napari-stitcher 0.1.0__tar.gz

napari_stitcher-0.1.0/.github/workflows/documentation_main.yml

@@ -0,0 +1,27 @@
+name: Generate main documentation
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  docs-main:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - name: Install dependencies
+      run: pip install -r docs/docs_requirements.txt
+    - name: Setup doc deploy
+      run: |
+        git config --global user.name Docs deploy
+        git config --global user.email docs@dummy.bot.com
+    - name: Build docs website
+      run: mike deploy main --push && mike set-default --push main

napari_stitcher-0.1.0/.github/workflows/documentation_release.yml

@@ -0,0 +1,31 @@
+name: Generate [version] documentation
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Deploy docs to GitHub Pages
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - name: Install dependencies
+      run: pip install -r docs/docs_requirements.txt
+    - name: Setup doc deploy
+      run: |
+        git config --global user.name Docs deploy
+        git config --global user.email docs@dummy.bot.com
+    - name: Set release notes tag
+      run: |
+        export RELEASE_TAG_VERSION="${{ github.event.release.tag_name }}"
+        echo RELEASE_TAG_VERSION="${RELEASE_TAG_VERSION:1}" >> "$GITHUB_ENV"
+    - name: Build docs website
+      run: mike deploy "${RELEASE_TAG_VERSION}" --push

napari_stitcher-0.1.0/.github/workflows/test_and_deploy.yml

@@ -0,0 +1,89 @@
+# This workflows will upload a Python Package 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: Test and Deploy
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        # platform: [ubuntu-latest, windows-latest, macos-latest]
+        platform: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11']
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v2
+
+  deploy:
+    # this will run when you have tagged a commit, starting with "v*"
+    # and requires that you have put your twine API key in your
+    # github secrets (see readme for details)
+    needs: [test]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+        run: |
+          git tag
+          python -m build .
+          twine upload dist/*

napari_stitcher-0.1.0/.gitignore

@@ -0,0 +1,87 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py
+
+src/napari_stitcher/_playground
+doc_old

napari_stitcher-0.1.0/.napari-hub/DESCRIPTION.md

@@ -0,0 +1,35 @@
+<!-- This file is a placeholder for customizing description of your plugin 
+on the napari hub if you wish. The readme file will be used by default if
+you wish not to do any customization for the napari hub listing.
+
+If you need some help writing a good description, check out our 
+[guide](https://github.com/chanzuckerberg/napari-hub/wiki/Writing-the-Perfect-Description-for-your-Plugin)
+-->
+
+# Description
+
+This plugin stitches images (napari layers) in 2/3D+t. Images can either be (pre-)aligned manually or on a grid.
+
+Here's it's [user guide](https://multiview-stitcher.github.io/napari-stitcher/) and [github repository](https://github.com/multiview-stitcher/napari-stitcher). napari-stitcher uses [`multiview-stitcher`](https://github.com/multiview-stitcher/multiview-stitcher) for registration and fusion.
+
+## Overview
+
+![](https://github.com/multiview-stitcher/napari-stitcher/raw/refs/heads/main/docs/images/napari-stitcher-loaded-mosaic-annotated.png)
+<small>Image data by Arthur Michaut @ Jérôme Gros Lab @ Institut Pasteur.</small>
+
+1. Directly stitch napari layers: Use napari to load, visualize and [preposition](prearrangement.md) the tiles to be stitched.
+2. When working with multi-channel data, stick to the following [naming convention](naming_convention.md): `{tile} :: {channel}`.
+3. Load either all or just a subset of the layers into the plugin.
+4. Choose registration options: registration channel, binning and more.
+5. Stitching = registration (refining the positions, optional) + fusion (joining the tiles into a single image).
+6. The registration result is shown in the viewer and the fused channels are added as new layers.
+
+## Demo
+
+[Link](https://github.com/user-attachments/assets/8773e49f-af18-4ff3-ab2f-2a5f1b1cadf2) to video demo.
+
+<video controls>
+<source src="https://github.com/multiview-stitcher/napari-stitcher/raw/refs/heads/main/docs/images/demo_3d.mp4" type="video/mp4">
+</video>
+
+<small>This demo uses the awesome [`napari-threedee`](https://github.com/napari-threedee/napari-threedee) for prepositioning the tiles. Image data: [BigStitcher](https://imagej.net/plugins/bigstitcher/).</small>

napari_stitcher-0.1.0/.napari-hub/config.yml

@@ -0,0 +1,18 @@
+# You may use this file to customize how your plugin page appears
+# on the napari hub: https://www.napari-hub.org/
+# See their wiki for details https://github.com/chanzuckerberg/napari-hub/wiki
+
+# Please note that this file should only be used IN ADDITION to entering
+# metadata fields (such as summary, description, authors, and various URLS)
+# in your standard python package metadata (e.g. setup.cfg, setup.py, or
+# pyproject.toml), when you would like those fields to be displayed
+# differently on the hub than in the napari application.
+
+# Add labels the plugin from the EDAM Bioimaging ontology
+labels:
+  ontology: EDAM-BIOIMAGING:alpha06
+  terms:
+  - Image registration
+  - Image reconstruction
+  - 2D image
+  - 3D image

