initial commit v1.0.0

Author: sophiamaedler

.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ main, release ]
+  pull_request:
+    branches: [ main, release ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install setuptools
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools
+    - name: Install dependencies
+      run: |
+        python -m pip install flake8 pytest setuptools
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install -e .
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Vs code
+.DS_Store
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/

LICENSE

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+MIT License
+
+Copyright (c) 2021 Georg Wallmann
+
+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.

README.md

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+
+[![Python package](https://github.com/MannLabs/py-lmd/actions/workflows/python-package.yml/badge.svg?branch=release)](https://github.com/MannLabs/py-lmd/actions/workflows/python-package.yml) [![Python package](https://img.shields.io/badge/version-v1.0.0-blue)](https://github.com/MannLabs/py-lmd/actions/workflows/python-package.yml) [![Python package](https://img.shields.io/badge/license-MIT-blue)](https://github.com/MannLabs/py-lmd/actions/workflows/python-package.yml)
+[![website](https://img.shields.io/website?url=https%3A%2F%2Fmannlabs.github.io/py-lmd/html/index.html)](https://mannlabs.github.io/py-lmd/html/index.html)
+
+![py-lmd_border](https://github.com/MannLabs/py-lmd/assets/15019107/035dfa13-c1a3-4ed0-8bbe-ddd5df29c367)
+
+Read, create and write cutting data for the Leica LMD6 & LMD7 microscope.
+Build reproducible workflows to calibrate, import SVG files and convert single-cell segmentation masks.
+
+
+Installation from Github
+========================
+py-lmd has been tested with **Python 3.8 and 3.9**.
+To install the py-lmd library clone the Github repository and use pip to install the library in your current environment.
+It is recommended to use the library with a conda environment. Please make sure that the package is installed editable
+like described. Otherwise static glyph files might not be available. 
+
+We recommend installing the non-python dependencies with conda before installing py-lmd:
+
+```
+git clone https://github.com/MannLabs/py-lmd
+
+conda create -n "py-lmd-env"
+conda activate py-lmd-env
+conda install python=3.9 scipy scikit-image>=0.19 numpy numba -c conda-forge
+pip install -e .
+
+```
+
+If you are installing on an M1 apple silicon Mac you will need to install `numba` via conda instead of pip before proceeding with the installation of the py-lmd library.
+
+```
+conda install numba
+```
+  
+Documentation
+========================
+The current documentation can be found under https://mannlabs.github.io/py-lmd/html/index.html.
+
+Citing our Work
+=================
+
+py-lmd was developed by Georg Wallmann, Sophia Mädler and Niklas Schmacke in the labs of Veit Hornung and Matthias Mann. If you use our code please cite the following manuscript:
+
+CITATION HERE