Absorption with cubepy #133

pawel21 · 2023-01-10T18:13:29Z

Hi,

I have created PR for my modification of code for absorption using cubepy.
I added example notebook in agnpy/docs/tutorials

…sorption_with_cubepy

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pawel21 · 2023-03-12T02:38:08Z

@cosimoNigro @jsitarek could you look on my PR? :)

cosimoNigro · 2023-03-19T18:50:13Z

I will @pawel21, sorry for the delay. I had little time in general and an issue to fix before this PR.
Will try in the next two weeks.

agnpy/absorption/absorption.py

docs/tutorials/absorption_in_BLR_with_cubepy.ipynb

jsitarek · 2023-03-31T15:35:06Z

docs/tutorials/absorption_in_BLR_with_cubepy.ipynb

+   "source": [
+    "SUM_RATIO_LINES_BLR = 30.652\n",
+    "\n",
+    "def get_absor_blrs(E, L_disk, R_line, r_blob_bh, z):\n",


this function would be useful to be included in the main code of agnpy
XI_LINE and eps_abs should be then among the function parameters

jsitarek · 2023-03-31T15:40:18Z

sorry for a very late feedback on this
@pawel21 - I left a few comments on the PR
@cosimoNigro - how do you prefer to proceed - should this function substitute the current integration? or should it be added as a separate function (like Paweł did now)? In the latter case a test comparing the two methods should be added.
The former case might be more reasonable, because this method is more precise and do not have those crazy memore requirements of the standard integration scheme.

…sorption_with_cubepy

jsitarek · 2023-07-06T09:15:24Z

digging through my old e-mails I realized that this PR is still pending.
@pawel21 I think that still 2 of my comments are not implemented/responded
@cosimoNigro any feedback about the general implementation and relation to the older code?

cosimoNigro · 2023-07-10T08:05:22Z

Sorry for letting it slip, will do the review later today.

cosimoNigro

Thanks a lot for your work @pawel21, and apologies again if I got disconnected and took a while to review it.

I think once you fix mine and @jsitarek's comments we can merge it in.
Discussing how to handle the general approach towards integration (e.g. allowing to choose between trapezoidal and adaptive integration) is something we should discuss together at a certain point in the future, along with the re-organisation of the package, not in this PR.

agnpy/absorption/absorption.py

docs/tutorials/absorption_in_BLR_with_cubepy.ipynb

cosimoNigro · 2023-07-16T16:34:18Z

Another thing that is missing is an absorption function returning the actual attenuation factor in the cubepy case, now only tau is computed.

…sorption_with_cubepy

jsitarek · 2024-10-03T01:00:30Z

Hi @pgliwny
The automatic CI checks fail:

FAILED agnpy/fit/tests/test_fit.py::TestFit::test_mrk_421_fit - IndexError: boolean index did not match indexed array along dimension 2; dimension is 1 but corresponding boolean dimension is 9
FAILED agnpy/fit/tests/test_fit.py::TestFit::test_pks_1510_fit - ValueError: non-broadcastable output operand with shape (6,1,1) doesn't match the broadcast shape (6,1,6)

maybe your PR changed something in the API

EDIT: I had a deeper look and the new code does not modify any of the existing functions so it should not be the reason for the fail of the tests.

agnpy/absorption/absorption.py

jsitarek · 2024-10-03T01:26:50Z

agnpy/absorption/absorption.py

+            **note** these are observed frequencies (observer frame)
+        z : float
+            redshift of the source
+        mu_s : float


I think this function is following evaluate_tau_blr that is only valid for mu_s=1 (otherwise integration over path of the photon and over the distance from the black hole is not equivalent), so it should not have it as a parameter (@cosimoNigro can you also have a look at this?)

agnpy/absorption/absorption.py

jsitarek · 2024-10-03T01:38:29Z

agnpy/absorption/absorption.py

+        XI_TARGET_LINE = self.target.xi_line
+        tau_z_all = np.zeros(nu.shape)
+
+        blr_shells = dict()


why do you define those dictionaries? I guess it is a remnant of a script where you were also plotting the effect of individual lines, but this is either way not possible this function.

here you are using the dictionaries only to sum up over all the lines, so you could instead created SphericalShellBLR and Absorption as temporary variables directly in the for loop

agnpy/absorption/absorption.py

agnpy/absorption/tests/test_absorption.py

jsitarek

I left some comments. In particular the test should be rewritten.

jsitarek · 2024-12-23T12:59:59Z

agnpy/absorption/absorption.py

+
+    def tau_blr_lines_cubepy(self, nu, lines_list, eps_abs=1e-6):
+        """
+        Calculate the absorption in all available BLR (Broad Line Region) shells.


"all available BLR shells" is a copy paste from the original function, better write "multiple BLR ..." or something like this since now you specify exaclty the list of lines to consider

it is still written "all available BLR shells"

jsitarek · 2024-12-23T13:04:34Z

agnpy/absorption/absorption.py

+             Optical depth values corresponding to the input frequencies.
+        """
+
+        sum_ratio_lines = sum(lines_dictionary[line]['L_Hbeta_ratio'] for line in lines_list)


you need to introduce a check or even better throw an exception if any of the requested line is not in lines_dictionary.keys()

I do not see the check

agnpy/absorption/absorption.py

codecov · 2025-01-21T15:14:24Z

Codecov Report

Attention: Patch coverage is 82.05128% with 14 lines in your changes missing coverage. Please review.

