Merge pull request #9 from SiLab-Bonn/development

v1.0.0

.github/workflows/main.yml

@@ -0,0 +1,54 @@
+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches:
+      - master
+      - development
+  pull_request:
+    branches:
+      - master
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  tests:
+    name: Testing on Python ${{matrix.python-version}} | ${{matrix.sim}}
+    runs-on: ubuntu-20.04
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, ubuntu-latest]
+        python-version: [3.7, 3.8, 3.9]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Anaconda ${{matrix.python-version}} setup
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{matrix.python-version}}
+
+      - name: Dependency installation
+        shell: bash -l {0}
+        run: |
+          conda info -a
+          conda install numpy scipy pyyaml matplotlib nose jupyter pandas
+          pip install -r requirements.txt
+
+      - name: Package installation
+        shell: bash -l {0}
+        run: |
+          python setup.py develop
+
+      - name: Testing
+        shell: bash -l {0}
+        run: nosetests

.gitignore

@@ -1,7 +1,7 @@
 # example checkpoints
-irrad_spectroscopy/examples/.ipynb_checkpoints/
+examples/.ipynb_checkpoints/
 # example output folder
-irrad_spectroscopy/examples/output/
+examples/output/
 # pyc
 *.pyc
 # pycharm

README.rst

@@ -1,19 +1,21 @@
 ==================================
-Irrad_Spectroscopy |travis-status|
+Irrad_Spectroscopy |test-status|
 ==================================
 
 Introduction
 ============
 
-``irrad_spectroscopy`` is a package intended to do gammma spectroscopy of (proton) irradiated samples such as chips, sensors,
-PCBs, etc. but can be also used for general gamma spectroscopy e.g. of radioactive sources. It consits of few independent
-methods which togehter allow for a complete spectroscopic analysis of radioactive gamma-spectra. A step-by-step full spectroscopy
-of an example spectrum can be found in the ``examples`` folder.
+``ìrrad_spectroscopy`` is a package which provides functions for gamma and X-ray spectroscopy, including isotope identification, activity determination and spectral dose calculations.
+Furthermore, it offers functions for calculating the gamma equivalent dose for given isotopes as a function of their initial activity.
+
+The package was developed for spectroscopic analysis or proton-irradiated semiconductor devices but can be used to analyze various samples,
+from radioactive sources to activated machine parts. It consits of few independent methods which togehter allow for a complete spectroscopic analysis, including plotting, of
+radioactive gamma-spectra. A step-by-step full spectroscopy of an example spectrum can be found in the ``examples`` folder.
 
 Installation
 ============
 
-You have to have Python 2/3 with the following packages installed:
+You have to have Python 3 with the following packages installed:
 
 - numpy
 - scipy
@@ -37,6 +39,9 @@ To finally install ``irrad_spectroscopy`` run the setup file
 Example usage
 =============
 
+Full spectroscopy
+-----------------
+
 Check the ``examples`` folder for several measured data sets of different sources for calibration and analysis. A `Jupyter Notebook <http://jupyter.org/>`_
 with a step-by-step analysis of an example spectrum of an irradiated chip is provided. Install jupyter and run
 
@@ -46,14 +51,86 @@ with a step-by-step analysis of an example spectrum of an irradiated chip is pro
 
 in order to open the web interface.
 
+Equivalent dose calculation
+--------------------------
+
+The package implements dose rate calculations for individual gamma lines as well as full gamma spectra of isotopes
+for various materials (search materials in `this table <https://github.com/SiLab-Bonn/irrad_spectroscopy/blob/development/irrad_spectroscopy/tables/xray_coefficient_table.yaml>`_)
+Dose rate calculations are implemented, assuming a point-like source!
+
+Calculating dose rate of an individual gamma line in air:
+
+.. code-block:: python
+
+   # Import 
+   from irrad_spectroscopy.physics import gamma_dose_rate
+
+   # Get dose rate of single gamma line in uSv/h
+   # Zn65 line at 1115.564 keV, prob 50.60%, activity of 20 kBq at a distance of 100 cm in air
+   res = gamma_dose_rate(energy=1115.546,
+                         probability=0.506,
+                         activity=20e3,
+                         distance=100,
+                         material='air')
+
+   print(res)  # Prints 1.515e-3  # uSv/h
+
+Calculating the (integrated) gamma dose rate of an isotope in air:
+
+.. code-block:: python
+
+   # Import 
+   from irrad_spectroscopy.physics import isotope_dose_rate
+
+   # Zn65 with activity of 20 kBq at a distance of 100 cm in air
+   res = isotope_dose_rate(isotope='65_Zn',
+                           activity=20e3,
+                           distance=100,
+                           material='air')
+   
+   print(res)  # Prints {'65_Zn': 1.515e-3}  # uSv/h
+
+   # Zn65 with activity of 20 kBq at a distance of 100 cm in air
+   # integrated over 2000 hours
+   res = isotope_dose_rate(isotope='65_Zn',
+                           activity=20e3,
+                           distance=100,
+                           material='air',
+                           time=2000)
+   
+   print(res)  # Prints {'65_Zn': 2.66}  # uSv
+
+Calculating the gamma dose rate of multiple isotopes in air:
+
+.. code-block:: python
+
+   # Import 
+   from irrad_spectroscopy.physics import isotope_dose_rate
+
+   # Multiple isotopes (Zn65 and Be7) with different activities
+   # (20 kBq, 100kBq) at a distance of 100 cm in air
+   res = isotope_dose_rate(isotope=('65_Zn', '7_Be'),
+                           activity=(20e3, 100e3),
+                           distance=100,
+                           material='air')
+   
+   print(res)  # Prints {'65_Zn': 1.515e-3, '7_Be': 0.73e-3}  # uSv/h
+
 Testing
 =======
 
