GetClusteringResults: Get clustering step result

Description

GetClusteringResults returns the results of the clustering procedure RunClustering

Usage

GetClusteringResults(data.array, res.listdenois, res.cluster)

Arguments

data.array

a (2D or 3D)+T array containing the original dynamic sequence of images (the dataset). The last dimension is the time.

res.listdenois

the list resulting from the RunDenoising procedure applied to data.array. This parameter may be replaced by the component info.den of the former.

res.cluster

the list resulting from a call to RunClustering

Value

a list containing two components clust.array and clust.map. clust.array is an array with same dimension as the original sequence data.array containing the clustered version. clust.map is an array with only spatial dimensions of data.array whose elements provide the cluster number at each location.

References

Rozenholc, Y. and Reiss, M. (2012) Preserving time structures while denoising a dynamical image, Mathematical Methods for Signal and Image Analysis and Representation (Chapter 12), Florack, L. and Duits, R. and Jongbloed, G. and van~Lieshout, M.-C. and Davies, L. Ed., Springer-Verlag, Berlin

Lieury, T. and Pouzat, C. and Rozenholc, Y. (submitted) Spatial denoising and clustering of dynamical image sequence: application to DCE imaging in medicine and calcium imaging in neurons

Examples

Run this code

# NOT RUN {
# }
# NOT RUN {
    library(DynClust)
    
    ## use fluorescence calcium imaging of neurons performed with Fura 2 excited at 340 nm
    data('adu340_4small',package='DynClust')
    
    ## Gain of the CCD camera:
    G <- 0.146
    ## readout variance of the CCD camera:
    sro2 <- (16.4)^2
    ## Stabilization of the variance to get a normalized dataset (variance=1)
    FT <- 2*sqrt(adu340_4small/G + sro2)
    FT.range = range(FT)
    
    ## launches the denoising step on the dataset with a statistical level of 5%
    FT.den.tmp <- RunDenoising(FT,1,mask.size=NA,nproc=2)
    
    ## launches the clustering step on the dataset with a statistical level of 5%
    FT.clust.tmp  <- RunClustering(FT,FT.den.tmp,nproc=2)
    n.cluster <- length(FT.clust.tmp$clusters)
    print(paste(n.cluster,'clusters using variance set to',sqrt(FT.den.tmp$var),'^2'))
    
    ## get the classified version of the data array and the map of the clusters
    FT.clust.res <- GetClusteringResults(FT,FT.den.tmp,FT.clust.tmp)
    
    ## plotting results of the clusterization
    par(mfrow=c(2,2))
    image(FT.clust.res$clust.map,col=rainbow(n.cluster))
    title('Cluster map')
    matplot(FT.clust.res$clust.center,col=rainbow(n.cluster),type="l",lwd=0.1,lty=1)
    title('Cluster centers')

    ## and more: original and clustered slices at time 50
    image(FT[,,50],zlim=FT.range,col=grey(seq(0,1,length=n.cluster)))
    title('Original sequence at time 50')
    image(FT.clust.res$clust.array[,,50],zlim=FT.range,col=grey(seq(0,1,length=n.cluster)))
    title('Clustered sequence at time 50')

    ####################################################################################
    ## reapply clustering with twice the nominal variance: forces stronger clustering ##
    ####################################################################################

    ## launches the denoising step on the dataset with a statistical level of 5%
    FT.den.tmp <- RunDenoising(FT,2,mask.size=NA,nproc=2)

    ## launches the clustering step on the dataset with a statistical level of 5%
    FT.clust.tmp  <- RunClustering(FT,FT.den.tmp,nproc=2)
    n.cluster <- length(FT.clust.tmp$clusters)
    print(paste(n.cluster,'clusters using twice the nominal variance'))
    
    ## get the classified version of the data array and the map of the clusters
    FT.clust.res <- GetClusteringResults(FT,FT.den.tmp,FT.clust.tmp)
    
    ## plotting results of the clusterization
    par(mfrow=c(2,2))
    image(FT.clust.res$clust.map,col=rainbow(n.cluster))
    title('Cluster map')
    matplot(FT.clust.res$clust.center,col=rainbow(n.cluster),type="l",lwd=0.1,lty=1)
    title('Cluster centers')

    ## and more: original and clustered slices at time 50
    image(FT[,,50],zlim=FT.range,col=grey(seq(0,1,length=n.cluster)))
    title('Original sequence at time 50')
    image(FT.clust.res$clust.array[,,50],zlim=FT.range,col=grey(seq(0,1,length=n.cluster)))
    title('Clustered sequence at time 50')
# }