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README
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galstar
=======
Setup and Build
===============
./configure --with-libpeyton=../libpeyton/optimized --optimized --prefix=`pwd`/staging
make -j install
This will configure and build an optimized version of galstar in
./optimized and install it in directory ./staging linking against
an optimized version of libpeyton from ../libpeyton/optimized
Quick Test
==========
greg@greg-G53JW:~/projects/galstar/build$ ./galstar --help
Usage: ./galstar <outfile1.txt:X1[,Y1]> [outfile2.txt:X2[,Y2] [...]]
Options:
--help produce this help message
--pdfs arg marginalized PDF to produce (can be given as the
command line argument)
--lf arg luminosity function file
--seds arg SEDs file
--thindisk arg Thin disk model parameters (l1 h1)
--thickdisk arg Thick disk model parameters, (f_thin l2 h2)
--halo arg Halo model parameters, (f_halo q n_inner R_br n_outer)
--test Assume the input contains (l b Ar DM Mr FeH uErr gErr
rErr iErr zErr) and generate test data
--range-M arg Range of absolute magnitudes to sample
--range-FeH arg Range of Fe/H to consider
--range-DM arg DM grid to sample
--range-Ar arg Ar grid to sample
--datafile arg Stellar magnitudes and errors file
--statsfile arg Base filename for statistics output
Quick Demo
==========
Running galstar on a pencil-beam catalog (test.in):
greg@greg-G53JW:~/projects/galstar/build$ ./galstar ../output/test/DM_Ar:DM,Ar --datafile ../test_input/test.in --statsfile ../output/test/stats
# Outputting P(DM, Ar) into file ../output/test/DM_Ar
# Loaded Phi(-1 <= Mr <= 28) LF from /home/greg/projects/galstar/staging/share/galstar/MrLF.MSandRGB_v1.0.dat
# Loaded 147951 SEDs from /home/greg/projects/galstar/staging/share/galstar/MSandRGBcolors_v1.3.dat
# Galactic structure: 8000 25 | 2150 245 | 0.13 3261 743 | 0.0051 0.7 -2.62
# Loading stellar magnitudes from ../test_input/test.in ...
# Sampler: DM=[5..20..0.02] Ar=[0..5..0.02] Mr=[ALL] FeH=[ALL]
=========================================
Calculating posterior for star #0
Mean:
13.7 +- 0.517
0.206 +- 0.093
3.8 +- 0.493
-1.32 +- 0.214
Covariance:
0.268 -0.0157 -0.251 -0.0295
-0.0157 0.00866 0.00719 -0.00353
-0.251 0.00719 0.243 0.0325
-0.0295 -0.00353 0.0325 0.0458
Gelman-Rubin diagnostic:
1.037 1.0459 1.049 1.0886
Acceptance rate: 18.4% 4.2% 4.04% 3.99%
Time elapsed for 2000000 steps (20 rounds) on 4 threads: 4.14 s
=========================================
Calculating posterior for star #1
Mean:
14.9 +- 0.549
0.185 +- 0.1
4.53 +- 0.584
-1.67 +- 0.265
Covariance:
0.302 0.0166 -0.317 0.0208
0.0166 0.0101 -0.0263 -0.00546
-0.317 -0.0263 0.341 -0.0158
0.0208 -0.00546 -0.0158 0.0703
Gelman-Rubin diagnostic:
1.0003 1.0001 1.0003 1.0001
Acceptance rate: 19.7% 19.6% 15.9% 17.6%
Time elapsed for 100000 steps (1 rounds) on 4 threads: 0.286 s
=========================================
Calculating posterior for star #2
Mean:
11.3 +- 0.712
0.25 +- 0.112
4.08 +- 0.691
-0.741 +- 0.15
Covariance:
0.506 -0.0186 -0.486 0.00625
-0.0186 0.0125 0.00631 0.00229
-0.486 0.00631 0.477 -0.00855
0.00625 0.00229 -0.00855 0.0225
Gelman-Rubin diagnostic:
1.1898 1.0141 1.1918 1.045
Acceptance rate: 4.02% 3.92% 4.05% 4.04%
Did not converge.
Time elapsed for 2000000 steps (20 rounds) on 4 threads: 3.56 s
=========================================
Calculating posterior for star #3
Mean:
15.2 +- 0.445
0.152 +- 0.076
3.96 +- 0.442
-1.48 +- 0.261
Covariance:
0.198 -0.00362 -0.194 0.00939
-0.00362 0.00578 -0.00203 -0.00731
-0.194 -0.00203 0.195 -0.00253
0.00939 -0.00731 -0.00253 0.0679
Gelman-Rubin diagnostic:
1.0002 1 1.0002 1.0001
Acceptance rate: 20.4% 19.5% 20.6% 18.6%
Time elapsed for 100000 steps (1 rounds) on 4 threads: 0.302 s
=========================================
Calculating posterior for star #4
Mean:
15.3 +- 0.614
0.225 +- 0.116
4.59 +- 0.642
-1.7 +- 0.274
Covariance:
0.377 0.0131 -0.388 0.0286
0.0131 0.0135 -0.0261 -0.00548
-0.388 -0.0261 0.412 -0.0235
0.0286 -0.00548 -0.0235 0.0753
Gelman-Rubin diagnostic:
