Gamma-ray packet source refactor #2546

andrewfullard · 2024-03-12T17:49:53Z

📝 Description

Type: 🎢 infrastructure

Refactors the gamma-ray packet creation to use a standard packet source-style setup.

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codecov · 2024-03-12T18:01:40Z

Codecov Report

Attention: Patch coverage is 21.89542% with 239 lines in your changes are missing coverage. Please review.

Project coverage is 66.77%. Comparing base (bf50d1e) to head (b1b3a9d).
Report is 4 commits behind head on master.

❗ Current head b1b3a9d differs from pull request most recent head d4ff4b8. Consider uploading reports for the commit d4ff4b8 to get more accurate results

Files	Patch %	Lines
tardis/energy_input/gamma_ray_packet_source.py	13.74%	182 Missing ⚠️
...energy_input/tests/test_gamma_ray_packet_source.py	36.36%	28 Missing ⚠️
tardis/energy_input/main_gamma_ray_loop.py	0.00%	15 Missing ⚠️
tardis/energy_input/GXPacket.py	15.38%	11 Missing ⚠️
tardis/energy_input/gamma_ray_transport.py	0.00%	1 Missing ⚠️
tardis/energy_input/samplers.py	0.00%	1 Missing ⚠️
tardis/montecarlo/montecarlo_numba/opacities.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2546      +/-   ##
==========================================
- Coverage   68.05%   66.77%   -1.29%     
==========================================
  Files         171      172       +1     
  Lines       14300    14453     +153     
==========================================
- Hits         9732     9651      -81     
- Misses       4568     4802     +234

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tardis/energy_input/gamma_ray_packet_source.py

tardis/energy_input/GXPacket.py

tardis/energy_input/gamma_ray_transport.py

tardis/energy_input/main_gamma_ray_loop.py

Radioactive packet source GXPacket collection Some initial methods

Creates a Packet collection with all necessary packet properties

tardis/energy_input/GXPacket.py

Knights-Templars · 2024-04-24T15:35:38Z

tardis/energy_input/GXPacket.py

+        self.nu_cmf = nu_cmf
+        self.status = status
+        self.shell = shell
+        self.time_current = time_current


What is time_current?

The current local time value of the packet, if there was a clock attached to it

Knights-Templars · 2024-04-24T15:37:55Z

tardis/energy_input/GXPacket.py

+        self.shell = shell
+        self.time_current = time_current
+        self.number_of_packets = len(self.energy_rf)
+        self.tau = -np.log(np.random.random(self.number_of_packets))


Is this tau same as the mean life of isotopes? Shall we give a separate name for this variable if this the optical depth?

Given that we are in a radiative transfer code, I think we should rename the mean lifetime instead

Knights-Templars · 2024-04-24T15:42:39Z

tardis/energy_input/gamma_packet_loop.py

@@ -289,9 +288,6 @@ def gamma_packet_loop(
                    energy_out[bin_index, time_index] += rest_energy / (


Instead of the energy_out, shall we dump the information into an array which which record the "escaping" packets information. That will help in getting the gamma-ray spectra in a post-processing step?

energy_out is such an array, but we can record more packet information if you want. I consider this out of scope for this PR though.

Knights-Templars · 2024-04-24T15:43:21Z

tardis/energy_input/gamma_packet_loop.py

@@ -322,7 +318,6 @@ def gamma_packet_loop(
        energy_plot_df_rows,
        energy_out,
        deposition_estimator,
-        packets_out,
        bin_width,


Do we need the bin_width as an output? WE can do that later in a post-processing step.

Probably not, but the blame said you added it. I can remove it, but it may be out of scope for this PR.

Knights-Templars · 2024-04-24T16:01:57Z

tardis/energy_input/gamma_ray_packet_source.py

+        nus_rf = np.zeros(number_of_packets)
+        nus_cmf = np.zeros(number_of_packets)
+        times = np.zeros(number_of_packets)
+        statuses = np.ones(number_of_packets, dtype=np.int64) * 3


Why it is multiplied by 3?

This is the default status of the packet. I will add a comment to clarify.

tardis/energy_input/gamma_ray_packet_source.py

Knights-Templars · 2024-04-24T16:03:27Z

tardis/energy_input/gamma_ray_packet_source.py

+        )
+
+        # get the time step index of the packets
+        initial_time_indexes = sampled_packets_df["time"]


time is an index of the data frame

They are actual times and not indices.

