Made notebooks run with current hera_sim #238

hughbg · 2022-09-12T13:32:42Z

Updated notebooks. They run, but may not make use of all the new features properly, so that needs to be examined.

review-notebook-app · 2022-09-12T13:32:48Z

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codecov · 2022-09-12T13:40:50Z

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All modified and coverable lines are covered by tests ✅

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steven-murray · 2022-09-12T19:36:54Z

Thanks @hughbg. I can't seem to make comments directly on the notebooks in reviewnb for some reason, so I will just leave comments here:

hera_sim_defaults

There's a cell with a comment "let's not the defaults are initially deactivated" but it prints out True.
It seems dodgy to have to define your own private functions (eg. _check_path and _read_npy). Where did these functions go (@r-pascua ?) and is there a better way to present this?
The values output by the H2C default bandpass/beam poly are the same as the H1C (whereas they used to be different). Is something going wrong there?

hera_sim_simulator

when printing all components (with list_all_components) there is a new section called "example" with entries testadd, testmult, testalias, which I presume aren't meant to be there? @r-pascua ? Hmmm, maybe it's due to running the notebook cells out of order? I think they're supposed to show up later.

hera_sim_tour

Note that there are private functions that are being defined here again (_check_path, _read_npy, _get_hera_bm_poly...)
The ptsrc foreground simulation looks very different. I presume this is because in the current version, the "defaults" get set automatically by default, and so perhaps the simulation is using a different beam. But I'd be curious to know if that's the reason.
For the noise simulation, the galaxy doesn't seem to appear in the updated plot, whereas it used to?
simulation of RFI seems to have changed substantially... can we verify why?

polybeam_simulation

You should probably try to follow the general black style in the notebooks as much as possible. When constructing the PerturbedPolyBeam, for instance, put the perturb_coeffs= on the next line indented.
When constructing the beam list in run_sim, you shouldn't make the list the same length as the number of antennas. You should only give unique beams. If there is only one unique beam, you can simply give it a list of one beam (if you have more than one unique beam, you also need to pass the beam_ids list). What you've done will work but it is not the most efficient.

visibility_simulator

The HealVis description should be prefaced with the warning that it is deprecated.
We should probably update the description of how to subclass the VisibilitySimulator class. But in another PR is fine.

r-pascua · 2022-09-14T06:17:24Z

Thanks for the updates @hughbg. I'm a little confused about some of the things that I'm seeing. According to some of the output from the Simulator tutorial notebook, it looks like your version is up-to-date, so I think the parts that are confusing me are likely the result of running cells out of order. When you get a chance, could you re-run the notebooks with freshly started kernels and push the results?

I'm just going to add some comments in response to the things @steven-murray raised in his review, as well as maybe a few of my own (or some suggestions), with the hope that the input is useful.

hera_sim_defaults

The current version of hera_sim does not initially set the defaults—I can't remember exactly why, but there was something in one of the changes that made it impossible (as far as I could tell) to set the defaults on importing hera_sim (so they're initially inactive). Running a test with a freshly installed version of hera_sim confirms that the defaults are not set when hera_sim is imported, so we can clear this up by running the notebook with a fresh kernel.
The _check_path and _read_npy functions live in the interpolators module, so there is no need to re-define those functions here. We shouldn't actually be using these anywhere in these notebooks—this issue is actually coupled with @steven-murray's next question...
The beam integral and bandpass fits look the same here because, with what's written in the notebook, they have no reason to look different. The _get_hera_bm_poly private function no longer exists, and neither does the one for getting the bandpass. Copying their old definitions here does not expose them to the defaults manager, so changing the defaults won't give you different results. The notebook should instead do something like this:

freqs = np.linspace(0.1, 0.2, 100)
hera_sim.defaults.set('h1c')
h1c_omega_p = hera_sim.defaults('omega_p')(freqs)
h1c_bandpass = hera_sim.defaults('bp_poly')(freqs)
hera_sim.defaults.set('h2c')
h2c_omega_p = hera_sim.defaults('omega_p')(freqs)
h2c_bandpass = hera_sim.defaults('bp_poly')(freqs)