1.0002 1.0003 1.0001 1.0001
Acceptance rate: 19.5% 19.2% 18.2% 18.7%
Time elapsed for 100000 steps (1 rounds) on 4 threads: 0.318 s
# Did not converge 1 times.
Create an input file from an SDSS fits file using the script read_sdss.py:
greg@greg-G53JW:~/projects/galstar/build$ ../scripts/read_sdss.py --help
usage: read_sdss [-h] [--filter FILT] [--toscreen] inputs [inputs ...]
Translate FITS files of SDSS objects to ASCII input for galstar
positional arguments:
inputs FITS files
optional arguments:
-h, --help show this help message and exit
--filter FILT Filter objects with errors greater than the specified amount
--toscreen Print results to screen, rather than outputting to ASCII
files
Another useful script is plotpdf.py:
greg@greg-G53JW:~/projects/galstar/build$ ../scripts/plotpdf.py --help
usage: plotpdf [-h] --output OUTPUT [--imgtype {png,pdf,eps}]
[--shape SHAPE SHAPE] [--xname XNAME] [--yname YNAME]
[--xmin XMIN] [--xmax XMAX] [--ymin YMIN] [--ymax YMAX]
files [files ...]
Plots posterior distributions produced by galstar
positional arguments:
files Input posterior distributions
optional arguments:
-h, --help show this help message and exit
--output OUTPUT Output image filename base (without extension)
--imgtype {png,pdf,eps}
Output image filetype
--shape SHAPE SHAPE # of rows and columns in figure
--xname XNAME Name of x-axis
--yname YNAME Name of y-axis
--xmin XMIN Lower bound of x in plots
--xmax XMAX Upper bound of x in plots
--ymin YMIN Lower bound of y in plots
--ymax YMAX Upper bound of y in plots
greg@greg-G53JW:~/projects/galstar/build$ ../scripts/plotpdf_greg.py ../output/test/DM_Ar_*.txt --output ../output/test/DM_Ar --shape 3 2 --xname '\mu' --yname 'A_r'
Plotting files 1 through 5...
Done.
To plot the stacked posteriors of the output marginalized along all but one dimension, run plot_hist.py:
greg@greg-G53JW:~/projects/galstar/build$ ../scripts/plot_hist.py --help
usage: plot_hist [-h] --xname XNAME --output OUTPUT [--xaxis {0,1}]
[--subtract-background SUBTRACT_BACKGROUND SUBTRACT_BACKGROUND SUBTRACT_BACKGROUND]
[--MLonly | --Pxonly]
files [files ...]
Plot stacked pdfs marginalized over one dimension and binned Maximum
Likelihoods
positional arguments:
files Input posterior distributions
optional arguments:
-h, --help show this help message and exit
--xname XNAME Name of x-axis
--output OUTPUT Output image filename (with extension)
--xaxis {0,1} Column to use as x-axis
--subtract-background SUBTRACT_BACKGROUND SUBTRACT_BACKGROUND SUBTRACT_BACKGROUND
Remove background, assuming line-of-sight (l, b,
radius), in degrees
--MLonly Only plot histogram of binned Maximum Likelihoods
--Pxonly Only plot stacked pdfs
greg@greg-G53JW:~/projects/galstar/build$ ../scripts/plot_hist.py ../output/test/DM_Ar_*.txt --output ../output/test/DM_hist.png --xname '\mu'
25th percentile: 13.62
Median: 14.53
75th percentile: 14.97
By the end of this demo, the following output has been produced:
greg@greg-G53JW:~/projects/galstar/build$ ls ../output/test/
DM_Ar_0.png DM_Ar_1.txt DM_Ar_3.txt DM_hist.png stats_1.dat stats_3.dat
DM_Ar_0.txt DM_Ar_2.txt DM_Ar_4.txt stats_0.dat stats_2.dat stats_4.dat
Input Files
==========
The --datafile option is used to pass a pencil-beam catalog of stellar magnitudes and errors. The format is:
l b
u g r i z u_err g_err r_err i_err z_err
u g r i z u_err g_err r_err i_err z_err
...
In the above demo, the following input file was given:
greg@greg-G53JW:~/projects/galstar/build$ cat ../test_input/test.in
60.169 40.978
19.163 18.067 17.743 17.557 17.564 0.033 0.016 0.013 0.015 0.033
20.834 20.016 19.653 19.471 19.539 0.115 0.031 0.022 0.025 0.069
17.290 16.043 15.605 15.410 15.395 0.017 0.014 0.012 0.014 0.030
20.664 19.623 19.356 19.190 19.168 0.099 0.025 0.019 0.022 0.054
21.195 20.540 20.097 19.962 19.844 0.155 0.046 0.030 0.034 0.086