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BOND

BOND infers oxygen and nitrogen abundances in giant HII regions by comparison with a large grid of photoionization models using strong and semi-strong lines.

Website: bond.ufsc.br

Natalia Vale Asari
natalia@astro.ufsc.br
04/May/2016

Quick start

1) Downloading

Download the code: bond v1.1

Download the initial octree grid and an example data table:

emission line table

grid

2) Installing

Unzip the code to a directory of yout choice.

[You also likely need to add bond/bond/ to your python path.]

Install these python libraries:

numpy (>= 1.10.1)
scipy (>= 0.16.1)
astropy (>= 1.0.dev11618)
matplotlib (>= 1.4.3)
seaborn (>= 0.6.0)
h5py (>= 2.4.0)

[Note: setup.py being tested]

3) Running the example

Go to the directory where you unzipped the bond code.

cd bond/example

Edit the configuration file (bond.cfg) to match your local directories, especially for the grid and sources. Try to run:

python fitting.py

4) Checking the results

You will find a few output files in your `outDir':

  • A directory with an individual fit for each source (./out/fit_sSPIRALS-HEBCD_gGoctree/*.hdf5 if you have not edited bond.cfg).

  • A .hdf5 file with the results for all sources combined (./out/fit_sSPIRALS-HEBCD_gGoctree.hdf5 if you have not edited bond.cfg).

  • A .txt file with a summary of the PDFs for all objects (./out/fit_sSPIRALS-HEBCD_gGoctree.txt if you have not edited bond.cfg).

  • A plot showing the N/O vs O/H PDFs for all sources in the current directory (NO_Vs_OH_BOND.pdf).

Improvements and fixes to come

1) What summaries from the output file should you use?

2) A better python installer.

3) Checking the PDFs object by object.

4) Using your own data tables

BOND needs the following data columns:

name      -- meaning
F3727     -- ([O II] 3726 + 3729)/Hb
F5007     -- [O III] 5007/Hb (not the sum of 4959 and 5007)
F6584     -- [N II] 6584/Hb (not the sum of 6548 and 6584)
F7135     -- [Ar III] 7135/Hb
F3869     -- [Ne III] 3869/Hb
F5876     -- He I 5876/Hb
eF3727    -- uncertainty in F3727 = ([O II] 3726 + 3729)/Hb
eF*       -- uncertainty in all the other emission line rations above
limF4363  -- * Detection limit for [O III] 4363/Hb, if 4363 has not been detected
limF5755  -- * Detection limit for [N II]  5755/Hb, if 5755 has not been detected
F4363     -- * [O III] 4363/Hb (this will not be used in the fit, but will be used to calculate an upper limit for 4363)
F5755     -- * [N II]  5755/Hb (this will not be used in the fit, but will be used to calculate an upper limit for 5755)
  • Highly recommended, but not essential.