Miscellaneous fixes following initial science validation comments.

[schlafly]

This PR makes a few changes following RTB comments.

I have added an additional sentence describing how maggies are converted into photons to the bandpass page at readthedocs.

The romanisim truncation support was half-baked and didn't propagate through to the places it needed to; this has been fixed.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.94%. Comparing base (0a1aac5) to head (1b2ffb4).
Report is 63 commits behind head on main.

Additional details and impacted files

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##             main     #131      +/-   ##
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+ Coverage   90.78%   90.94%   +0.15%     
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  Files          17       17              
  Lines        1671     1700      +29     
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+ Hits         1517     1546      +29     
  Misses        154      154              

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[schlafly]

@AndreaBellini, I think this addresses your requested doc change.

@ojustino, thanks for noticing the issue with the read_pattern not being correctly propagated through in the truncated case. Please see if this addresses your issue.

[PaulHuwe]

LGTM

[ojustino]

Hi @schlafly, no problem, and thanks for making these fixes. The read_pattern-related additions make sense to me, and a quick check with my validation code now shows truncation working as intended.

[schlafly]

Thanks Justin. @AndreaBellini, if the addition to the bandpass docs here
https://romanisim--131.org.readthedocs.build/en/131/romanisim/bandpass.html
addresses your concerns, I'll go ahead and merge this.

[AndreaBellini]

Hi Eddie, I’m currently on travel with (at the mint) intermittent internet connection. Thanks for adding extra information. The text mentions photons, but there is no mention of DN and DN/s, which are the units in L1 and L2 data. Unless I missed it, the text does not tell the user how to convert from DN/s to AB mag. Cheers, Andrea

…

--- Dr. Andrea Bellini Space Telescope Science Institute 3700 San Martin Drive Baltimore MD 21210 Tel: +1 410 338 4431 On Jul 11, 2024, at 17:08, Eddie Schlafly ***@***.***> wrote:  Thanks Justin. @AndreaBellini<https://urldefense.com/v3/__https://github.com/AndreaBellini__;!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!00UYy-MDIBvWqZ-DRtJ9ERoMZxkepcTviClwHeRFp55MnxXX5YSqUaAjUzvkhQnG1P2hrVX0e5rZ_kB7R2gDo6Dz$>, if the addition to the bandpass docs here https://romanisim--131.org.readthedocs.build/en/131/romanisim/bandpass.html<https://urldefense.com/v3/__https://romanisim--131.org.readthedocs.build/en/131/romanisim/bandpass.html__;!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!00UYy-MDIBvWqZ-DRtJ9ERoMZxkepcTviClwHeRFp55MnxXX5YSqUaAjUzvkhQnG1P2hrVX0e5rZ_kB7R8w0eEEP$> addresses your concerns, I'll go ahead and merge this. — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/spacetelescope/romanisim/pull/131*issuecomment-2223189127__;Iw!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!00UYy-MDIBvWqZ-DRtJ9ERoMZxkepcTviClwHeRFp55MnxXX5YSqUaAjUzvkhQnG1P2hrVX0e5rZ_kB7R6z3oGhG$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AE37OQQ5SVR3BAUORT5H3IDZL2NXVAVCNFSM6AAAAABKKICCRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRTGE4DSMJSG4__;!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!00UYy-MDIBvWqZ-DRtJ9ERoMZxkepcTviClwHeRFp55MnxXX5YSqUaAjUzvkhQnG1P2hrVX0e5rZ_kB7R7uHn27B$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[schlafly]

Thanks Andrea. I've now added a section to the L1 page that has the conversion from photons to DN via the gain.
https://romanisim--131.org.readthedocs.build/en/131/romanisim/l1.html#gain

[AndreaBellini]

Hi Eddie, please double check what is currently meant by “photons” then. The gain is only used to convert electrons to DNs. Are you sure you mean photons and not electrons? If you really mean photons, then there is a further conversion factor that depends on the wavelength of the photons for shortish wavelengths. I think I read somewhere that the average for Roman is 4,7 electrons per photons, but I might be wrong. Cheers, Andrea

