Add sdec visualisation notebook

[KasukabeDefenceForce]

📝 Description

Type: 🪲 bugfix | 🚀 feature | ☣️ breaking change | 🚦 testing | 📝 documentation | 🎢 infrastructure

This PR aims at adding a notebook which analyses the sdec data and provides a simple way to plot that data

Also, link issues affected by this pull request by using the keywords: close, closes, closed, fix, fixes, fixed, resolve, resolves or resolved.

📌 Resources

Examples, notebooks, and links to useful references.

🚦 Testing

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☑️ Checklist

• I requested two reviewers for this pull request
• I updated the documentation according to my changes
• I built the documentation by applying the build_docs label

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[tardis-bot]

*beep* *bop*
Hi human,
I ran ruff on the latest commit (4eb4d30).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

7	W291  	[*] Trailing whitespace
6	W293  	[*] Blank line contains whitespace
4	E999  	[ ] SyntaxError: Expected a statement
2	RET506	[ ] Unnecessary `else` after `raise` statement

Complete output(might be large):

docs/analysing_tardis_outputs/index.rst:1:1: E999 SyntaxError: Expected an expression
docs/analysing_tardis_outputs/index.rst:12:1: W293 [*] Blank line contains whitespace
docs/analysing_tardis_outputs/spectrum/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/analysing_tardis_outputs/spectrum/index.rst:7:1: W293 [*] Blank line contains whitespace
docs/analysing_tardis_outputs/spectrum/sdec_notebook.ipynb:cell 20:6:67: W291 [*] Trailing whitespace
docs/analysing_tardis_outputs/visualization/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/analysing_tardis_outputs/visualization/index.rst:25:1: W293 [*] Blank line contains whitespace
docs/index.rst:1:1: E999 SyntaxError: Expected a statement
docs/index.rst:21:51: W291 [*] Trailing whitespace
docs/index.rst:43:76: W291 [*] Trailing whitespace
docs/index.rst:44:64: W291 [*] Trailing whitespace
docs/index.rst:45:71: W291 [*] Trailing whitespace
docs/index.rst:46:69: W291 [*] Trailing whitespace
docs/index.rst:47:68: W291 [*] Trailing whitespace
docs/index.rst:66:1: W293 [*] Blank line contains whitespace
docs/index.rst:88:1: W293 [*] Blank line contains whitespace
docs/index.rst:112:1: W293 [*] Blank line contains whitespace
tardis/visualization/sdec/util.py:115:9: RET506 Unnecessary `else` after `raise` statement
tardis/visualization/sdec/util.py:273:9: RET506 Unnecessary `else` after `raise` statement
Found 19 errors.
[*] 13 fixable with the `--fix` option.

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 96 lines in your changes missing coverage. Please review.

Project coverage is 68.76%. Comparing base (cec8b53) to head (4eb4d30).

Files with missing lines	Patch %	Lines
tardis/visualization/sdec/util.py	0.00%	96 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2968      +/-   ##
==========================================
- Coverage   69.52%   68.76%   -0.76%     
==========================================
  Files         228      229       +1     
  Lines       16429    16525      +96     
==========================================
- Hits        11422    11364      -58     
- Misses       5007     5161     +154     

☔ View full report in Codecov by Sentry.
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[tardis-bot]

*beep* *bop*

Hi, human.

The docs workflow has succeeded ✔️

Click here to see your results.

[tardis-bot]

*beep* *bop*
Hi human,
I ran benchmarks as you asked comparing master (cec8b53) and the latest commit (4eb4d30).
Here are the logs produced by ASV.
Results can also be downloaded as artifacts here.

Significantly changed benchmarks:

All benchmarks:

Benchmarks that have stayed the same:

| Change   | Before [cec8b531] <master>   | After [4eb4d307]    | Ratio   | Benchmark (Parameter)                                                                                                               |
|----------|------------------------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------|
|          | 1.27±0.4μs                   | 1.66±0.4μs          | ~1.31   | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_line                    |
|          | 1.82±0.9μs                   | 2.28±1μs            | ~1.25   | transport_montecarlo_estimators_radfield_estimator_calcs.BenchmarkMontecarloMontecarloNumbaPacket.time_update_line_estimators       |
|          | 5.68±1μs                     | 6.54±1μs            | ~1.15   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket                                           |
|          | 7.39±2μs                     | 8.39±2μs            | ~1.13   | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_volley                                    |
|          | 57.2±20μs                    | 46.1±30μs           | ~0.81   | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_scatter                                          |
|          | 5.49±0.9ms                   | 3.88±0ms            | ~0.71   | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('macroatom')                                   |
|          | 3.27±0.4μs                   | 3.55±0.3μs          | 1.09    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_bad_vpacket                                       |
|          | 561±200ns                    | 591±100ns           | 1.05    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_photoabsorption_opacity_calculation                              |
|          | 541±200ns                    | 561±200ns           | 1.04    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_pair_creation_opacity_calculation                                |
|          | 1.19±0μs                     | 1.23±0μs            | 1.03    | transport_geometry_calculate_distances.BenchmarkTransportGeometryCalculateDistances.time_calculate_distance_boundary                |
|          | 732±0.4ns                    | 751±0.8ns           | 1.03    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_thomson_scatter                                       |
|          | 1.67±0.01ms                  | 1.72±0.01ms         | 1.03    | transport_montecarlo_main_loop.BenchmarkTransportMontecarloMontecarloMainLoop.time_montecarlo_main_loop                             |
|          | 2.62±0.5ms                   | 2.70±0.5ms          | 1.03    | transport_montecarlo_single_packet_loop.BenchmarkTransportMontecarloSinglePacketLoop.time_single_packet_loop                        |
|          | 1.03±0m                      | 1.05±0m             | 1.01    | run_tardis.BenchmarkRunTardis.time_run_tardis_rpacket_tracking                                                                      |
|          | 204±0.07ns                   | 206±0.4ns           | 1.01    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_intensity_black_body                                       |
|          | 40.8±10μs                    | 41.1±20μs           | 1.01    | transport_montecarlo_interaction.BenchmarkTransportMontecarloInteraction.time_line_emission                                         |
|          | 20.6±5μs                     | 20.8±5μs            | 1.01    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_last_interaction_tracker_list |
|          | 38.8±0.01μs                  | 39.0±0.09μs         | 1.01    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_generate_rpacket_tracker_list                  |
|          | 38.4±0.08s                   | 38.5±0.2s           | 1.00    | run_tardis.BenchmarkRunTardis.time_run_tardis                                                                                       |
|          | 2.09±0m                      | 2.09±0m             | 1.00    | spectrum_formal_integral.BenchmarkTransportMontecarloFormalIntegral.time_FormalIntegrator_functions                                 |
|          | 62.6±0.1ms                   | 62.8±0.06ms         | 1.00    | transport_montecarlo_packet_trackers.BenchmarkTransportMontecarloPacketTrackers.time_rpacket_trackers_to_dataframe                  |
|          | 551±200ns                    | 511±100ns           | 0.93    | opacities_opacity.BenchmarkMontecarloMontecarloNumbaOpacities.time_compton_opacity_calculation                                      |
|          | 3.73±0.4μs                   | 3.46±0.9μs          | 0.93    | transport_montecarlo_vpacket.BenchmarkMontecarloMontecarloNumbaVpacket.time_trace_vpacket_within_shell                              |
|          | 2.72±0.05ms                  | 2.50±0.01ms         | 0.92    | opacities_opacity_state.BenchmarkOpacitiesOpacityState.time_opacity_state_initialize('scatter')                                     |

If you want to see the graph of the results, you can check it here