timeserieswindow2matrix: Time-series image to matrix of time windows around...

In neuroconductor-devel/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Description

Extract a matrix from a time-series image after applying a mask where each row is a space-time vector

Usage

timeserieswindow2matrix(
  timeseriesmatrix,
  mask,
  eventlist,
  timewindow,
  zeropadvalue = 0,
  spacing = NA
)

Arguments

timeseriesmatrix	Input timeseriesmatrix from timeseries2matrix
mask	Input mask of type 'antsImage' ... the mask will be replicated into a 4D image of length timewindow + zeropadvalue.
eventlist	time indices for the events to extract
timewindow	n-timepoints around each event, forward in time.
zeropadvalue	pads the mask by this amount fwd and bwd in time.
spacing	optional 4d spacing vector that will impact smoothing parameters

Value

Success – an R matrix of dimensions ntimewindow*sizeofnonzerovaluesinmask*nevents

Author(s)

Avants BB

Examples

img <- makeImage( c(10,10,10,50) , 0 )
mask <- as.antsImage( array( 1 , dim(img)[1:3] ) )
mat<-timeseries2matrix( img, mask )
mat <- timeserieswindow2matrix( mat , mask, c(1, 4, 5 ), 2, 0 )
print( dim(mat$eventmatrix) )
print( dim(mat$mask4d) )

##### another approach
dim4<-c( 20, 30, 10, 100 )
i1<-10:15
i2<-11:18
i3<-4:8
i4<-10:90
arr3d<-array(data = 0, dim = dim4[1:3] )
arr3d[i1,i2,i3]<-1
arr<-array(data = 0, dim =dim4 )
for ( t in i4 ) arr[,,,t]<-t
nois<-which( arr > 0 )
noisv<-rnorm( length(nois) )
arr[ nois ]<-arr[ nois ]+noisv*0.0
msk <- as.antsImage( arr3d )
img <- as.antsImage( arr )
mat<-timeseries2matrix( img, msk )
eanat<-sparseDecom(  mat, msk, sparseness=0.1, z=0.5,nvecs=2, its=5,cthresh=0, mycoption=1)
eanat2<-sparseDecom( mat,  sparseness=0.1,z=0.5,nvecs=2, its=5,cthresh=0, mycoption=1)
enomask<-eanat2$eigenanatomyimages[1,]
emask<-eanat$eigenanatomyimages[1,]
print( enomask[31:40] )
print(   emask[31:40] )

# same thing with event matrices ....
ttt<-timeserieswindow2matrix( mat, msk, c(20,40,60,70) , 6, 0 )
tte<-ttt$eventmatrix
eanat<-sparseDecom(  tte, ttt$mask4d, sparseness=-0.9, z=0.5,nvecs=2, its=5,cthresh=0, mycoption=1)
eanat2<-sparseDecom( tte,  sparseness=-0.9, z=0.5,nvecs=2, its=5,cthresh=0, mycoption=1)
enomask<-eanat2$eigenanatomyimages[,1]
# back to timematrix
tmat<-matrix( enomask,  nrow=6 )
# back to image
eimg<-antsImageClone( msk )
eimg[ msk == 1 ]<-tmat[1,]
# convert image space to evec space
emat<-eanat2$eigenanatomyimages
# convert emat to events FIXME this does not currently work
# eavent<-timeserieswindow2matrix( data.matrix(emat) , msk, 1 , 6, 0 )
# emask<-eavent$eventmatrix[1,]
#############################

neuroconductor-devel/ANTsR documentation built on April 1, 2021, 1:02 p.m.