[R] Creating Movies with R

Sat Sep 23 18:05:49 CEST 2006

On 9/22/06, Gabor Grothendieck <ggrothendieck at gmail.com> wrote:
> See the flag= argument on formatC:
>
> n <- 10
> formatC(1:n, dig = nchar(n)-1, flag = 0)
>
> # Here is another way:
>
> n <- 10
> sprintf(paste("%0", nchar(n), ".0f", sep = ""), 1:n)

sprintf("%0*.0f", nchar(n), 1:n)

or even

sprintf("%0*d", nchar(n), 1:n)

/H

>
> On 9/22/06, J.R. Lockwood <lockwood at rand.org> wrote:
> > An alternative that I've used a few times is the jpg() function to
> > create the sequence of images, and then converting these to an mpeg
> > movie using "mencoder" distributed with "mplayer".  This works on both
> > windows and linux.  I have a pretty self-contained example file
> > written up that I can send to anyone who is interested.  Oddly, the
> > most challenging part was creating a sequence of file names that would
> > be correctly ordered - for this I use:
> >
> > lex <- function(N){
> >  ## produce vector of N lexicograpically ordered strings
> >  ndig <- nchar(N)
> >  substr(formatC((1:N)/10^ndig,digits=ndig,format="f"),3,10000000)
> > }
> >
> >
> > On Fri, 22 Sep 2006, Jeffrey Horner wrote:
> >
> > > Date: Fri, 22 Sep 2006 13:46:52 -0500
> > > From: Jeffrey Horner <jeff.horner at vanderbilt.edu>
> > > To: Lorenzo Isella <lorenzo.isella at gmail.com>, r-help at stat.math.ethz.ch
> > > Subject: Re: [R] Creating Movies with R
> > >
> > > If you run R on Linux, then you can run the ImageMagick command called
> > > convert. I place this in an R function to use a sequence of PNG plots as
> > > movie frames:
> > >
> > > make.mov.plotcol3d <- function(){
> > >      unlink("plotcol3d.mpg")
> > >      system("convert -delay 10 plotcol3d*.png plotcol3d.mpg")
> > > }
> > >
> > > Examples can be seen here:
> > >
> > > http://biostat.mc.vanderbilt.edu/JrhRgbColorSpace
> > >
> > > Look for the 'Download Movie' links.
> > >
> > > Cheers,
> > >
> > > Jeff
> > >
> > > Lorenzo Isella wrote:
> > > > Dear All,
> > > >
> > > > I'd like to know if it is possible to create animations with R.
> > > > To be specific, I attach a code I am using for my research to plot
> > > > some analytical results in 3D using the lattice package. It is not
> > > > necessary to go through the code.
> > > > Simply, it plots some 3D density profiles at two different times
> > > > selected by the user.
> > > > I wonder if it is possible to use the data generated for different
> > > > times to create something like an .avi file.
> > > >
> > > > Here is the script:
> > > >
> > > > rm(list=ls())
> > > > library(lattice)
> > > >
> > > > # I start defining the analytical functions needed to get the density
> > > > as a function of time
> > > >
> > > > expect_position <- function(t,lam1,lam2,pos_ini,vel_ini)
> > > > {1/(lam1-lam2)*(lam1*exp(lam2*t)-lam2*exp(lam1*t))*pos_ini+
> > > > 1/(lam1-lam2)*(exp(lam1*t)-exp(lam2*t))*vel_ini
> > > > }
> > > >
> > > > sigma_pos<-function(t,q,lam1,lam2)
> > > > {
> > > > q/(lam1-lam2)^2*(
> > > > (exp(2*lam1*t)-1)/(2*lam1)-2/(lam1+lam2)*(exp(lam1*t+lam2*t)-1) +
> > > > (exp(2*lam2*t)-1)/(2*lam2) )
> > > > }
> > > >
> > > > rho_x<-function(x,expect_position,sigma_pos)
> > > > {
> > > > 1/sqrt(2*pi*sigma_pos)*exp(-1/2*(x-expect_position)^2/sigma_pos)
> > > > }
> > > >
> > > > #### Now the physical parameters
> > > > tau<-0.1
> > > > beta<-1/tau
> > > > St<-tau ### since I am in dimensionless units and tau is already in
> > > > units of 1/|alpha|
> > > > D=2e-2
> > > > q<-2*beta^2*D
> > > > ############### Now the grid in space and time
> > > > time<-5  # time extent
> > > > tsteps<-501 # time steps
> > > > newtime<-seq(0,time,len=tsteps)
> > > > #### Now the things specific for the dynamics along x
> > > > lam1<- -beta/2*(1+sqrt(1+4*St))
> > > > lam2<- -beta/2*(1-sqrt(1+4*St))
> > > > xmin<- -0.5
> > > > xmax<-0.5
> > > > x0<-0.1
> > > > vx0<-x0
> > > > nx<-101 ## grid intervals along x
> > > > newx<-seq(xmin,xmax,len=nx) # grid along x
> > > >
> > > > # M1 <- do.call("g", c(list(x = newx), mypar))
> > > >
> > > >
> > > > mypar<-c(q,lam1,lam2)
> > > > sig_xx<-do.call("sigma_pos",c(list(t=newtime),mypar))
> > > > mypar<-c(lam1,lam2,x0,vx0)
> > > > exp_x<-do.call("expect_position",c(list(t=newtime),mypar))
> > > >
> > > > #rho_x<-function(x,expect_position,sigma_pos)
> > > >
> > > > #NB: at t=0, the density blows up, since I have a delta as the initial state!
