From 1a4b78fc11a04d2de0b735151cc4037306f8b612 Mon Sep 17 00:00:00 2001
From: Joerg Polzehl <polzehl@wias-berlin.de>
Date: Mon, 17 Oct 2022 10:40:23 -0500
Subject: [PATCH] new function setmask to include mask definition, e.g.
 generated by fsl_bet, in dtiData object

---
 DESCRIPTION            |  4 ++--
 NAMESPACE              |  2 +-
 R/io.r                 |  5 ++++-
 R/utilities.r          | 25 ++++++++++++++++++++++++-
 man/setmask-methods.Rd | 41 +++++++++++++++++++++++++++++++++++++++++
 5 files changed, 72 insertions(+), 5 deletions(-)
 create mode 100644 man/setmask-methods.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 298b264..0f2a8bb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dti
-Version: 1.5.2
-Date: 2020-05-19
+Version: 1.5.3
+Date: 2022-10-17
 Title: Analysis of Diffusion Weighted Imaging (DWI) Data
 Authors@R: c(person("Karsten", "Tabelow", role = c("aut", "cre"),
                     email = "karsten.tabelow@wias-berlin.de"),
diff --git a/NAMESPACE b/NAMESPACE
index 3b78fb3..e62f8c5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -31,7 +31,7 @@ exportMethods("show", "plot", "print", "summary", "dti.smooth", "dtiTensor",
               "dtiIndices", "dwiQball", "dwiMixtensor", "dwiMtCombine",
               "dwiRiceBias", "dkiTensor", "dkiIndices", "dwiMD")
 exportMethods("extract", "show3d", "tracking", "selectFibers", "reduceFibers",
-              "touchingFibers", "combineFibers", "getmask", "sdpar",
+              "touchingFibers", "combineFibers", "getmask", "setmask", "sdpar",
               "getsdofsb", "dwi.smooth", "dwi.smooth.ms")
 export(dtiData, readDWIdata, subsetg, combineDWIdata, awssigmc, awslsigmc, afsigmc,
        aflsigmc, dkiIndices, showFAColorScale, tensor2medinria, medinria2tensor)
diff --git a/R/io.r b/R/io.r
index 8283ca6..ac89c68 100644
--- a/R/io.r
+++ b/R/io.r
@@ -4,7 +4,10 @@
 #                                                              #
 ################################################################
 
-dtiData <- function(gradient,imagefile,ddim,bvalue=NULL,xind=NULL,yind=NULL,zind=NULL,level=0,mins0value=1,maxvalue=32000,voxelext=c(1,1,1),orientation=c(0L,2L,5L),rotation=diag(3)) {
+dtiData <- function(gradient,imagefile,ddim,bvalue=NULL,xind=NULL,
+                    yind=NULL,zind=NULL,level=0,mins0value=1,
+                    maxvalue=32000,voxelext=c(1,1,1),
+                    orientation=c(0L,2L,5L),rotation=diag(3)) {
   args <- list(sys.call())
   if (any(sort((orientation)%/%2) != 0:2)) stop("invalid orientation \n")
   if (dim(gradient)[2]==3) gradient <- t(gradient)
diff --git a/R/utilities.r b/R/utilities.r
index a639b74..6a4559c 100644
--- a/R/utilities.r
+++ b/R/utilities.r
@@ -1084,6 +1084,28 @@ setMethod("extract","dwiQball",function(x,
   invisible(z)
 })
 
+setmask <- function(object,  ...) cat("No method defined for class:",class(object),"\n")
+
+setGeneric("setmask", function(object,  ...) standardGeneric("getmask"))
+
+setMethod("setmask","dtiData",function(object, maskfile){
+  ddim <- object@ddim0
+  xind <- object@xind
+  yind <- object@yind
+  zind <- object@zind
+  mask <- oro.nifti::readNIfTI(maskfile, reorient = FALSE)
+  dmask <- mask@dim_
+  if(all(ddim == dmask)){
+    object@mask <- mask[xind,yind,zind] > 0
+  } else if(all(dmask == object@ddim)){
+    object@mask <- mask > 0
+  } else {
+    stop("Incorrect dimensions of mask file")
+  }
+  object
+}
+)
+
 getmask <- function(object,  ...) cat("No method defined for class:",class(object),"\n")
 
 setGeneric("getmask", function(object,  ...) standardGeneric("getmask"))
@@ -1110,6 +1132,7 @@ setMethod("getmask","dtiData",function(object, level=NULL, prop=.4, size=3){
   z
 }
 )
+
 setMethod("getmask","array",function(object, level=NULL, prop=.4, size=3){
   if(length(dim(object))!=3){
     level <- NULL
@@ -1144,7 +1167,7 @@ selectCube <- function(xind,yind,zind,ddim,maxobj){
   n1 <- length(xind)
   n2 <- length(yind)
   n3 <- length(zind)
-  if(any(c(xind[1],yind[1],zind[1]) < 1 || any(c(xind[n1]-ddim[1],yind[n2]-ddim[2],zind[n3]-ddim[3])>0))){
+  if(any(c(xind[1],yind[1],zind[1]) < 1) || any(c(xind[n1]-ddim[1],yind[n2]-ddim[2],zind[n3]-ddim[3])>0)){
     stop("Error in index specification, specified cube exceeds dimensions of object")
   }
   l1 <- (xind[n1]-xind[1]+1-n1) == 0
diff --git a/man/setmask-methods.Rd b/man/setmask-methods.Rd
new file mode 100644
index 0000000..64631eb
--- /dev/null
+++ b/man/setmask-methods.Rd
@@ -0,0 +1,41 @@
+%- Also NEED an '\alias' for EACH other topic documented here.
+\name{setmask-methods}
+\docType{methods}
+\alias{setmask}
+\alias{setmask-methods}
+\alias{setmask,ANY-method}
+\alias{setmask,dtiData-method}
+\title{ Methods for Function `setmask' in Package `dti' }
+\description{
+   Read mask definition from NIfTI file and include it in dtiData object
+}
+\usage{
+\S4method{setmask}{dtiData}(object, maskfile)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{object}{an object of class \code{"dtiData"}}
+  \item{maskfile}{NIfTI file containing mask definition. Dimension need to be 
+  compatible, i.e. either equal \code{object@ddim0} or \code{object@ddim}}
+}
+\section{Methods}{
+\describe{
+
+  \item{obj = "ANY"}{ Returns a warning }
+
+  \item{obj = "dtiData"}{Set mask definition in dtiObject using information provided as NIfTI file as e.g. provided by \code{fsl_bet}. }
+
+}
+}
+\value{
+  The function returns an object of class \code{dtiData}.
+}
+\author{ 
+  Karsten Tabelow \email{tabelow@wias-berlin.de}\cr 
+  J\"org Polzehl \email{polzehl@wias-berlin.de}
+}
+\seealso{ 
+  \code{\link{dtiData}},
+  \code{\link{readDWIdata}},
+}
+\keyword{ methods }