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## ---- eval=FALSE---------------------------------------------------------
# library(devtools)
# install_github('asgr/ProFound')
# install_github('ICRAR/ProFit')
## ------------------------------------------------------------------------
evalglobal=FALSE
## ------------------------------------------------------------------------
library(ProFound)
## ---- eval=evalglobal----------------------------------------------------
# library(ProFit)
# library(LaplacesDemon)
## ---- eval=TRUE, fig.width=6, fig.height=6, dpi=40-----------------------
set.seed(666)
sky=c(rnorm(5e5,mean=0,sd=1),(rnorm(5e5,mean=0,sd=1)+runif(5e5,0,100)))
maghist(sky, xlab='Pixel Value', ylab='Counts', grid=TRUE)
## ---- eval=TRUE----------------------------------------------------------
sky_clip_both=magclip(sky)
sky_clip_lo=magclip(sky, estimate='lo')
## ---- eval=TRUE, fig.width=6, fig.height=6, dpi=40-----------------------
magplot(density(sky_clip_both$x), col='red', grid=TRUE, xlab='Pixel Value', ylab='PDF')
lines(density(sky_clip_lo$x), col='blue')
## ---- eval=TRUE, fig.width=6, fig.height=6, dpi=40-----------------------
magplot(density(sky_clip_lo$x), col='blue', grid=TRUE, xlab='Sky Pixel Value', ylab='PDF')
lines(seq(-5,5,len=1e3), dnorm(seq(-5,5,len=1e3)), col='black')
## ---- eval=TRUE----------------------------------------------------------
median(sky_clip_lo$x)
diff(quantile(sky_clip_lo$x, pnorm(c(-1,0))))
## ---- eval=TRUE----------------------------------------------------------
mean(sky_clip_lo$x)
sd(sky_clip_lo$x)
## ---- eval=evalglobal----------------------------------------------------
# image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound"))
# profound=profoundProFound(image, skycut=1, magzero=30, plot=TRUE)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magimage(profound$sky)
# magimage(profound$skyRMS)
#
# maghist(profound$sky, xlab='Pixel Value', ylab='Counts', grid=TRUE)
# maghist(profound$skyRMS, xlab='Pixel Value', ylab='Counts', grid=TRUE)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# ExamplePSF=profitMakeGaussianPSF(fwhm=5)
# ExamplePSF=ExamplePSF/sum(ExamplePSF)
#
# model_test=list(
# sersic=list(
# xcen=runif(67,0,356),
# ycen=runif(67,0,356),
# mag=profound$segstats$mag,
# re=profound$segstats$R50,
# nser=runif(67,0.5,4),
# ang=runif(67,0,180),
# axrat=runif(67,0.3,1),
# box=rep(0,67)
# )
# )
#
# im_test<-profitMakeModel(modellist=model_test, psf=ExamplePSF, dim=c(356,356), magzero = 30)$z
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magimage(im_test)
## ---- eval=evalglobal----------------------------------------------------
# im_test_noise=im_test+rnorm(356^2, mean=profound$sky, sd=profound$skyRMS)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magimage(im_test_noise)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# profound_resim=profoundProFound(im_test_noise, skycut=1, magzero=30, plot=TRUE)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magimage(profound$sky)
# magimage(profound$skyRMS)
#
# magimage(profound_resim$sky)
# magimage(profound_resim$skyRMS)
#
# magimage(profound$sky-profound_resim$sky)
# magimage(profound$skyRMS-profound_resim$skyRMS)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# maghist(profound$sky, xlab='Pixel Value', ylab='Counts', grid=TRUE)
# maghist(profound$skyRMS, xlab='Pixel Value', ylab='Counts', grid=TRUE)
#
# maghist(profound_resim$sky, xlab='Pixel Value', ylab='Counts', grid=TRUE)
# maghist(profound_resim$skyRMS, xlab='Pixel Value', ylab='Counts', grid=TRUE)
#
# maghist(profound$sky-profound_resim$sky, xlab='Pixel Value', ylab='Counts', grid=TRUE)
# maghist(profound$skyRMS-profound_resim$skyRMS, xlab='Pixel Value', ylab='Counts', grid=TRUE)