> > > > # At any t>0, instead, the result is finite.
> > > > #for this reason I now redefine time by getting rid of the istant t=0
> > > > to work out
> > > > # the density
> > > >
> > > >
> > > > rho_x_t<-matrix(ncol=nx,nrow=tsteps-1)
> > > > for (i in 2:tsteps)
> > > > {mypar<-c(exp_x[i],sig_xx[i])
> > > > myrho_x<-do.call("rho_x",c(list(x=newx),mypar))
> > > > rho_x_t[ i-1, ]<-myrho_x
> > > > }
> > > >
> > > > ### Now I also define a scaled density
> > > >
> > > > rho_x_t_scaled<-matrix(ncol=nx,nrow=tsteps-1)
> > > > for (i in 2:tsteps)
> > > > {mypar<-c(exp_x[i],sig_xx[i])
> > > > myrho_x<-do.call("rho_x",c(list(x=newx),mypar))
> > > > rho_x_t_scaled[ i-1, ]<-myrho_x/max(myrho_x)
> > > > }
> > > >
> > > > ###########Now I deal with the dynamics along y
> > > >
> > > > lam1<- -beta/2*(1+sqrt(1-4*St))
> > > > lam2<- -beta/2*(1-sqrt(1-4*St))
> > > > ymin<- 0
> > > > ymax<- 1
> > > > y0<-ymax
> > > > vy0<- -y0
> > > >
> > > > mypar<-c(q,lam1,lam2)
> > > > sig_yy<-do.call("sigma_pos",c(list(t=newtime),mypar))
> > > > mypar<-c(lam1,lam2,y0,vy0)
> > > > exp_y<-do.call("expect_position",c(list(t=newtime),mypar))
> > > >
> > > >
> > > > # now I introduce the function giving the density along y: this has to
> > > > include the BC of zero
> > > > # density at wall
> > > >
> > > > rho_y<-function(y,expect_position,sigma_pos)
> > > > {
> > > > 1/sqrt(2*pi*sigma_pos)*exp(-1/2*(y-expect_position)^2/sigma_pos)-
> > > > 1/sqrt(2*pi*sigma_pos)*exp(-1/2*(y+expect_position)^2/sigma_pos)
> > > > }
> > > >
> > > > newy<-seq(ymin,ymax,len=nx) # grid along y with the same # of points
> > > > as the one along x
> > > >
> > > >
> > > > rho_y_t<-matrix(ncol=nx,nrow=tsteps-1)
> > > > for (i in 2:tsteps)
> > > > {mypar<-c(exp_y[i],sig_yy[i])
> > > > myrho_y<-do.call("rho_y",c(list(y=newy),mypar))
> > > > rho_y_t[ i-1, ]<-myrho_y
> > > > }
> > > >
> > > > rho_y_t_scaled<-matrix(ncol=nx,nrow=tsteps-1)
> > > > for (i in 2:tsteps)
> > > > {mypar<-c(exp_y[i],sig_yy[i])
> > > > myrho_y<-do.call("rho_y",c(list(y=newy),mypar))
> > > > rho_y_t_scaled[ i-1, ]<-myrho_y/max(myrho_y)
> > > > }
> > > >
> > > >
> > > > # The following 2 plots are an example of the plots I'd like to use to
> > > > make an animation
> > > >
> > > >
> > > > g <- expand.grid(x = newx, y = newy)
> > > >
> > > > instant<-100
> > > > mydens<-rho_x_t[ instant, ]%o%rho_y_t[ instant, ]/(max(rho_x_t[
> > > > instant, ]%o%rho_y_t[ instant, ]))
> > > >
> > > >
> > > > lentot<-nx^2
> > > > dim(mydens)<-c(lentot,1)
> > > >
> > > > g$z<-mydens
> > > > jpeg("dens-t-3.jpeg")
> > > > print(wireframe(z ~ x * y, g, drape = TRUE,shade=TRUE,
> > > > scales = list(arrows = FALSE),pretty=FALSE, aspect = c(1,1), colorkey = TRUE
> > > > ,zoom=0.8, main=expression("Density at t=2"), zlab =
> > > > list(expression("density"),rot = 90),distance=0.0,
> > > > perspective=TRUE,#screen = list(z = 150, x = -55,y= 0)
> > > > ,zlim=range(c(0,1))))
> > > > dev.off()
> > > >
> > > >
> > > > instant<-300
> > > > mydens<-rho_x_t[ instant, ]%o%rho_y_t[ instant, ]/(max(rho_x_t[
> > > > instant, ]%o%rho_y_t[ instant, ]))
> > > >
> > > >
> > > > lentot<-nx^2
> > > > dim(mydens)<-c(lentot,1)
> > > >
> > > > g$z<-mydens
> > > > jpeg("dens-t-3.jpeg")
> > > > print(wireframe(z ~ x * y, g, drape = TRUE,shade=TRUE,
> > > > scales = list(arrows = FALSE),pretty=FALSE, aspect = c(1,1), colorkey = TRUE
> > > > ,zoom=0.8, main=expression("Density at t=3"), zlab =
> > > > list(expression("density"),rot = 90),distance=0.0,
> > > > perspective=TRUE,#screen = list(z = 150, x = -55,y= 0)
> > > > ,zlim=range(c(0,1))))
> > > > dev.off()
> > > >
> > > >
> > > >
> > > >
> > > > Kind Regards
> > > >
> > > > Lorenzo
> > > >
> > > > ______________________________________________
> > > > R-help at stat.math.ethz.ch mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > > > and provide commented, minimal, self-contained, reproducible code.
> > >
> > >
> > > --
> > > http://biostat.mc.vanderbilt.edu/JeffreyHorner
> > >
> > > ______________________________________________
> > > R-help at stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> >
> > J.R. Lockwood
> > 412-683-2300 x4941
> > lockwood at rand.org
> > http://www.rand.org/statistics/bios/
> >
> > --------------------
> >
> > This email message is for the sole use of the intended recip...{{dropped}}
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>