The suggestion above is not the only way to get the beam integral and bandpass fits, but I think it is the most straightforward option, shows a neat feature of the defaults object, and doesn't require using private methods.
Something completely unrelated to this PR, but which I want to bring up: I think that as we start building out the H4C validation simulations, we should be updating the defaults-related stuff to know about the models we're using.

hera_sim_simulator

The example_blah stuff definitely is not in there when you do a fresh import of hera_sim. This has to be due to the cells being run out of order.
Everything else looks fine here.

hera_sim_tour

The private function (and related) issues should be able to be resolved by adapting the code snippet I provided above.
Regarding the point source simulation: remember that the defaults are not set when importing the module. I think the original set of point source visibilities were made with a buggy version of the function—it's hard-coded to smear the sources by the HERA beam (see line 269 in foregrounds.py), so no point source simulation should look so stripy.
The new noise simulation doesn't have the galaxy in it because it doesn't use the sky model it used to use, so it's defaulting to just a power-law sky temperature model. This can be fixed by adding Tsky_mdl=hera_sim.noise.HERA_Tsky_mdl['xx'] to the function call.
The RFI functions were normalized to have their signature follow rfi_func(lsts, freqs, **kwargs). So the call signature is wrong, and we shouldn't expect the simulation to give something sensible. Maybe we could protect against this a bit by adding something like if np.any(lsts < 0) or np.any(lsts > 2*np.pi): raise ValueError(...) to things that require both lsts and freqs.
The style in this notebook could do with some updating, and we could also move to using uvtools.plot.labeled_waterfall for generating the waterfalls (so that the waterfall axes are... labeled). Definitely not a priority, but at some point I'd like to see these improvements implemented.

As for the other notebooks, I don't have any comments beyond what @steven-murray has pointed out. Thanks again for your work @hughbg! Hopefully it'll only be a few iterations for us to get everything wrangled.

hughbg · 2022-09-22T13:55:57Z

I've uploaded a new version of hera_sim_defaults. Rerunning the cells in order fixed some issues. I switched the beam and bandpass code to

freqs = np.linspace(0.1, 0.2, 100)
hera_sim.defaults.set('h1c')
h1c_omega_p = hera_sim.defaults('omega_p')(freqs)
h1c_bandpass = hera_sim.defaults('bp_poly')(freqs)
hera_sim.defaults.set('h2c')
h2c_omega_p = hera_sim.defaults('omega_p')(freqs)
h2c_bandpass = hera_sim.defaults('bp_poly')(freqs)

The old code was returning model values whereas this code is returning values interpolated from the models. That is in accord with the y-label axes which have always referred to beam and bandpass values (area and gains) rather than models. The plots are quite different now.

steven-murray · 2024-08-27T11:29:33Z

@r-pascua and @hughbg, I have finally gotten back to this PR.

I did the following:

Formatted each notebook with ruff so they all look a bit better now.
Re-ran all the notebooks locally to make sure they run through fine with the recent updates to hera_sim.
Went through mine and @r-pascua's suggestions above and implemented them
Added a new CI test that runs each of the notebook demos, so we can keep track of when they break.

r-pascua · 2024-08-27T22:44:20Z

docs/tutorials/end_to_end_example.ipynb

@@ -26,7 +26,7 @@
  },


Change vis_cpu to matvis, add fftvis to the list of supported simulators, and maybe note that healvis is deprecated (or just remove it from the list)?

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Good catch. Changed to matvis,added fftvis and removed healvis.

r-pascua · 2024-08-27T22:44:20Z

docs/tutorials/end_to_end_example.ipynb

@@ -26,7 +26,7 @@
  },


Line #1. vis_cpu_sim = VisibilitySimulation(data_model=data_model, simulator=MatVis())
Should we change this (and following occurrences) to matvis_sim?

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r-pascua · 2024-08-27T22:44:20Z

docs/tutorials/end_to_end_example.ipynb

@@ -26,7 +26,7 @@
  },


Line #1. %%timeit
I think we want to do %%time instead of %%timeit

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Woops! Good catch.

r-pascua · 2024-08-27T22:44:20Z

docs/tutorials/end_to_end_example.ipynb

@@ -26,7 +26,7 @@
  },


Do we think it's worthwhile for me to edit the figure caption with a better description of how to interpret the simulation data?

