
+importFrom(raster,mask)
+importFrom(raster,plotRGB)
+importFrom(raster,projectRaster)
+importFrom(raster,projection)
+importFrom(raster,raster)
+importFrom(raster,rasterToPolygons)
+importFrom(raster,res)
+importFrom(raster,stack)
+importFrom(raster,values)
+importFrom(raster,xyFromCell)
+importFrom(sp,Polygon)
+importFrom(sp,Polygons)
+importFrom(sp,SpatialPointsDataFrame)
+importFrom(sp,SpatialPolygons)
+importFrom(sp,SpatialPolygonsDataFrame)
+importFrom(sp,bbox)
+importFrom(sp,over)
+importFrom(sp,proj4string)
+importFrom(sp,spsample)
+importFrom(stats,dist)
+importFrom(utils,read.csv)

R/fieldArea.R → R/fct_fieldArea.R

@@ -1,4 +1,35 @@
-fieldArea<-function(mosaic, areaValue=0, fieldShape=NULL, n.core=NULL, plot=T, na.rm=FALSE){
+#' fieldArea
+#' 
+#' @title Percentage of object area 
+#' 
+#' @description It calculates the percentage of object area in the entire mosaic or per plot using the fieldShape file.
+#' 
+#' @param mosaic object mask of class stack from the function \code{\link{fieldMask}}.
+#' @param areaValue referent value of object area in the image.
+#' @param fieldShape evaluate the object area percentage per plot using the fieldShape as reference. If fieldShape=NULL, 
+#'  the object area percentage will be calculated directly for the entire original image.
+#' @param n.core number of cores to use for multicore processing (Parallel).
+#' @param plot if is TRUE the crop image and fieldShape will be plotted.
+#' @param na.rm logical. Should missing values (including NaN) be used?. 
+#' 
+#' @importFrom raster stack extract crop
+#' @importFrom parallel detectCores
+#' @importFrom graphics par 
+#' @importFrom foreach %dopar% foreach
+#' @importFrom doParallel registerDoParallel
+#' @importFrom grDevices grey
+#'
+#' 
+#'
+#' @return A list with two element
+#' \itemize{
+#'   \item \code{areaPorcent} is the percentage of object area per plot represented in \code{DataFrame}.
+#'   \item \code{fieldShape} is the new \code{fieldShape} format \code{SpatialPolygonsDataFrame}.
+#' }
+#' 
+#'
+#' @export
+fieldArea <- function(mosaic, areaValue = 0, fieldShape = NULL, n.core = NULL, plot = TRUE, na.rm = FALSE) {
   mosaic <- stack(mosaic)
   num.band<-length(mosaic@layers)
   print(paste(num.band," layer available", sep = ""))
@@ -28,7 +59,8 @@ fieldArea<-function(mosaic, areaValue=0, fieldShape=NULL, n.core=NULL, plot=T, n
       if(n.core>detectCores()){stop(paste(" 'n.core' must be less than ",detectCores(),sep = ""))}
       cl <- parallel::makeCluster(n.core, output = "", setup_strategy = "sequential")
       registerDoParallel(cl)
-      extM <- foreach(i = 1:length(fieldShape), .packages = c("raster")) %dopar% 
+      i = 1:length(fieldShape)
+      extM <- foreach(i, .packages = c("raster")) %dopar% 
         {
           single <- fieldShape[i, ]
           CropPlot <- crop(x = mosaic, y = single)

R/fieldCount.R → R/fct_fieldCount.R

@@ -1,4 +1,37 @@
-fieldCount<-function(mosaic, fieldShape, value=0, minSize=0.01, n.core=NULL, pch=16, cex=0.7, col="red", na.rm=FALSE){
+#' fieldCount 
+#' 
+#' @title Calculating number of objects per plot
+#' 
+#' @description The mask from function \code{\link{fieldMask}} is used to identify the number of objects per plot..
+#' 
+#' @param mosaic object mask of class stack from the function \code{\link{fieldMask}}.
+#' @param fieldShape plot shape file.
+#' @param value referent value to vegetation pixels in the mask. If "HUE" was used on 
+#'   \code{\link{fieldMask}} the value=0.
+#' @param minSize used to set the minimum size percentage of plant canopy  (to remove weeds and more).
+#' @param n.core number of cores to use for multicore processing (Parallel). 
+#' @param pch point symbol, please check \code{help("points")}.
+#' @param cex character (or symbol) expansion: a numerical vector, please check \code{help("points")}.
+#' @param col color code or name, please check \code{help("points")}.
+#' @param na.rm logical. Should missing values (including NaN) be removed?.
+#' 
+#' @importFrom raster projection extract xyFromCell
+#' @importFrom EBImage distmap watershed
+#'
+#' 
+#' @return A list with five element
+#' \itemize{
+#'   \item \code{fieldCount} is the number of objects per plot represented in DataFrame.
+#'   \item \code{fieldShape} is the new shapeFile with stand count.
+#'   \item \code{mosaic} is the Watershed layer.
+#'   \item \code{objectSel} is the objects area per plot.
+#'   \item \code{objectReject} is the objects position in the image.
+#' }
+#' 
+#'
+#' @export
+fieldCount <- function(mosaic, fieldShape, value = 0, minSize = 0.01, n.core = NULL, pch = 16, 
+                       cex = 0.7, col = "red", na.rm = FALSE) {
   if(!is.na(projection(fieldShape))&is.na(projection(mosaic))){
     if(projection(fieldShape)!=projection(mosaic)){stop("fieldShape and mosaic must have the same projection CRS, strongly suggested to use fieldRotate() for both files.")}}
   mosaic <- stack(mosaic)
@@ -81,6 +114,10 @@ fieldCount<-function(mosaic, fieldShape, value=0, minSize=0.01, n.core=NULL, pch
   print(paste("Number of objects: ", sum(field), sep = ""))
   graphics::points(do.call(rbind,objectSel)[,c(2,3)], pch=pch, cex=cex, col=col)
   sp::plot(fieldShape, add=T)
-  Out <- list(fieldCount=field, fieldShape=fieldShape, mosaic=mosaic$watershed, objectSel=objectSel, objectReject=objectReject)
+  Out <- list(fieldCount=field, 
+              fieldShape=fieldShape, 
+              mosaic=mosaic$watershed, 
+              objectSel=objectSel, 
+              objectReject=objectReject)
   return(Out)
 }

