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Adding a NV plugin (hitlet simulator) #292

Merged
merged 128 commits into from
Feb 13, 2025
Merged

Adding a NV plugin (hitlet simulator) #292

merged 128 commits into from
Feb 13, 2025

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Before you submit this PR: make sure to put all XENONnT specific information in a wiki-note as the repo is publicly accessible

What does the code in this PR do / what does it improve?

Can you briefly describe how it works?

Can you give a minimal working example (or illustrate with a figure)?

Please include the following if applicable:

  • Update the docstring(s)
  • Bump plugin version(s)
  • Update the documentation
  • Tests to check the (new) code is working as desired.
  • Does it solve one of the GitHub open issues?

HenningSE and others added 30 commits January 24, 2024 16:22
@HenningSE @ramirezdiego
Refactor pmt_transit_time_spread V2 (#93)
75df0ef 
* Remove unused WFSim functions

* Refactor pmt_transit_time_spread

* Keep only photons with positive photon_gain

---------

Co-authored-by: Diego Ramírez García <[email protected]>
@dachengx
Add pytest GitHub action (#104)
5cc78d3 
* Add pytest GitHub action

* Minor debug

* Use poetry

* Not really poetry

* Add straxen in dependencies

* Add scikit-learn to pyproject.toml

* Also update a bit of .gitignore

* Install nestpy 2.0.1 following XENONnT/montecarlo_environment#8

* Try https://stackoverflow.com/a/77575403/16515081

* Change directory

* Update actions version

* Debug for nestpy installation

* Use numpy.testing to test arrays with different length

* Minor change of a warning

* Combine warnings

* Add tearDown to remove temp folder after each test function

* Use root file provided in XENONnT/private_nt_aux_files#299

* Patch secret file like straxen

* Add create_readonly_utilix_config.sh

* Check the downloaded file

* Debug

* Add timeout, copied from 47bc007

* Add timeout_decorator
@HenningSE @dachengx
Add fuse base plugins to reduce duplicate code (#112)
0861489 
* Add fuseBasePlugin and fuseBaseDownChunkingPlugin

* update volume and merger plugins

* Update microphysics plugins

* update detectorphysics plugins

* update waveform building plugins

* loosen save_when for Volume and Merger Plugins

* Try to set the nestpy random seed in compute function

* Set a timeout for the tests

* Increase timeout for deterministic seed tests

* Longer timeout

* Use CamelCase for base plugins

* Bugfix

* Disable st.make in tests for secondary plugin output

* Increase timeout for fullchain tests

* Lock and Unlock the nestpy random seed

* remove unnecessary setup functions

* multi class inheritance for FuseBaseDownChunkingPlugin

* remove duplicate code

* Bump version: 0.2.5 → 0.3.0

---------

Co-authored-by: dachengx <[email protected]>
@dachengx
Add timeout for the action (#113)
8240715 
* Add timeout for the action
* Shorten timelimit to 15min
@dachengx
Only install fuse (#114)
1dd603e
@dachengx
Use poetry to install the package (#115)
e228974
@dachengx @ramirezdiego
Use numba.typed.List to fix a deprecation (#116)
eae20ed 
Co-authored-by: Diego Ramírez García <[email protected]>
@dachengx @ramirezdiego
Faster horizontal shift calculation (#117)
1f601d0 
Co-authored-by: Diego Ramírez García <[email protected]>
@ramirezdiego @HenningSE
Update installation instructions (#120)
9f9cca1 
* Small update to the readme
* Minor update
* Development status alpha

---------

Co-authored-by: Henning Schulze Eißing <[email protected]>
@HenningSE
Binomial process for CIV and removal of Pandas in find_cluster (#119)
cae2564 
* Binomial process for CIV

* Remove Pandas from _find_cluster()
@ramirezdiego
Change name for pypi build
dd201bf
@ramirezdiego @HenningSE
PyPI build (#121)
e62c2d0 
* Update README with pypi badge

* Create python_publish.yml


---------

Co-authored-by: Henning Schulze Eißing <[email protected]>
@HenningSE @ramirezdiego
Release 1.0.0 (#122)
57a064f 
* Update README for release