## ---- eval=evalglobal----------------------------------------------------
# sd(profound$sky)
# sd(profound$sky-profound_resim$sky)
#
# sd(profound$skyRMS)
# sd(profound$skyRMS-profound_resim$skyRMS)
## ---- eval=evalglobal----------------------------------------------------
# contam=seq(1e5, 2e6, by=1e5)
# N=length(contam)
# output=cbind(contam,rep(0,N), rep(0,N), rep(0,N), rep(0,N))
# for(i in 1:N){
# sky=c(rnorm(5e5,mean=0,sd=1),(rnorm(contam[i],mean=0,sd=1)+runif(contam[i],0,100)))
# sky_clip_lo=magclip(sky, estimate='lo')
# output[i,2]=as.numeric(median(sky_clip_lo$x))
# output[i,3]=as.numeric(diff(quantile(sky_clip_lo$x, pnorm(c(-1,0)))))
# output[i,4]=as.numeric(mean(sky_clip_lo$x))
# output[i,5]=as.numeric(sd(sky_clip_lo$x))
# }
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magplot(1-output[,1]/(5e5+output[,1]),output[,2], log='y', grid=TRUE, xlab='Nsky/Ntotal', ylab='(Sky Estimate) - (Sky Input)', type='l', col='red')
# lines(1-output[,1]/(5e5+output[,1]),output[,4], col='blue')
# legend('topright', legend=c('Median','Mean'), lty=1, col=c('red','blue'))
#
# magplot(1-output[,1]/(5e5+output[,1]),output[,3]-1, log='y', grid=TRUE, xlab='Nsky/Ntotal', ylab='(Sky-RMS Estimate) - (Sky-RMS Input)', type='l', col='red')
# lines(1-output[,1]/(5e5+output[,1]),output[,5]-1, col='blue')
# legend('topright', legend=c('Quantile Range','Standard-Deviation'), lty=1, col=c('red','blue'))
## ---- eval=evalglobal----------------------------------------------------
# profound_median_clip=profoundProFound(image, skycut=1.0, magzero=30, skytype='median', doclip=TRUE) #The default mode
# profound_median_noclip=profoundProFound(image, skycut=1.0, magzero=30, skytype='median', doclip=FALSE)
# profound_mean_clip=profoundProFound(image, skycut=1.0, magzero=30, skytype='mean', doclip=TRUE)
# profound_mean_noclip=profoundProFound(image, skycut=1.0, magzero=30, skytype='mean', doclip=FALSE)
# profound_mode_clip=profoundProFound(image, skycut=1.0, magzero=30, skytype='mode', doclip=TRUE)
# profound_mode_noclip=profoundProFound(image, skycut=1.0, magzero=30, skytype='mode', doclip=FALSE)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# maghist(profound_median_clip$sky-profound_median_noclip$sky, grid=TRUE)
# maghist(profound_mean_clip$sky-profound_mean_noclip$sky, grid=TRUE)
# maghist(profound_mode_clip$sky-profound_mode_noclip$sky, grid=TRUE)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# maghist(profound_mean_clip$sky-profound_median_clip$sky, grid=TRUE)
# maghist(profound_mode_clip$sky-profound_median_clip$sky, grid=TRUE)
# maghist(profound_mean_clip$sky-profound_mode_clip$sky, grid=TRUE)
## ---- eval=evalglobal, fig.width=8, fig.height=5, dpi=40-----------------
# magplot(profound_median_clip$segstats$mag, profound_median_clip$segstats$mag-profound_mean_clip$segstats$mag, ylim=c(-0.1,0.1), xlab='Median mag', ylab='(Median mag) - (Mean mag)', grid=TRUE)
# lines(magrun(profound_median_clip$segstats$mag, profound_median_clip$segstats$mag-profound_mean_clip$segstats$mag), col='red')
## ---- eval=evalglobal----------------------------------------------------
# profound=profoundProFound(image, type="bicubic")
# newsky=profoundSkySplitFFT(image$imDat, objects=profound$objects_redo, sky=profound$sky, skyRMS=profound$skyRMS)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magimage(profound$sky)
# magimage(newsky$sky)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magimage(image$imDat)
# magimage(image$imDat-profound$sky)
# magimage(image$imDat-newsky$sky)
## ---- eval=evalglobal, fig.width=6, fig.height=6, dpi=40-----------------
# magimage(profoundSkySplitFFT(image$imDat)$sky_lo)
# magimage(profoundSkySplitFFT(image$imDat)$sky_hi)
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