Okay. I think they would be more useful as indices instead of actual times. Times are useful for plotting but not much else in my opinion. I know I am probably referencing the index incorrectly regardless and will fix the code here.

tardis/energy_input/gamma_ray_packet_source.py

* First steps Radioactive packet source GXPacket collection Some initial methods * Add more methods to the packet source * Documentation, cleanup, positronium handling * Black formatting, cleanup * Fix kappa_calculation import loop * Working packet source Creates a Packet collection with all necessary packet properties * Positron deposition and packet tracker arrays * Fix parents dict * Result now mostly consistent with master * Fix kappa calculation test * Adds missing docstring for calculate_energy_factors * Fix util tests and black * Testing skeleton for packet source * black tests * Address comments * Beginnings of an alternate packet source for the dataframe * Possible deposition fix, import fixes * Added old functions * Cleanup, comments, and more dataframe sampling setup * Corrected packet time computation * Modified sampling to use positron information * Remove packet sampling call and replace with dataframe method * Update method call to match current usage * Comment responses * More comments, improve packet dataframe index handling --------- Co-authored-by: Knights-Templars <[email protected]>

andrewfullard added nebular restructure labels Mar 12, 2024

andrewfullard requested review from wkerzendorf and Knights-Templars March 12, 2024 17:49

andrewfullard self-assigned this Mar 12, 2024

andrewfullard changed the title ~~First steps~~ Gamma-ray packet source refactor Mar 12, 2024

Knights-Templars reviewed Mar 13, 2024

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andrewfullard requested a review from Knights-Templars March 27, 2024 19:29

andrewfullard marked this pull request as ready for review March 27, 2024 19:29

Knights-Templars reviewed Mar 29, 2024

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andrewfullard force-pushed the gamma-packet-source branch from 329e557 to 7ad25a0 Compare April 3, 2024 19:06

andrewfullard added 15 commits April 22, 2024 16:07

First steps

5b3351a

Radioactive packet source GXPacket collection Some initial methods

Add more methods to the packet source

14f81c8

Documentation, cleanup, positronium handling

c135284

Black formatting, cleanup

ddd2c23

Fix kappa_calculation import loop

4055329

Working packet source

f1edb89

Creates a Packet collection with all necessary packet properties

Positron deposition and packet tracker arrays

4a0624d

Fix parents dict

72148c1

Result now mostly consistent with master

70a0dfe

Fix kappa calculation test

2ee34f5

Adds missing docstring for calculate_energy_factors

485157a

Fix util tests and black

2ead93b

Testing skeleton for packet source

cdb3b10

black tests

ac403be

Address comments

88e9023

andrewfullard and others added 6 commits April 22, 2024 16:07

Beginnings of an alternate packet source for the dataframe

45b0c34

Possible deposition fix, import fixes

0e9149a

Added old functions

0555b22

Cleanup, comments, and more dataframe sampling setup

4f66494

Corrected packet time computation

33213d6

Modified sampling to use positron information

cc27c05

andrewfullard force-pushed the gamma-packet-source branch from ddb64ca to cc27c05 Compare April 22, 2024 20:07

andrewfullard added 2 commits April 22, 2024 16:15

Remove packet sampling call and replace with dataframe method

4dd6bc6

Update method call to match current usage

0576977

andrewfullard requested a review from Knights-Templars April 22, 2024 20:41

Knights-Templars reviewed Apr 24, 2024

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tardis/energy_input/GXPacket.py Show resolved Hide resolved

Knights-Templars reviewed Apr 24, 2024

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tardis/energy_input/gamma_ray_packet_source.py Outdated Show resolved Hide resolved

Knights-Templars reviewed Apr 24, 2024

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Comment responses

25804e3

Knights-Templars reviewed Apr 24, 2024

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tardis/energy_input/gamma_ray_packet_source.py Show resolved Hide resolved

More comments, improve packet dataframe index handling

d4ff4b8

Knights-Templars approved these changes Apr 24, 2024

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andrewfullard merged commit b8788a1 into tardis-sn:master Apr 24, 2024
8 of 9 checks passed

andrewfullard mentioned this pull request Apr 24, 2024

Fixed the broken import modules in main gamma ray loop. #2591

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Gamma-ray packet source refactor #2546

Gamma-ray packet source refactor #2546

andrewfullard commented Mar 12, 2024

codecov bot commented Mar 12, 2024 •

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Knights-Templars Apr 24, 2024

andrewfullard Apr 24, 2024

		@@ -289,9 +288,6 @@ def gamma_packet_loop(
		energy_out[bin_index, time_index] += rest_energy / (

Gamma-ray packet source refactor #2546

Gamma-ray packet source refactor #2546

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andrewfullard commented Mar 12, 2024

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codecov bot commented Mar 12, 2024 •

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