* Update README.md

* Update HISTORY.md for the release

* Bump version: 0.3.1 → 1.0.0

---------

Co-authored-by: ramirezdiego <[email protected]>
@dachengx
Simplify pytest and coveralls to shorten time usage (#123)
7f4eb42 
* Simplify the pytest and coveralls to shorten the time usage

* Run only coveralls
@mhliu0001 @HenningSE
Some code improvements for better performance (#125)
e6aea36 
* Minor fixes

* Minor improvements for code style & performance

* Remove useless comments

* bump plugin versions

---------

Co-authored-by: Henning Schulze Eißing <[email protected]>
@HenningSE @ramirezdiego
Bring the documentation to readthedocs (#124)
6e98efc 
* Update documentation so it can be displayed at readthedocs

* Update plugin versions as the dtype was changed

---------

Co-authored-by: Diego Ramírez García <[email protected]>
@ramirezdiego @HenningSE
Add missing badges and tests (#127)
0c7736a 
* Update testing batch

* Docs badge

* Fix link of testing badge

* Add again test_plugin_versions_in_doc.py

Using @dachengx's trick to solve the testing issues

* S2PhotonPropagation plugin update

* Update MicrophysicsSummary.rst

* Rename MicrophysicsSummary.rst to MicroPhysicsSummary.rst

* Update s1_photon_propagation version

* Bufix

---------

Co-authored-by: Henning Schulze Eißing <[email protected]>
@HenningSE
Save electric field as float16 instead of int64 (#133)
82eed8f
@HenningSE @ramirezdiego
CSV input plugin update (#132)
85a2f5c 
* Update dtype of ChunkCsvInput

* Add test for csv input

---------

Co-authored-by: Diego Ramírez García <[email protected]>
@HenningSE
Change electric field dtype to float32 (#135)
36f3308 
* Save electric field as float16 instead of int64

* Change electric field dtype to float32

* Change missing dtypes

---------

Co-authored-by: Henning Schulze Eißing <[email protected]>
@HenningSE @KaraMelih
Fix csv timing (#137)
838c072 
* Fix csv timing

* fix cm->mm add comments

---------

Co-authored-by: KaraMelih <[email protected]>
@HenningSE
No rechunking for microphysics summary & e_field NaNs to zero (#140)
002b91f 
* no rechunking for microphysics summary

* remove nan field values
@cfuselli @ramirezdiego
Increase size of string fields in geant4_interactions (#142)
f5558cb 
* Increase size of string fields in geant4_interactions

---------

Co-authored-by: Diego Ramírez García <[email protected]>
@sebvetter
Changed place of exit condition for no S1s to avoid locking nest rnd …
7c17b65 
…seed
@sebvetter
Merge pull request #146 from XENONnT/issue145
a9dc17a 
Prevent empty instructions to lock NEST random seed
@HenningSE @ramirezdiego
Handle missing corrections_version and cleanup (#143)
05a5e9e 
* Raise error when corrections_version is missing

* remove unnecessary parentheses

* bugfix

---------

Co-authored-by: Diego Ramírez García <[email protected]>
@HenningSE @dachengx @ramirezdiego
Addition of truth plugins (#99)
7c97473 
* Correctly sort photons into pulses

* Propagate cluster number up to propagated photons

* Avoid 0 as cluster id.

* Add contributing_clusters to PMTResponseAndDAQ output

* Add truth output to PMTResponseAndDAQ

* Add draft for PeakTruth plugin

* code cleanup

* Save number of S1 S2 and AP photons

* Update PeakTruth plugin

* Add example notebook

* Add SurvivingClusters plugin

* Extend the example notebook and some bugfixing

* Sort cluster_ids and cluster_photons by number of photons

* Add average observed position to PeakTruth

* Update example notebook

* Add draft for EventTruth plugin

* Register truth plugins in the context

* Make cluster ids unique for a whole run of data

* Remove duplicate config args

* We can not use the fuse base plugin right now. Fix timeout and rechunk

* Reduce propagated_s2_photons_file_size_target to 200 MB

* Add event truth to example notebook.