…

--- Dr. Andrea Bellini Space Telescope Science Institute 3700 San Martin Drive Baltimore MD 21210 Tel: +1 410 338 4431 On Jul 11, 2024, at 20:33, Eddie Schlafly ***@***.***> wrote:  Thanks Andrea. I've now added a section to the L1 page that has the conversion from photons to DN via the gain. https://romanisim--131.org.readthedocs.build/en/131/romanisim/l1.html#gain<https://urldefense.com/v3/__https://romanisim--131.org.readthedocs.build/en/131/romanisim/l1.html*gain__;Iw!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!2Ryk7W9oWQX7d0q3UJGtHXKqlXVicbBswv-rLMupG5eKcDXAzNGyKWqf_oFhJWMBxwZFr_YByTL_SeLKCxUjPImV$> — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/spacetelescope/romanisim/pull/131*issuecomment-2223632250__;Iw!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!2Ryk7W9oWQX7d0q3UJGtHXKqlXVicbBswv-rLMupG5eKcDXAzNGyKWqf_oFhJWMBxwZFr_YByTL_SeLKC7nLwOea$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AE37OQVCJY7ZYQNPL5KIK7DZL3FY3AVCNFSM6AAAAABKKICCRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRTGYZTEMRVGA__;!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!2Ryk7W9oWQX7d0q3UJGtHXKqlXVicbBswv-rLMupG5eKcDXAzNGyKWqf_oFhJWMBxwZFr_YByTL_SeLKC1kSRqm2$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[schlafly]

We are currently treating the system as if a photon generates an electron. Yes, if there's an additional level in the chain from DN to photons, it's not presently included; can you point me to some documentation?

[schlafly]

This paper finds quantum yields peaking at 1.05 at 550 nm, with an average in the F062 band of probably around 1.03.
https://iopscience.iop.org/article/10.1088/1538-3873/ac46ba#paspac46baf7
In other bands they find ~1.003%. That's certainly an effect I'm neglecting, assuming a quantum yield of 1. The fact that the quantum yields are not exactly one means to me that there's some ~imprecision in the notion of gain and ramp fitting; when we pretend that the electrons are Poisson distributed, in fact they have some slightly more complex distribution. It doesn't seem to me that this is an effect that we should be simulating at this stage---we certainly don't have requirements about modeling quantum yields, etc..

Is this in fact the effect you're concerned about here?

[AndreaBellini]

Hi Eddie, I’m ok if you assume 1 photon = 1 electron if it is supported in the literature. Just add this information in the documentation and, as far as I am concerned, go ahead and merge the pull request. Thank you for adding all of this into the documentation. Roman I-Sim will certainly benefit from it. Cheers, Andrea

…

--- Dr. Andrea Bellini Space Telescope Science Institute 3700 San Martin Drive Baltimore MD 21210 Tel: +1 410 338 4431 On Jul 12, 2024, at 18:07, Eddie Schlafly ***@***.***> wrote:  This paper finds quantum yields peaking at 1.05 at 550 nm, with an average in the F062 band of probably around 1.03. https://iopscience.iop.org/article/10.1088/1538-3873/ac46ba#paspac46baf7<https://urldefense.com/v3/__https://iopscience.iop.org/article/10.1088/1538-3873/ac46ba*paspac46baf7__;Iw!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!3zr0xbnNEUUFtFbNkRnA0QiC0DRyeyUYrZY7y4nQ5NNNfMdKhXvP33gHfKXHyuketJ69ePanMZrpJQJ6_sms4TJm$> In other bands they find ~1.003%. That's certainly an effect I'm neglecting, assuming a quantum yield of 1. The fact that the quantum yields are not exactly one means to me that there's some ~imprecision in the notion of gain and ramp fitting; when we pretend that the electrons are Poisson distributed, in fact they have some slightly more complex distribution. It doesn't seem to me that this is an effect that we should be simulating at this stage---we certainly don't have requirements about modeling quantum yields, etc.. Is this in fact the effect you're concerned about here? — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/spacetelescope/romanisim/pull/131*issuecomment-2225896423__;Iw!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!3zr0xbnNEUUFtFbNkRnA0QiC0DRyeyUYrZY7y4nQ5NNNfMdKhXvP33gHfKXHyuketJ69ePanMZrpJQJ6_huuPZyX$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AE37OQQBRF5SUH7B6QJZ5RLZL75NTAVCNFSM6AAAAABKKICCRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRVHA4TMNBSGM__;!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!3zr0xbnNEUUFtFbNkRnA0QiC0DRyeyUYrZY7y4nQ5NNNfMdKhXvP33gHfKXHyuketJ69ePanMZrpJQJ6_hNrgzBi$>. You are receiving this because you were mentioned.Message ID: ***@***.***>