 The code in this package has unit-tests. These tests contain a benchmark with actual gamma-spectroscopy data of
 two calibrated, radioactive sources, namely 22-Na and 133-Ba. The activity reconstruction efficiencies for the 
 tested data sets are tested to be above 90%.
 
-
-.. |travis-status| image:: https://api.travis-ci.com/SiLab-Bonn/irrad_spectroscopy.svg?branch=master
-    :target: https://travis-ci.com/SiLab-Bonn/irrad_spectroscopy
+.. |test-status| image:: https://github.com/Silab-Bonn/irrad_spectroscopy/actions/workflows/main.yml/badge.svg?branch=development
+    :target: https://github.com/SiLab-Bonn/irrad_spectroscopy/actions
     :alt: Build status
+
+Example spectrum
+================
+
+Generated spectrum, including background and identified peaks, of a radioactive sample after proton irradiation.
+Multiple isotopes can be assigned to one peak due to the uncertaiunty of the energy calibration.
+
+.. image:: static/figs/sample_spectrum.png

irrad_spectroscopy/examples/example_spectroscopy.ipynb → examples/example_spectroscopy.ipynb

@@ -74,10 +74,7 @@
     "# name\n",
     "SAMPLE_NAME = 'example_sample'\n",
     "\n",
-    "# paths\n",
-    "package_path = isp.package_path\n",
-    "\n",
-    "example_path = os.path.join(package_path, 'examples')\n",
+    "example_path = os.getcwd()\n",
     "\n",
     "data_path = os.path.join(example_path, 'example_data')\n",
     "\n",
@@ -276,21 +273,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15"
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,

irrad_spectroscopy/__init__.py

@@ -2,14 +2,7 @@
 import yaml
 
 
-# paths
-package_path = os.path.dirname(__file__)
-
-examples_path = os.path.join(package_path, 'examples')
-
-testing_path = os.path.join(package_path, 'testing')
-
-tables_path = os.path.join(package_path, 'tables')
+tables_path = os.path.join(os.path.dirname(__file__), 'tables')
 
 # table files paths
 gamma_table_file = os.path.join(tables_path, 'gamma_table.yaml')

setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import setup, find_packages  # This setup relies on setuptools since distutils is insufficient and badly hacked code
 
-version = '0.1.0'
+version = '1.0.0'
 author = 'Pascal Wolf'
 author_email = '[email protected]'
 
@@ -11,7 +11,7 @@
 setup(
     name='irrad_spectroscopy',
     version=version,
-    description='Gamma spectroscopy of irradiated sensors, chips and PCBs.',
+    description='Gamma and X-ray spectroscopy as well as dose rate calculations of radioactive samples.',
     url='https://github.com/SiLab-Bonn/irrad_spectroscopy',
     license='MIT License',
     long_description='',

irrad_spectroscopy/testing/test_spectroscopy.py → tests/test_spectroscopy.py

@@ -6,10 +6,10 @@
 import irrad_spectroscopy.spectroscopy as sp
 from irrad_spectroscopy.spec_utils import get_measurement_time, source_to_dict, select_peaks
 from irrad_spectroscopy.physics import decay_law
-from irrad_spectroscopy import testing_path, gamma_table
+from irrad_spectroscopy import gamma_table
 
 
-test_data_path = os.path.join(testing_path, 'test_data')
+test_data_path = os.path.join(os.path.dirname(__file__), 'test_data')
 
 
 class TestSpectroscopy(unittest.TestCase):