* Add draft for cluster tagging plugin

* Squashed commit of the following:

commit 388945d
Author: Henning Schulze Eißing <[email protected]>
Date:   Tue Feb 13 11:28:54 2024 -0600

    Update example notebook

commit 0587859
Author: Henning Schulze Eißing <[email protected]>
Date:   Tue Feb 13 11:28:45 2024 -0600

    Bugfixing

commit b74c7a3
Author: Henning Schulze Eißing <[email protected]>
Date:   Tue Feb 13 11:28:33 2024 -0600

    revert PMTResponseAndDAQ changes

commit 8cf3586
Author: Henning Schulze Eißing <[email protected]>
Date:   Tue Feb 13 11:02:42 2024 -0600

    Refactor EventTruth

commit 45d816a
Author: Henning Schulze Eißing <[email protected]>
Date:   Tue Feb 13 10:57:39 2024 -0600

    Refactor SurvivingClusters

commit f656ae7
Author: Henning Schulze Eißing <[email protected]>
Date:   Tue Feb 13 10:42:16 2024 -0600

    Refactor ClusterTagging

commit de29c75
Author: Henning Schulze Eißing <[email protected]>
Date:   Tue Feb 13 07:49:45 2024 -0600

    Refactor peak and records truth

* rename get_cluster_information to _get_cluster_information

* loop s1 s2 ap in PeakTruth

* update plugin versions

* Update figures

* Update S2PhotonPropagation.rst

* Update S1PhotonPropagation.rst

* clean outputs of example notebook

* Add changes from delayed_electrons PR

* Update secondary_scintillation.py

* Add cluster_id

* Fix bug in s2 photon timing

* fix typo in example notebook

* add cluster_id to markdown cell

---------

Co-authored-by: Dacheng Xu <[email protected]>
Co-authored-by: mhliu0001 <[email protected]>
Co-authored-by: Diego Ramírez García <[email protected]>
Changes in map interpolation methods (#152)
fe15130 
* Proposed changes for interpolation methods

* Bug fix

* Add missing interpolation method for S2PhotonPropagationSimple
@dachengx
Proposal to use pre-commit for continuous integration (#155)
44e6d2a 
* Add pre-commit configuration

* Proposal to use pre-commit for continuous integration

* Add commit hash to .git-blame-ignore-revs

* Bug fix for inverse_field_distortion_correction
@cfuselli @HenningSE
Change raw_records to save_when TARGET (#148)
bd20347 
Co-authored-by: Henning Schulze Eißing <[email protected]>
dachengx and others added 28 commits August 2, 2024 18:48
@dachengx
Poetry does not understand requires-python (#252)
86ede28
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#253)
9087091 
updates:
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- [github.com/pre-commit/mirrors-mypy: v1.11.0 → v1.11.1](pre-commit/mirrors-mypy@v1.11.0...v1.11.1)
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[pre-commit.ci] pre-commit autoupdate (#255)
da6ea85 
updates:
- [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.11.2](pre-commit/mirrors-mypy@v1.11.1...v1.11.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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[pre-commit.ci] pre-commit autoupdate (#256)
293a625 
updates:
- [github.com/pycqa/doc8: v1.1.1 → v1.1.2](PyCQA/doc8@v1.1.1...v1.1.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@cfuselli @pre-commit-ci
@HenningSE @ramirezdiego
Update yields and clustering (#245)
5923e2f 
* add option to turn off recombination fluctuation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* remove urlconfig duplicate

* do not create electrons in betayields if creates2 is false

* only use custom yield above 10kev

* use getquanta with beta yields

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* line too long

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* plugin version bump

* plugin version bump

* sorry was testing version changes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add nest free parameters and option to fix yields

* do not break photoabsorbtion clusters

* if gamma phot, give gamma - no matter what creaproc

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix none default option

* bug fix

* add ERYieldsParameters and move fix gamma to nestyields

* typo fix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* avoid infinite logging and remove unnecessary check

* do not mess with option

* readd default none

* error with new default

* avoid negative field due to nest nice feature

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* cleanup betayields

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix lineage algo - RadioactiveDecayBase (#254)

* add classification via secondaries

* remove prints

* make more gammas...