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Yeah, that would be great!

r-pascua · 2024-08-27T22:44:21Z

docs/tutorials/hera_sim_defaults.ipynb

@@ -18,36 +18,15 @@
   "cell_type": "code",


While not necessary, I would like to update this to make better plots in the future.

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r-pascua · 2024-08-27T22:44:21Z

docs/tutorials/hera_sim_defaults.ipynb

@@ -18,36 +18,15 @@
   "cell_type": "code",


Something got messed up here. Instead of plotting np.polyval(...),we should just be plotting bps[seas] and beams[seas],since they were evaluated a few cells up via h1c_beam = hera_sim.defaults("omega_p")(fqs) and so on. hera_sim.defaults.("omega_p") will return an instance of a subclass of hera_sim.interpolators.FreqInterpolator which may then be called to interpolate to the desired frequencies.

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Totally! OK fixed that.

r-pascua · 2024-08-27T22:44:21Z

docs/tutorials/hera_sim_defaults.ipynb

@@ -18,36 +18,15 @@
   "cell_type": "code",


Line #6. sim1.run_sim(**sim1params)
This should be moved between line 3 and line 4. I'm pretty sure the main reason the two plots look different is that the random seed is different.

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Got it. Fixed.

review-notebook-app · 2024-08-27T22:44:23Z

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r-pascua commented on 2024-08-27T22:44:23Z
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Line #7.        ax1.set_xlabel(None)

I think a better way to do this is to replace this line and line 8 with ax1.xaxis.set_visible(False)

review-notebook-app · 2024-08-27T22:44:24Z

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r-pascua commented on 2024-08-27T22:44:23Z
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Is the change to np.int64(ant) a ruff formatting thing?

steven-murray commented on 2024-09-09T12:54:56Z
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no, it's a numpy 2 thing.

review-notebook-app · 2024-08-27T22:44:24Z

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r-pascua commented on 2024-08-27T22:44:24Z
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I'm guessing False -> np.False_ is another ruff thing?

steven-murray commented on 2024-09-09T12:55:12Z
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Also a numpy 2 thing.

review-notebook-app · 2024-08-27T22:44:25Z

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r-pascua commented on 2024-08-27T22:44:25Z
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Something has broken. I'm suspecting that it has to do with the change to (baseline, pol) evident from all the warning messages, but this needs to be dug into. The simplest check is to see whether these two are equivalent by relaxing the check from a == b to np.isclose(a,b).

steven-murray commented on 2024-09-09T13:08:28Z
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OK, I tried some stuff out and it turns out that the differences are due to the original simulation having some negative real parts of the autos. When this is saved to file and re-read, the imaginary parts are forced to zero, and the real parts are made positive. Not sure what to do about that.

r-pascua commented on 2024-09-09T21:32:29Z
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OK, my fix was pretty coarse: I just made it so that autocorrelations are modified via vis = np.abs(vis).astype(complex) in the hera_sim.eor.NoiselikeEoR.__call__ method. Figure it shouldn't be too much of an issue since I imagine this functionality really isn't used all that frequently.

steven-murray commented on 2024-09-10T10:29:34Z
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That sounds fine to me

review-notebook-app · 2024-08-27T22:44:26Z

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r-pascua commented on 2024-08-27T22:44:25Z
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Something has broken here--the first value should be False. Will need to dig into this.

r-pascua commented on 2024-09-09T21:33:19Z
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Fixed this issue. The Simulator just wasn't caching the baseline filters.

review-notebook-app · 2024-08-27T22:44:26Z

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r-pascua commented on 2024-08-27T22:44:26Z
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Line #5.        np.any(vis_A[blt_inds]),  # The first application give (0, 1) noise,

Looks like I forgot to add "didn't" to the comment.

review-notebook-app · 2024-08-27T22:44:27Z

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r-pascua commented on 2024-08-27T22:44:27Z
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Line #18.        Smin=0.5,

Might be a good idea to bump this up quite a bit, since it leads to a bit of cognitive dissonance in the following plot (not all parts of the "bright sources" plot are higher amplitude than any part of the "faint sources" plot---this is fine, but the reason why it's fine is perhaps a bit nuanced).

