microssim 0.0.1__tar.gz

microssim-0.0.1/.github/pull_request_template.md

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+### Description
+
+Please provide a brief description of the changes in this PR. Include any relevant context or background information.
+
+- **What**: Clearly and concisely describe what changes you have made.
+- **Why**: Explain the reasoning behind these changes. What problem are you solving? Why is this change necessary?
+- **How**: Describe how you implemented these changes. Provide an overview of the approach and any important implementation details.
+
+### Changes Made
+
+- **Added**: List new features or files added.
+- **Modified**: Describe existing features or files modified.
+- **Removed**: Detail features or files that were removed.
+
+### Related Issues
+
+Link to any related issues or discussions. Use keywords like "Fixes", "Resolves", or "Closes" to link to issues automatically.
+
+- Fixes #
+- Resolves #
+- Closes #
+
+### Breaking changes
+
+Describe any breaking change.
+
+
+### Additional Notes and Examples
+
+Include any additional notes or context that reviewers should be aware of, including snippets of code illustrating your new feature.
+
+---
+
+**Please ensure your PR meets the following requirements:**
+
+- [ ] Code builds and passes tests locally, including doctests
+- [ ] New tests have been added (for bug fixes/features)
+- [ ] Pre-commit passes
+- [ ] PR to the documentation exists (for bug fixes / features)

microssim-0.0.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
+        platform: [ubuntu-latest, macos-13, windows-latest]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          # if running a cron job, we add the --pre flag to test against pre-releases
+          python -m pip install .[dev] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing 
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+        with:
+          version: v0.7.3
+
+  deploy:
+    name: Release
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+
+      - name: Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

microssim-0.0.1/.gitignore

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+# VSCode
+.vscode
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff
+.ruff_cache

microssim-0.0.1/.pre-commit-config.yaml

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+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.18
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
+    hooks:
+      - id: ruff
+        args: [--fix, --unsafe-fixes, --select, I]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        files: "^src/ri_ssim/.*\\.py$"
+        additional_dependencies:
+          - numpy
+          - types-tqdm
+
+  # check docstrings
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.7.0
+    hooks:
+      - id: numpydoc-validation
+        exclude: "^notebooks/.*"

microssim-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 JugLab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

microssim-0.0.1/PKG-INFO

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+Metadata-Version: 2.3
+Name: microssim
+Version: 0.0.1
+Summary: Improved structural similarity metrics for comparing microscopy data.
+Project-URL: homepage, https://github.com/juglab/MicroSSIM
+Project-URL: repository, https://github.com/juglab/MicroSSIM
+Author: Ashesh, Joran Deschamps, Florian Jug
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: numpy<2
+Requires-Dist: scikit-image
+Requires-Dist: scipy
+Requires-Dist: torch
+Requires-Dist: torchmetrics
+Requires-Dist: tqdm
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: sybil; extra == 'dev'
+Provides-Extra: examples
+Requires-Dist: jupyter; extra == 'examples'
+Requires-Dist: matplotlib; extra == 'examples'
+Requires-Dist: pooch; extra == 'examples'
+Requires-Dist: seaborn; extra == 'examples'
+Requires-Dist: tifffile; extra == 'examples'
+Description-Content-Type: text/markdown
+
+# MicroSSIM
+
+[![License](https://img.shields.io/pypi/l/microssim.svg?color=green)](https://github.com/juglab/MicroSSIM/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/microssim.svg?color=green)](https://pypi.org/project/microssim)
+[![Python Version](https://img.shields.io/pypi/pyversions/microssim.svg?color=green)](https://python.org)
+[![CI](https://github.com/juglab/MicroSSIM/actions/workflows/ci.yml/badge.svg)](https://github.com/juglab/MicroSSIM/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/juglab/MicroSSIM/branch/main/graph/badge.svg)](https://codecov.io/gh/juglab/MicroSSIM)
+
+
+
+MicroSSIM is an image measure aimed at addressing the shortcomings of the Structural
+Similarity Index Measure (SSIM), in particular in the context of microscopy images. Indeed,
+in microscopy, degraded images (e.g. lower signal to noise ratio) often have a different
+dynamic range than the original images. This can lead to a poor performance of SSIM.
+
+The measure normalizes the images using background subtraction and a more appropriate 
+range estimation. It then estimates a scaling factor used to scale the image
+to the target (original image or ground truth). The metric is then computed
+similarly to the SSIM. 
+
+MicroSSIM is easily extensible to other SSIM-like measures, such as Multi-Scale SSIM 
+(MS-SSIM), for which we provide an example.
+
+See the [paper](https://arxiv.org/abs/2408.08747) for more details.
+
+## Installation
+
+```bash
+pip install microssim
+```
+
+
+## Usage
+
+```python
+import numpy as np
+from microssim import MicroSSIM, micro_structural_similarity
+from skimage.metrics import structural_similarity
+
+rng = np.random.default_rng(42)
+N = 5
+gt = 200 + rng.integers(0, 65535, (N, 256, 256)) # stack of different images
+pred = rng.poisson(gt) / 10
+
+# using the convenience function
+result = micro_structural_similarity(gt, pred)
+print(f"MicroSSIM: {result} (convenience function)")
+
+# using the class allows fitting a large dataset, then scoring a subset
+microssim = MicroSSIM()
+microssim.fit(gt, pred) # fit the parameters
+
+for i in range(N):
+    score = microssim.score(gt[i], pred[i]) # score a single pair
+    print(f"MicroSSIM ({i}): {score}")
+
+# compare with SSIM from skimage
+for i in range(N):
+    score = structural_similarity(gt[i], pred[i], data_range=65535)
+    print(f"SSIM ({i}): {score}")
+```
+
+The code is similar for MicroMS3IM.
+
+## Tips for deep learning
+
+MicroSSIM was developed in the context of deep-learning, in which SSIM is often used
+as a measure to compare denoised and ground-truth images. The tips presented here are
+valid beyond deep-learning.
+
+The larger the dataset, the better the estimate of the scaling factor will be. Therefore,
+it is recommended to fit the measure on the entire dataset (e.g. the whole training 
+dataset). Once the data fitted, the `MSSIM` class has registered the parameters used
+for normalization and scaling. You can then score a subset of the data (e.g. the validation
+or test datasets) using the `score` method.
+
+
+
+## Cite us
+
+If you use MicroSSIM in your research, please cite us:
+
+Ashesh, Ashesh, Joran Deschamps, and Florian Jug. "MicroSSIM: Improved Structural Similarity for Comparing Microscopy Data." arXiv preprint arXiv:2408.08747 (2024). [link](https://arxiv.org/abs/2408.08747).

