Merge pull request #14 from rhoitink/develop

Pull request for v1.6.0

.github/workflows/deploydocs.yml

@@ -12,9 +12,9 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.x
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
         architecture: 'x64'

.github/workflows/pythonpackage.yml

@@ -9,12 +9,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.gitignore

@@ -14,3 +14,4 @@ htmlcov
 site
 *.xyz
 *.ipynb
+src/simulatedmicroscopy/_version.py

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml # checks for correct yaml syntax for github actions ex.
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.2.2
+    hooks:
+      - id: ruff
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black

CITATION.cff

@@ -28,5 +28,5 @@ keywords:
   - point spread function
   - image generation
 license: MIT
-version: "v1.5.0"
-date-released: '2023-04-26'
+version: "v1.6.0"
+date-released: '2024-02-19'

docs/data-generation-example.md

@@ -86,12 +86,13 @@ You convolved image is now saved in the `image` variable.
 
 ## 4. Optional: adding noise and downsampling the image
 
-Adding Poisson noise and downsampling the image to a lower pixel size is included as well and can be done as follows:
+Adding noise and downsampling the image to a lower pixel size is included as well and can be done as follows:
 
 ```python
-# add Poisson noise with λ = 50
 # downsample by a factor 2 in z and factor 3 in xy
-image.noisify(50).downsample([2, 3, 3])
+# add Poisson noise (shot noise) with a signal-to-noise ratio of 30
+# add Gaussian noise (read noise, additive) with a mean value of 1e-5 and a signal-to-noise ratio of 50
+image.downsample([2, 3, 3]).add_shot_noise(SNR = 30.0).add_read_noise(SNR = 50.0, background = 1e-5)
 ```
 
 The downsampling by a factor two along a dimension, means that the number of pixels along that dimension is divided by two, which leads to an increase of the pixel size by a factor or two.

pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "src/simulatedmicroscopy/_version.py"
+
+[tool.black]
+line-length = 79
+target-version = ['py38', 'py39', 'py310', 'py311']
+
+[tool.ruff]
+line-length = 79
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+
+ignore = [
+    "E501",
+    "E203",
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py38"
+fix = true

setup.cfg

@@ -1,2 +1,61 @@
-[flake8]
-ignore=E501,E203,W503
+[metadata]
+name = simulatedmicroscopy
+
+description =  Python package to create synthetic (fluorescence) microscopy images of (nano)particles and convolution with a point spread function
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/rhoitink/simulatedmicroscopy
+author = Roy Hoitink
+author_email = L.D.Hoitink@uu.nl
+license = MIT
+license_files = LICENSE
+classifiers =
+    Development Status :: 4 - Beta
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Topic :: Scientific/Engineering :: Image Processing
+project_urls =
+    Bug Tracker = https://github.com/rhoitink/simulatedmicroscopy/issues
+    Documentation = https://github.com/rhoitink/simulatedmicroscopy#README.md
+    Source Code = https://github.com/rhoitink/simulatedmicroscopy
+    User Support = https://github.com/rhoitink/simulatedmicroscopy/issues
+
+[options]
+packages = find:
+install_requires =
+    numpy
+    matplotlib
+    h5py
+    scipy
+    scikit-image>=0.20.0
+
+python_requires = >=3.8
+include_package_data = True
+package_dir =
+    =src
+setup_requires = setuptools_scm
+
+[options.packages.find]
+where = src
+
+[options.extras_require]
+dev =
+    black
+    flake8
+    pytest
+    pytest-cov
+docs =
+    mkdocs
+    mkdocs-material
+    mkdocstrings[python]
+    mkdocs-gen-files
+    mkdocs-literate-nav

src/simulatedmicroscopy/__init__.py

@@ -0,0 +1,22 @@
+from .image import HuygensImage, Image
+from .input import Coordinates
+from .particle import Cube, PointParticle, Shell, Sphere, Spherocylinder
+from .psf import GaussianPSF, HuygensPSF
+
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+__all__ = [
+    "Coordinates",
+    "Image",
+    "HuygensImage",
+    "HuygensPSF",
+    "GaussianPSF",
+    "PointParticle",
+    "Sphere",
+    "Shell",
+    "Spherocylinder",
+    "Cube",
+]