Modified gleam #117
Modified gleam #117
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@@ Coverage Diff @@
## main #117 +/- ##
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- Coverage 99.71% 99.51% -0.20%
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Files 5 6 +1
Lines 1399 1448 +49
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+ Hits 1395 1441 +46
- Misses 4 7 +3
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Thanks for putting this together @samirchoudhuri!
I have a few comments about the code, particularly around better integrating it with the SkyModel object. Also, we'll need to get all the new lines covered with tests.
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| def modified_gleam( | ||
| gleam_filename="gleamegc.dat", |
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Where do you get this file from? We have a method in this utils module to download the GLEAM catalog as a VOT table from Vizier. But it isn't just a text file like it looks like you're expecting this one to be.
| raise ValueError("File not found") | ||
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| # read array of RA (deg), Dec (deg), Flux at 100 MHz (Jy), sp. index | ||
| aa = np.genfromtxt(gleam_filename, usecols=usecols) |
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Is there a good reason not to use the VOT table and the read_gleam_catalog method on SkyModel to get the values you need here?
| aa = np.genfromtxt(gleam_filename, usecols=usecols) | ||
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| # use sources with finite flux and sp. index values | ||
| cat_gleam = aa[(aa[:, 2] >= 0.0) & np.isfinite(aa[:, 2]) & np.isfinite(aa[:, 3])] |
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So leaving out the sources without a spectral index concerns me. This is ¼-⅓ of the catalog and it is not limited to dim sources. Bright sources that have peaked spectra or broken power law shapes also end up without a spectral index. The read_gleam_catalog method on SkyModel can read in all the subband fluxes and you can interpolate between them if needed.
| [201.3667, -43.0192, 1937.472, -0.50], # Centaurus A | ||
| [139.5250, -12.0956, 544.686, -0.96], # Hydra A | ||
| [79.9583, -45.7789, 774.612, -0.99], # Pictor A | ||
| [252.7833, 4.9925, 791.486, -1.07], # Hercules A | ||
| [187.7042, 12.3911, 1562.747, -0.86], # Virgo A | ||
| [83.6333, 22.0144, 1560.743, -0.22], # Crab | ||
| [299.8667, 40.7339, 13599.676, -0.78], # Cygnus A | ||
| [350.8667, 58.8117, 15811.361, -0.41], # Cassiopeia A | ||
| [50.6708, -37.2083, 1256.016, -0.81], | ||
| ] | ||
| ) # Fornax A |
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Where did these come from? I'd really like to document the source of these in the code. We actually have some other students working on getting better (multi-component) models for these sources into SkyModel objects, so I've been thinking about making a function to add them to GLEAM. We don't have those ready yet, so we can start with these and then replace them with better ones, but I'm insisting that we have a documentation trail for our sky models.
| # save in a file | ||
| if modified_gleam_filename != "": | ||
| np.savetxt(modified_gleam_filename, cat_gleam) |
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I feel pretty strongly that we want to actually use the SkyModel object here. It is similar to UVData in that it requires that all the necessary metadata are set and then it has write methods (I'd prefer to use the write_skyh5 method) to write to standardized file formats that can be read back into a SkyModel object in the future.
| if modified_gleam_filename != "": | ||
| np.savetxt(modified_gleam_filename, cat_gleam) | ||
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| return cat_gleam |
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And this should return a SkyModel object, not a numpy array.
| Write modified gleam catalogue to fill the blank regions, and also to add the peeled sources. | ||
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Can you fill out this docstring a little more to describe the algorithm in a bit more detail? You can even put in a reference to your paper if you like. But other people are much more likely to use it if they understand what it's doing and what problem it's trying to solve.
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Hey @samirchoudhuri Bryna is offline for now, but I'm around to help you get this over the finish line once you get back around to it. Great place to start by addressing all of her last comment :D |
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Thanks, @mkolopanis. Sure, I will get back to you soon. |
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@samirchoudhuri I'm back and happy to help push this forward if needed. It looks like it needs to be rebased again which I can also help with. |
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Thanks @bhazelton. I was working on this PR, but got stuck in converting to SkyModel object. I will resume and update. |
A method added in the utils.py to generate a modified GLEAM catalogue which fills the blank regions.