microssim-0.0.1/README.md

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+# MicroSSIM
+
+[![License](https://img.shields.io/pypi/l/microssim.svg?color=green)](https://github.com/juglab/MicroSSIM/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/microssim.svg?color=green)](https://pypi.org/project/microssim)
+[![Python Version](https://img.shields.io/pypi/pyversions/microssim.svg?color=green)](https://python.org)
+[![CI](https://github.com/juglab/MicroSSIM/actions/workflows/ci.yml/badge.svg)](https://github.com/juglab/MicroSSIM/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/juglab/MicroSSIM/branch/main/graph/badge.svg)](https://codecov.io/gh/juglab/MicroSSIM)
+
+
+
+MicroSSIM is an image measure aimed at addressing the shortcomings of the Structural
+Similarity Index Measure (SSIM), in particular in the context of microscopy images. Indeed,
+in microscopy, degraded images (e.g. lower signal to noise ratio) often have a different
+dynamic range than the original images. This can lead to a poor performance of SSIM.
+
+The measure normalizes the images using background subtraction and a more appropriate 
+range estimation. It then estimates a scaling factor used to scale the image
+to the target (original image or ground truth). The metric is then computed
+similarly to the SSIM. 
+
+MicroSSIM is easily extensible to other SSIM-like measures, such as Multi-Scale SSIM 
+(MS-SSIM), for which we provide an example.
+
+See the [paper](https://arxiv.org/abs/2408.08747) for more details.
+
+## Installation
+
+```bash
+pip install microssim
+```
+
+
+## Usage
+
+```python
+import numpy as np
+from microssim import MicroSSIM, micro_structural_similarity
+from skimage.metrics import structural_similarity
+
+rng = np.random.default_rng(42)
+N = 5
+gt = 200 + rng.integers(0, 65535, (N, 256, 256)) # stack of different images
+pred = rng.poisson(gt) / 10
+
+# using the convenience function
+result = micro_structural_similarity(gt, pred)
+print(f"MicroSSIM: {result} (convenience function)")
+
+# using the class allows fitting a large dataset, then scoring a subset
+microssim = MicroSSIM()
+microssim.fit(gt, pred) # fit the parameters
+
+for i in range(N):
+    score = microssim.score(gt[i], pred[i]) # score a single pair
+    print(f"MicroSSIM ({i}): {score}")
+
+# compare with SSIM from skimage
+for i in range(N):
+    score = structural_similarity(gt[i], pred[i], data_range=65535)
+    print(f"SSIM ({i}): {score}")
+```
+
+The code is similar for MicroMS3IM.
+
+## Tips for deep learning
+
+MicroSSIM was developed in the context of deep-learning, in which SSIM is often used
+as a measure to compare denoised and ground-truth images. The tips presented here are
+valid beyond deep-learning.
+
+The larger the dataset, the better the estimate of the scaling factor will be. Therefore,
+it is recommended to fit the measure on the entire dataset (e.g. the whole training 
+dataset). Once the data fitted, the `MSSIM` class has registered the parameters used
+for normalization and scaling. You can then score a subset of the data (e.g. the validation
+or test datasets) using the `score` method.
+
+
+
+## Cite us
+
+If you use MicroSSIM in your research, please cite us:
+
+Ashesh, Ashesh, Joran Deschamps, and Florian Jug. "MicroSSIM: Improved Structural Similarity for Comparing Microscopy Data." arXiv preprint arXiv:2408.08747 (2024). [link](https://arxiv.org/abs/2408.08747).