* v24

* v25

* v26

* v27

* v28

* v28

* v29

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* remove njit

* cleanup

* change logic for alpha and resolve comments pr

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* remove unnecessary beta classification

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* dietrofront conversion electrons

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* add only beta and ic options

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Remove legacy BetaYields plugin

* Better variable name for y

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Henning Schulze Eißing <[email protected]>
Co-authored-by: Diego Ramírez García <[email protected]>
@HenningSE
Take yield and width parameters from config file (#257)
2f651b0 
* Take yield and width parameters from config file

* Density from config

* Add a workaround for yield parameters in vectorized function
@cfuselli @pre-commit-ci
Faster lineage clustering (#258)
4cd68b6 
* faster lineage

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@HenningSE
Release 1.4.0 (#259)
c3ad03f 
* Update HISTORY.md

* Bump version: 1.3.0 → 1.4.0
@SaelMo
typo found with pulse_id, may be related to out_of_order errors (#260)
d622926
@HenningSE @pre-commit-ci
Make sure CDF goes to 1 smoothly (#261)
beb8b43 
* Make sure CDF goes to 1 smoothly

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@HenningSE @pre-commit-ci @ramirezdiego
Option to replace maps by constant dummy map (#262)
49c8bde 
* Add Dummy Map protocol

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Diego Ramírez García <[email protected]>
@HenningSE
Release 1.4.1 (#265)
73a345f 
* Update HISTORY.md

* Bump version: 1.4.0 → 1.4.1
@HenningSE
Change logging_level to DEBUG in utilix config (#267)
6b5ecc1
@pre-commit-ci @HenningSE
[pre-commit.ci] pre-commit autoupdate (#266)
b0114e2 
updates:
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- [github.com/psf/black: 24.8.0 → 24.10.0](psf/black@24.8.0...24.10.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Henning Schulze Eißing <[email protected]>
@yuema137 @dachengx
Import MongoDownloader from utilix (#271)
733ec56 
* import mongodownloader from utilix

* add utilix dependency

* Upgrade utilix

---------

Co-authored-by: dachengx <[email protected]>
@HenningSE
Remove WFSim connection (#268)
fd40b75 
* Remove WFSim connection

* Remove test
@HenningSE @ramirezdiego
Area correction override (#269)
205afa5 
* Draft for processing override

* Set logging to info when setting up the context

* Add alt fields and extend the docstring.

---------

Co-authored-by: Diego Ramírez García <[email protected]>
@ramirezdiego
Release 1.4.2 (#272)
36ac25c 
* Push HISTORY for the release

* Bump version: 1.4.1 → 1.4.2
@ramirezdiego
change trackid in csv generator (#273)
4209bec
@dachengx
Constraint strax(en) to be less than 2.0.0(3.0.0) (#276)
8705be0
@HenningSE @pre-commit-ci
Use master for docformatter (#277)
5b5e3e8 
* Use master for docformatter

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@cfuselli
increase min_electron_gap_length_for_splitting (#275)
084662e
@pre-commit-ci @HenningSE
[pre-commit.ci] pre-commit autoupdate (#274)
ccbc24b 
updates:
- [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Henning Schulze Eißing <[email protected]>
@HenningSE
Release 1.4.3 (#284)
77b198f 
* Update HISTORY.md

* Bump version: 1.4.2 → 1.4.3
@dachengx @HenningSE
Be compatible with straxen >= 3 (#282)
124edb0 
* Be compatible with straxen >= 3

* Record `corrections_run_id`

* Record `simulation_config_file`

* Add padding of chunks in lineage

* Constraint strax(en) versions

* Need straxen 3.0.1 for common_config to exist

---------

Co-authored-by: Henning Schulze Eißing <[email protected]>
@dachengx
Remove CMT URLs, drop python 3.9 (#285)
2cdc339 
* Remove CMT URLs

* Drop python 3.9

* Back to 3.10

* Enlarge timeout tolerance

* Constraint timeout

* Further constraint timeout

* Have to enlarge timeout
@dachengx
Bump to 1.4.4 (#286)
50021ec 
* Update HISTORY.md

* Bump version: 1.4.3 → 1.4.4
@dachengx
Only simulate a part of the PI train (#287)
ad1789c
@HenningSE HenningSE merged commit aabe102 into nv_plugins Feb 13, 2025
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