Get data / Define model / ??? / ProFit!
ProFit is a Bayesian galaxy fitting tool that uses a fast C++ image generation library and a flexible interface to a large number of likelihood samplers.
First things first, you will probably want to install a recent version of R that lets you build packages from source. The advantage of choosing this route is you can then update bleeding edge versions directly from GitHub. If you rely on the pre-build binaries on CRAN you might be waiting much longer.
Pretty simple, go here and install the most relevant pkg file: https://cloud.r-project.org/bin/macosx/
Pretty simple, go here and install the most relevant exe file: https://cloud.r-project.org/bin/windows/base/
Varies a bit by platform. All the info on binaries is here: https://cloud.r-project.org/bin/linux/
Debian: sudo apt-get install r-base r-base-dev
Fedora: sudo yum install R
Suse: More of a pain, see here https://cloud.r-project.org/bin/linux/suse/README.html
Ubuntu: sudo apt-get install r-base-dev
If you have a poorly supported version of Linux (e.g. CentOS) you will need to install R from source with the development flags (this bit is important). You can read more here: https://cloud.r-project.org/sources.html
Now you have the development version of R installed (hopefully) I would also suggest you get yourself R-Studio. It is a very popular and well maintained R IDE that gives you a lot of helpful shortcuts to scripting and analysing with R. The latest version can be grabbed from https://www.rstudio.com/products/rstudio/ where you almost certainly want the free Desktop version.
You can start R simply by typing "R" in your terminal. I would advocate running it from R-Studio though (a much nicer IDE experience for most people).
Within R you can get the v1.1.0 pre-built binary from CRAN by running (note as of 20/02/2018 it is not on CRAN. It might reappear at a future date though- basically CRAN removed support for some of the packages we use):
install.packages('ProFit')The above variant of R will work easily even when you do not have the buld tools or root permission etc. The downside is the version hosted on CRAN is not the bleeding edge variant (CRAN do not allow very regular updating).
There is a pre-built for R 3.4 and Mac OSX Siera (10.12+) v1.1.0 ProFit package (close to the most recent source version) available on Dropbox. You can download it to a local directory from https://www.dropbox.com/s/gsniyhctsrg77qq/ProFit_1.1.0.tgz?dl=0. Once downloaded you can install it within R via:
install.packages('PATH-TO-PACKAGE/ProFit_1.1.0.tgz', repos=NULL, type='mac.binary')The above might work with different versions of R (fairly likely) and different versions of OSX (not so likely), but it cannot be guaranteed (sorry). It might be worth giving it a try if you are not savvy with compiling code and fiddling with Makevars and flags (this might not be necessary, but in general installing from binary is much easier, when it works).
If you do have the build tools, a development version of R, useful permissions, and a bit of bravery then you will be able to install the latest variants directly from the main ICRAR GitHub branch. You need a version of GCC or Clang that supports vaguely modern C++11 features. For Linux users this should be the case for any OS installed in the last 5 years, but for OSX the tool chain tends to be a fair amount older. If you have 10.9 (Mavericks) or newer and the associated X-Code (6+) then you should probably be fine. Other options might be to install a set of more recent tools from Homebrew (see instructions on installing a more modern Clang in the OpenCLMaybe 0.0 and OpenMP document).
First you should make sure you have a sensible looking Makevars file in ~/.R/Makevars:
For GCC it should probably look like this:
CC = gcc
CXX = g++
CXX1X = g++
CXX11 = g++
CFLAGS = -O3 -Wall -mtune=native -march=native -Ofast -std=gnu99
CXXFLAGS = -O3 -Wall -mtune=native -march=native -Ofast -std=c++0x
CXX1XFLAGS = -O3 -Wall -mtune=native -march=native -Ofast -std=c++0x
CXX11FLAGS = -O3 -Wall -mtune=native -march=native -Ofast -std=c++0x
For Clang it should probably look like this:
CC = clang
CXX = clang++
CXX1X = clang++
CXX11 = clang++
CFLAGS = -O3 -Wall -mtune=native -march=native -Ofast
CXXFLAGS = -O3 -Wall -mtune=native -march=native -Ofast
CXX1XFLAGS = -O3 -Wall -mtune=native -march=native -Ofast
CXX11FLAGS = -O3 -Wall -mtune=native -march=native -Ofast
With this setup, you can then have a go at building ProFit from source:
install.packages('devtools')
library(devtools)
install_github("ICRAR/ProFit")
library(ProFit)The above (binary or source install) should also install the required packages. If you have trouble with this you can try installing the required packages manually first and then retry the installation for ProFit:
install.packages(c('fftw', 'R2Cuba', 'RColorBrewer', 'LaplacesDemon', 'imager', 'magicaxis', 'FITSio', 'data.table'))
install.packages('devtools')
library(devtools)
install_github("ICRAR/ProFit")To use the profitMakeSegim and profitProFound function for image segmentation you will need to have EBImage installed. Since this can be a bit cumbersome on some platforms (given its dependencies) this is only listed as a suggested package. You can have a go at installing it by running:
source("https://bioconductor.org/biocLite.R")
biocLite("EBImage")Be warned, it will probably ask you to update a whole bunch of stuff. Just say no and only install EBImage for now. If something else needs updating or is missing you will get a warning when trying to use it, and you can update those packages as neccessary. If you say yes you will probably sit there for an hour whilst it builds dozens of packages from source that you do not need to really update.
Linux users might also need to install some non-standard graphics libraries (depending on your install). If you do not have them already, you should look to install Cairo, jpeg and tiff libraries (these are apparently technically not entirely free, hence not coming by default on some strictly open source Linux variants). For Cairo you might need to install the development version, so check this if you are having issues.
Assuming this has all installed successfully, you should now be able to load ProFit within R with the usual:
library(ProFit)modellist = list(
sersic = list(
xcen = c(180, 60),
ycen = c(90, 10),
mag = c(15, 13),
re = c(14, 5),
nser = c(3, 10),
ang = c(46, 80),
axrat = c(0.4, 0.6),
box = c(0.5,-0.5)
),
pointsource = list(
xcen = c(34,10,150),
ycen = c(74,120,130),
mag = c(10,13,16)
),
sky = list(
bg = 3e-12
)
)Without a PSF provided only the extended sources are shown, with no convolution:
magimage(profitMakeModel(modellist=modellist, dim=c(200,200)))With a PSF provided the PSFs are displayed and the extended sources are convolved with the PSF:
magimage(profitMakeModel(modellist=modellist, psf=profitMakePointSource(), dim=c(200,200)))To find more long-form examples, including complicated fitting use-cases, please check the vignettes provided. You can browse these with:
browseVignettes('ProFit')Or if that does not work they are all hosted externally at http://rpubs.com/asgr/
This package is designed to offer a fully featured Bayesian interface to galaxy model fitting (also called profiling). It mostly uses the same standard inputs as other popular codes (e.g. GALFIT) but can use complex priors and a number of likelihoods.
A.S.G. Robotham, D. Taranu, R. Tobar
To see where our efforts have gone, check out our gource video!
https://www.dropbox.com/s/75kdcx57cwka01m/gource_comp.mp4?dl=0
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