steven-murray commented on 2024-09-09T13:11:46Z
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I set it to 5-20 instead of 0.5-10. I think it looks pretty reasonable now.

review-notebook-app · 2024-08-27T22:44:28Z

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r-pascua commented on 2024-08-27T22:44:27Z
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Ah. I think in order to fix this bug we need to add attrs_to_pull = dict(ants="antpos") as a class attribute after line 3. I forget exactly when I added this change, but it's a more explicit way of telling the Simulator which of its attributes need to be used as parameter values when adding a particular systematic effect. When the Simulator is trying to figure out how to set all of the model parameters, it first queries the model to see which parameters can be retrieved from the Simulator (meta)data and determines the default parameter settings according to the defaults singleton, then modifies the parameters that are passed to the model in accordance with any keyword arguments provided by the user.

steven-murray commented on 2024-09-09T13:17:26Z
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Good - fixed.

review-notebook-app · 2024-08-27T22:44:29Z

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r-pascua commented on 2024-08-27T22:44:28Z
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It looks like mutual coupling isn't showing up in the list for some reason?

steven-murray commented on 2024-09-09T13:19:10Z
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Huh. Just ran it again and it's there

r-pascua commented on 2024-09-09T17:45:40Z
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weird

review-notebook-app · 2024-08-27T22:44:29Z

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r-pascua commented on 2024-08-27T22:44:29Z
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Line #1.    print("\n".join(str(f) for f in tempdir.iterdir()))

Maybe change this to sorted(tempdir.iterdir()) so it looks more sensible?

steven-murray commented on 2024-09-09T13:20:19Z
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DOne.

review-notebook-app · 2024-08-27T22:44:30Z

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r-pascua commented on 2024-08-27T22:44:29Z
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Line #1.    print("\n".join(str(f) for f in tempdir.iterdir() if str(f).endswith("files.uvh5")))

Same as previous comment

steven-murray commented on 2024-09-09T13:20:23Z
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Done

review-notebook-app · 2024-08-27T22:44:30Z

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r-pascua commented on 2024-08-27T22:44:30Z
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Maybe change the reflections to a bandpass, or make the reflection amplitude lower, since the 1%-level reflections are making the figure below look kind of insane.

steven-murray commented on 2024-09-09T13:21:43Z
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I set it to amp=1e-4

r-pascua commented on 2024-09-09T21:36:51Z
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Huh, looks like that didn't help much. Probably some annoying thing with a small set of observing times leading to the mock EoR component dominating the signal? Looks like this has been an issue for a while, so I suppose I'm fine with leaving it as-is.

steven-murray commented on 2024-09-10T10:30:17Z
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Yeah, something to dig into later if we need to.

review-notebook-app · 2024-08-27T22:44:32Z

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r-pascua commented on 2024-08-27T22:44:31Z
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Line #2.    import aipy

We're not using aipy anymore, are we?

steven-murray commented on 2024-09-09T13:24:44Z
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Not in general. I've swapped this out to use astropy.units.sday

review-notebook-app · 2024-08-27T22:44:32Z

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r-pascua commented on 2024-08-27T22:44:32Z
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Line #1.    uvtools.plot.labeled_waterfall(nos_jy, mode="log", freqs=fqs*1e9, lsts=lsts)

Can we restrict the dynamic range on this plot? Right now we have too much dynamic range, so it's very hard to see that there are noise fluctuations (it just looks kind of grainy). I think it's as simple as setting dynamic_range=3 in the call to labeled_waterfall.

steven-murray commented on 2024-09-09T13:27:15Z
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Done.

review-notebook-app · 2024-08-27T22:44:33Z

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r-pascua commented on 2024-08-27T22:44:33Z
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Looks like we lost the impulse and scatter RFI? I'm guessing that it's there, but the amplitude is too low.

steven-murray commented on 2024-09-09T14:32:35Z
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I can see it if I take the other RFI components away, so it is there. Their magnitude is so different that they don't show well in this plot. Plotting on log scale doesn't work either because most of the array is zero so it just bombs out.

r-pascua commented on 2024-09-09T21:39:01Z
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Gotcha. Thanks for checking!

steven-murray · 2024-09-09T12:55:13Z

Also a numpy 2 thing.

