Fix classification of alpha events

.bumpversion.cfg

@@ -1,5 +1,6 @@
 [bumpversion]
-current_version = 0.3.3
+current_version = 0.3.8
 files = setup.py epix/__init__.py
 commit = True
 tag = True
+

.github/workflows/python-publish.yml

@@ -1,33 +1,33 @@
 # This workflow will upload epix to PyPi using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
-name: Upload Python Package
+name: PyPI
 
 on:
-  release:
-    types: [created]
-  # Allow manual build if tests are failing first time
   workflow_dispatch:
+  release:
+    types: [ created ]
 
 jobs:
-  deploy:
-
+  build:
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.8'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      # Setup steps
+      - name: Setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: pip install wheel
+
+      - name: Build package
+        run: python setup.py sdist bdist_wheel
+
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

HISTORY.md

@@ -1,7 +1,31 @@
+0.3.8 (2024-02-23)
+==================
+* Propagate defaults for energy range arguments (#82)
+
+0.3.7 (2024-02-08)
+==================
+* Selection based on total energy deposit in sensitive volume (#76)
+* Fix cut_by_eventid again (#80)
+
+0.3.6 (2024-01-15)
+==================
+* Fix G4 event number selection with cut_by_eventid (#75)
+* `np.int` is deprecated (#78)
+* Fix epix to allow version bump (#77)
+
+0.3.5 (2023-09-13)
+==================
+* Custom microclustering and beta-yields generator (#73)
+
+0.3.4 (2023-03-28)
+==================
+* Fix calculation for cluster weighted average time (#65)
+* Add zenodo badge
+
 0.3.3 (2023-01-09)
 ==================
-* Specify not working numba in req. file by @JoranAngevaare in https://github.com/XENONnT/epix/pull/62
-* Install scikit-learn by @JoranAngevaare in https://github.com/XENONnT/epix/pull/63
+* Specify not working numba in req. file (#62)
+* Install scikit-learn (#63)
 
 0.3.2 (2022-08-15)
 ==================

README.md

@@ -39,7 +39,10 @@ The other keyword arguments are:
 | `--MicroSeparationTime`  | Clustering time (ns) | `10` |
 | `--TagClusterBy`  | decide if you tag the cluster (particle type, energy depositing process) according to first interaction in it (`time`) or most energetic (`energy`) | `energy` |
 | `--MaxDelay`  | Time after which we cut the rest of the event (ns) | `1e7` |
-| `--YieldModel` | Model for yield/quanta generationg (nest or bbf) | `nest` |
+| `--MaxEnergy`  | Upper range for energy selection _in sensitive volume_ (keV) | `inf` |
+| `--MinEnergy`  | Lower range for energy selection _in sensitive volume_ (keV) | `-1`  |
+| `--YieldModel` | Model for yield/quanta generation (nest / bbf / beta) | `nest` |
+| `--ClusterMethod` | Microclustering method (dbscan / betadecay / brem) | `dbscan` |
 | `--SourceRate`  | Event rate for event separation<br /> - `0` for no time shift (G4 time remains)<br /> - `-1` for clean time shift between events<br /> - `>0` (Hz) for random spacing | `0` |
 | `--CutNeutron` | Add if you want to filter only nuclear recoil events (maximum ER energy deposit 10 keV) | `false` |
 | `--JobNumber`  | Job number in full chain simulation. Offset is computed as `JobNumber * n_simulated_events/SourceRate`, where `n_simulated_events` is read from file. | `0` |

bin/run_epix

@@ -48,7 +48,17 @@ def pars_args():
                         help='Event rate for event separation. 0 (default) means no time shift is applied for the '
                              'different events. Use -1 for clean spacing or give a rate >0 to space events randomly.')
     parser.add_argument('--YieldModel', dest='yield', type=str, 
-                        default='nest', help = 'Switch between BBF and NEST yield model')
+                        default='nest', help = 'Switch between NEST, BBF, and BETA yield model, '
+                                               '[ nest | bbf | beta ]')
+    parser.add_argument('--ClusterMethod', dest='cluster_method', type=str,
+                        default='dbscan', help = 'Switch between DBSCAN, BETA-DECAY, '
+                                                 'and BREMSSTRAHLUNG microclustering, [ dbscan | betadecay | brem ]')
+    parser.add_argument('--MaxEnergy', dest='max_energy', type=float,
+                        action='store', default=float('inf'), #keV
+                        help='Maximum energy in sensitive volume to be stored [keV].')
+    parser.add_argument('--MinEnergy', dest='min_energy', type=float,
+                        action='store', default=-1, #keV
+                        help='Minimum energy in sensitive volume to be stored [keV].')
     parser.add_argument('--JobNumber', dest='job_number', type=int,
                         action='store', default=0,
                         help='Job number in full chain simulation. Offset is computed as '

epix/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.3.3'
+__version__ = '0.3.8'
 
 from .common import *
 from .io import *
@@ -10,3 +10,5 @@
 from .detectors import *
 from .run_epix import *
 from .quantgen_wrapper import BBF_quanta_generator
+from .quantgen_wrapper import BETA_quanta_generator
+from .quantgen_wrapper import NEST_quanta_generator

epix/betadecay_cluster.py

@@ -0,0 +1,40 @@
+import numpy as np
+import pandas as pd
+import uproot
+import time
+import os
+import re
+import awkward as ak
+import collections
+
+
+class BetaDecayClustering():
+
+    def __init__(self):
+        pass
+
+    def cluster(self, event_tracks_df):
+        betagamma_df = event_tracks_df[
+            ((event_tracks_df.type == 'e-') & (event_tracks_df.creaproc == 'RadioactiveDecayBase'))
+            | ((event_tracks_df.type == 'gamma') & (event_tracks_df.creaproc == 'RadioactiveDecayBase'))]
+        betagamma_df = betagamma_df[
+            ~((betagamma_df.edproc == "Rayl") | (betagamma_df.edproc == "Transportation"))]
+
+        betagamma_df['ed'] = betagamma_df.PreStepEnergy - betagamma_df.PostStepEnergy
+        betagamma_df.loc[betagamma_df.type == 'e-', 'ed'] = betagamma_df.loc[
+            betagamma_df.type == 'e-', 'PreStepEnergy']
+        betagamma_df = betagamma_df[betagamma_df.ed > 1e-6]
+
+        beta_trackid = []
+        for ind, row in betagamma_df.iterrows():
+            if row['type'] == 'gamma':
+                pass
+            elif row['type'] == 'e-':
+                if row['trackid'] in beta_trackid:
+                    betagamma_df.drop(ind, inplace=True)
+                else:
+                    beta_trackid.append(row['trackid'])
+            else:
+                betagamma_df.drop(ind, inplace=True)
+
+        return betagamma_df