Project coverage is 96.80%. Comparing base (506c038) to head (a2b1aaf).

Files with missing lines	Patch %	Lines
agnpy/absorption/absorption.py	67.44%	14 Missing ⚠️

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@@            Coverage Diff             @@
##           master     #133      +/-   ##
==========================================
- Coverage   97.13%   96.80%   -0.34%     
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  Files          42       42              
  Lines        3459     3535      +76     
==========================================
+ Hits         3360     3422      +62     
- Misses         99      113      +14

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…gnpy into absorption_with_cubepy

jsitarek · 2025-08-20T08:04:01Z

agnpy/absorption/tests/test_absorption.py

+        nu = E.to("Hz", equivalencies=u.spectral())
+        tau_blr = abs_blr.tau(nu)
+        tau_blr_cubepy = abs_blr.tau_blr_cubepy(nu, eps_abs=1e-3)
+        assert np.allclose(tau_blr, tau_blr_cubepy, rtol=1e-1, atol=1e-1)


have you checked what are the tau values obtained in this case? It might happen that there is very little absorption with tau << 1 and then the test will pass always even if the two numbers are far from one another because of atol.

jsitarek · 2025-08-20T08:08:35Z

agnpy/absorption/absorption.py

+            radius of the BLR spherical shell
+        r : :class:`~astropy.units.Quantity`
+            distance between the Broad Line Region and the blob
+        mu, phi : :class:`~numpy.ndarray`


those two are not in the list of parameters

jsitarek · 2025-08-20T08:09:03Z

agnpy/absorption/absorption.py

+        # set boundary for integration
+        low = np.array(
+            [
+                [min(mu_to_integrate)],


the integration of mu and phi should be simply -1 to 1 and 0 to 2 pi.

jsitarek · 2025-08-20T08:14:18Z

agnpy/absorption/tests/test_absorption.py

        # requires a 10% deviation from the two SED points
        assert check_deviation(nu, tau_dt, tau_ps_dt, 0.1)

+    def test_abs_blr_cubepy(self):


now that you added test_tau_accuracy_standard_vs_cubepy this test does not seem to add anything to it, so I think you can remove test_abs_blr_cubepy

pawel21 added 8 commits November 26, 2021 15:56

Merge branch 'pylint_and_flake8' of https://github.com/cosimoNigro/agnpy

9bfc005

Merge branch 'master' of https://github.com/cosimoNigro/agnpy

3bb4a33

calcurate absorption using cubepy

a23cab0

add set up error to integrate

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iterate freq to compute tau_blr

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Merge branch 'master' of https://github.com/cosimoNigro/agnpy into ab…

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…sorption_with_cubepy

Merge branch 'master' of https://github.com/cosimoNigro/agnpy into ab…

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…sorption_with_cubepy

add notebook with absorption in BLR with cubepy

bcd1888

jsitarek requested changes Mar 31, 2023

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pawel21 added 5 commits April 6, 2023 14:39

Merge branch 'master' of https://github.com/cosimoNigro/agnpy into ab…

ffdecbe

…sorption_with_cubepy

remove l_size

403a0bb

start develop funtion to calcurate absorption over all line for BLR

c0b6cfa

added fun to calculate absorption in all BLR lines

8e21ba8

nodified notebook to new function

57d67bc

cosimoNigro reviewed Jul 16, 2023

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pawel21 added 7 commits April 26, 2024 16:07

add test for absorption in BLR with cubepy

7039b98

remove not used parameters

dd28724

Add more clear explanations for docs string about calc tau in BLR

92eb17b

Add function to compute inegrand for cubepy

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Merge branch 'master' of https://github.com/cosimoNigro/agnpy into ab…

d5b4778

…sorption_with_cubepy

Add environment dependencies for cubepy

a81e789

Fix environment dependencies

eeed0a9

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pawel21 added 2 commits October 9, 2024 16:58

make code more concise and renamed function

ede4818

add unit in doc and add tau_blr_lines_cubepy_function

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pawel21 added 2 commits January 21, 2025 15:56

Merge branch 'master' into absorption_with_cubepy

ea38e31

improved docs description

af96f66

pawel21 added 6 commits January 22, 2025 17:25

start write test for compare tau blr standard with cubepy

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test

1ca2ef9

Merge branch 'absorption_with_cubepy' of https://github.com/pawel21/a…

9cd77ea

…gnpy into absorption_with_cubepy

add test for tau calcuration with standard and cubepy method

fe80a75

remove function for all lines and remove unnecessary objects

d9584a8

pass line_dict.keys() as default argument

a2b1aaf

jsitarek reviewed Aug 20, 2025

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Absorption with cubepy #133

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Absorption with cubepy #133

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