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steven-murray · 2024-09-09T13:08:30Z

OK, I tried some stuff out and it turns out that the differences are due to the original simulation having some negative real parts of the autos. When this is saved to file and re-read, the imaginary parts are forced to zero, and the real parts are made positive. Not sure what to do about that.

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steven-murray · 2024-09-09T13:11:48Z

I set it to 5-20 instead of 0.5-10. I think it looks pretty reasonable now.

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steven-murray · 2024-09-09T13:17:27Z

Good - fixed.

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steven-murray · 2024-09-09T13:19:11Z

Huh. Just ran it again and it's there

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steven-murray · 2024-09-09T13:20:20Z

DOne.

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steven-murray · 2024-09-09T13:20:24Z

Done

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steven-murray · 2024-09-09T13:21:44Z

I set it to amp=1e-4

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steven-murray · 2024-09-09T13:24:45Z

Not in general. I've swapped this out to use astropy.units.sday

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steven-murray · 2024-09-09T13:27:16Z

Done.

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steven-murray · 2024-09-09T14:32:36Z

I can see it if I take the other RFI components away, so it is there. Their magnitude is so different that they don't show well in this plot. Plotting on log scale doesn't work either because most of the array is zero so it just bombs out.

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steven-murray · 2024-09-09T14:33:57Z

Yup, good.

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steven-murray · 2024-09-09T14:36:01Z

Done

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steven-murray · 2024-09-09T14:36:07Z

Done

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r-pascua · 2024-09-09T17:45:41Z

weird

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Prior to this commit, any vis_filter keys provided when simulating an effect were not saved in the Simulator._components dictionary, so retrieving effects that were only applied to a subset of the array via Simulator.get would give incorrect results.

r-pascua · 2024-09-09T21:32:30Z

OK, my fix was pretty coarse: I just made it so that autocorrelations are modified via vis = np.abs(vis).astype(complex) in the hera_sim.eor.NoiselikeEoR.__call__ method. Figure it shouldn't be too much of an issue since I imagine this functionality really isn't used all that frequently.

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r-pascua · 2024-09-09T21:33:20Z

Fixed this issue. The Simulator just wasn't caching the baseline filters.

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r-pascua · 2024-09-09T21:36:52Z

Huh, looks like that didn't help much. Probably some annoying thing with a small set of observing times leading to the mock EoR component dominating the signal? Looks like this has been an issue for a while, so I suppose I'm fine with leaving it as-is.

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r-pascua · 2024-09-09T21:39:02Z

Gotcha. Thanks for checking!

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r-pascua · 2024-09-09T22:00:03Z

OK, I think I've fixed the last of the issues and removed debug things from the notebooks. @steven-murray please take one last look to ensure we didn't miss anything before merging!

steven-murray · 2024-09-10T10:29:35Z

That sounds fine to me

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steven-murray · 2024-09-10T10:30:18Z

Yeah, something to dig into later if we need to.

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steven-murray

All looks good now.

Made notebooks run with current hera_sim

2bc46f2

Updates for hera_sim_defaults

0ca55ce

steven-murray added 4 commits December 16, 2022 09:06

Merge branch 'main' into updated-notebooks

e6b5855

merge main

1a36168

docs: update all docs notebooks

c3f17ca

docs: updated hera_sim_tour

17b28e5

ci: install mpi4py properly

42a9a46

r-pascua reviewed Aug 27, 2024

View reviewed changes

docs: update docs form Bobby's comments

056caaa

r-pascua added 3 commits September 9, 2024 16:50

fix: make sure noiselike_eor is positive for autos

6813e6c

nb: fix issues with hera_sim_simulator tutorial

be6a9b2

nb: add some extra text to end-to-end Fig. 2

1bd2bc7

style: run ruff --check

b950bff

steven-murray approved these changes Sep 10, 2024

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steven-murray merged commit 91e1c4e into main Sep 10, 2024
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Made notebooks run with current hera_sim #238

Made notebooks run with current hera_sim #238

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