R/fct_fieldCrop.R

@@ -0,0 +1,74 @@
+#' fieldCrop 
+#' 
+#' @title Selecting experimental field from original image
+#' 
+#' @description It calculates the percentage of object area in the entire mosaic or per plot using the fieldShape file.
+#' 
+#' @param mosaic object mask of class stack from the function \code{\link{fieldMask}}.
+#' @param fieldShape crop the image using the fieldShape as reference. If fieldShape=NULL, four points should be selected 
+#'  directly on the original image to determine the experimental field.
+#' @param nPoint number of points necessary to select field boundaries or area to remove (4 >= nPoint <= 50).
+#' @param remove if TRUE the selected area will be removed from the image.
+#' @param plot if \code{TRUE} (by default) plots the original and cropped image.
+#' @param type character indicating the type of plotting, please check help("lines").
+#' @param lty line types, please check help("lines").
+#' @param lwd line width, please check help("lines").
+#' @param fast.plot  if TRUE only the grey scale image will be plotted as reference (faster approach).
+#'  if TRUE only the grey scale image will be plotted as reference (faster approach).
+#' 
+#' @importFrom raster plotRGB mask
+#' @importFrom graphics locator lines 
+#' @importFrom sp Polygons Polygon SpatialPolygonsDataFrame SpatialPolygons
+#'
+#' 
+#' @return A image format stack.
+#' 
+#' @export
+fieldCrop <- function(mosaic, fieldShape = NULL, nPoint = 4, plot = TRUE, remove = FALSE, type = "l", 
+                      lty = 2, lwd = 3, fast.plot = FALSE) {
+  mosaic <- stack(mosaic)
+  num.band <- length(mosaic@layers)
+  print(paste(num.band," layers available", sep = ""))
+  if(nPoint<4|nPoint>50){stop("nPoint must be >= 4 and <= 50")}
+  par(mfrow=c(1,2))
+  if(is.null(fieldShape)|plot){
+    if(fast.plot){
+      raster::plot(mosaic[[1]], col=grey(1:100/100), axes=FALSE, box=FALSE, legend=FALSE)}
+    if(!fast.plot){
+      if(num.band>2){plotRGB(RGB.rescale(mosaic,num.band=3), r = 1, g = 2, b = 3)}
+      if(num.band<3){raster::plot(mosaic, axes=FALSE, box=FALSE)}}
+  }
+  if(!is.null(fieldShape)){
+    if(raster::projection(fieldShape) != raster::projection(mosaic)){
+      stop("fieldShape and mosaic must have the same raster::projection CRS. Use fieldRotate() for both files.")
+      }
+    r <- crop(x = mosaic, y = fieldShape)
+  }
+  c1 <- NULL
+  if(is.null(fieldShape)) {
+    print(paste("Select ",nPoint," points at the corners of field of interest in the plots space.",sep = ""))
+    for(i in 1:nPoint){
+      c1.1<-locator(type="p",n = 1, col="red",pch=19)
+      c1<-rbind(c1,c(c1.1$x,c1.1$y))
+    }
+    c1<-rbind(c1,c1[1,])
+    colnames(c1)<-c("x","y")
+    lines(c1, col= "red", type=type, lty=lty, lwd=lwd)
+  }
+  if(!is.null(c1)) {
+    p1 <- Polygons(list(Polygon(c1)), "x")
+    f1 <- SpatialPolygonsDataFrame( SpatialPolygons(list(p1)), data.frame( z=1, row.names=c("x") ) )
+    raster::projection(f1) <- raster::projection(mosaic)
+    if(!remove){r <- crop(x = mosaic, y = f1)}
+    if(remove){r <- mask(x = mosaic, mask = f1, inverse = remove)}
+  }
+  r <- stack(r)
+  if(plot){
+    if(fast.plot) {
+      raster::plot(r[[1]], col=grey(1:100/100), axes=FALSE, box=FALSE, legend=FALSE)}
+    if(!fast.plot){
+      if(num.band>2){plotRGB(RGB.rescale(r,num.band=3), r = 1, g = 2, b = 3)}
+      if(num.band<3){raster::plot(r, axes=FALSE, box=FALSE)}}}
+  par(mfrow=c(1,1))
+  return(r)
+}