napari_stitcher-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,41 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: ^\.napari-hub/.*
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.32.1
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus, --keep-runtime-typing]
+  - repo: https://github.com/myint/autoflake
+    rev: v1.4
+    hooks:
+      - id: autoflake
+        args: ["--in-place", "--remove-all-unused-imports"]
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-typing-imports>=1.9.0]
+  - repo: https://github.com/tlambert03/napari-plugin-checks
+    rev: v0.2.0
+    hooks:
+      - id: napari-plugin-checks
+  # https://mypy.readthedocs.io/en/stable/introduction.html
+  # you may wish to add this as well!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v0.910-1
+  #   hooks:
+  #     - id: mypy

napari_stitcher-0.1.0/LICENSE

@@ -0,0 +1,28 @@
+
+Copyright (c) 2022, Marvin Albert
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

napari_stitcher-0.1.0/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

napari_stitcher-0.1.0/PKG-INFO

@@ -0,0 +1,102 @@
+Metadata-Version: 2.1
+Name: napari-stitcher
+Version: 0.1.0
+Summary: Stitch napari image layers in 2-3D+t
+Author: Marvin Albert
+Author-email: marvin.albert@gmail.com
+License: BSD-3-Clause
+Project-URL: Bug Tracker, https://github.com/multiview-stitcher/napari-stitcher/issues
+Project-URL: Documentation, https://multiview-stitcher.github.io/napari-stitcher/
+Project-URL: Source Code, https://github.com/multiview-stitcher/napari-stitcher
+Project-URL: User Support, https://github.com/multiview-stitcher/napari-stitcher/issues
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.18
+Requires-Dist: magicgui
+Requires-Dist: qtpy
+Requires-Dist: tifffile>=2022.7.28
+Requires-Dist: multiview-stitcher[aicsimageio]==0.1.14
+Requires-Dist: spatial_image==0.3.0
+Requires-Dist: multiscale_spatial_image==0.11.2
+Provides-Extra: testing-no-gui
+Requires-Dist: tox; extra == "testing-no-gui"
+Requires-Dist: pytest; extra == "testing-no-gui"
+Requires-Dist: pytest-cov; extra == "testing-no-gui"
+Requires-Dist: pytest-qt; extra == "testing-no-gui"
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-qt; extra == "testing"
+Requires-Dist: napari; extra == "testing"
+Requires-Dist: pyqt5; extra == "testing"
+
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-stitcher)](https://napari-hub.org/plugins/napari-stitcher)
+[![License {{cookiecutter.license}}](https://img.shields.io/pypi/l/napari-stitcher.svg?color=green)](https://github.com/multiview-stitcher/napari-stitcher/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-stitcher.svg?color=green)](https://pypi.org/project/napari-stitcher)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-stitcher.svg?color=green)](https://python.org)
+[![tests](https://github.com/multiview-stitcher/napari-stitcher/actions/workflows/test_and_deploy.yml/badge.svg)](https://github.com/multiview-stitcher/napari-stitcher/actions)
+[![codecov](https://codecov.io/gh/multiview-stitcher/napari-stitcher/branch/main/graph/badge.svg)](https://codecov.io/gh/multiview-stitcher/napari-stitcher)
+[![DOI](https://zenodo.org/badge/697999800.svg)](https://zenodo.org/doi/10.5281/zenodo.13151252)
+
+
+# napari-stitcher
+
+A napari plugin for stitching large multi-positioning datasets in 2/3D+t using [`multiview-stitcher`](https://github.com/multiview-stitcher/multiview-stitcher).
+
+![](docs/images/napari-stitcher-loaded-mosaic-annotated.png)
+<small>Image data by Arthur Michaut @ Jérôme Gros Lab @ Institut Pasteur.</small>
+
+#### Quick guide:
+
+1. Directly stitch napari layers: Use napari to load, visualize and [preposition](prearrangement.md) the tiles to be stitched.
+2. When working with multi-channel data, stick to the following [naming convention](naming_convention.md): `{tile} :: {channel}`.
+3. Load either all or just a subset of the layers into the plugin.
+4. Choose registration options: registration channel, binning and more.
+5. Stitching = registration (refining the positions, optional) + fusion (joining the tiles into a single image).
+6. The registration result is shown in the viewer and the fused channels are added as new layers.
+
+## Demo
+
+https://github.com/user-attachments/assets/8773e49f-af18-4ff3-ab2f-2a5f1b1cadf2
+
+<small>This demo uses the awesome [`napari-threedee`](https://github.com/napari-threedee/napari-threedee) for prepositioning the tiles. Image data: [BigStitcher](https://imagej.net/plugins/bigstitcher/).</small>
+
+## Documentation
+
+Head over to the [user guide](https://multiview-stitcher.github.io/napari-stitcher/main/) for more details.
+
+## Installation
+
+You can install `napari-stitcher` via `pip`:
+
+```bash
+pip install napari-stitcher
+```
+
+For more installation options, see the [installation docs](https://multiview-stitcher.github.io/napari-stitcher/main/installation/).
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with `tox`.
+
+## License
+
+Distributed under the terms of the [BSD-3] license, "napari-stitcher" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue](https://github.com/multiview-stitcher/napari-stitcher/issues) along with a detailed description.

napari_stitcher-0.1.0/README.md

@@ -0,0 +1,56 @@
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-stitcher)](https://napari-hub.org/plugins/napari-stitcher)
+[![License {{cookiecutter.license}}](https://img.shields.io/pypi/l/napari-stitcher.svg?color=green)](https://github.com/multiview-stitcher/napari-stitcher/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-stitcher.svg?color=green)](https://pypi.org/project/napari-stitcher)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-stitcher.svg?color=green)](https://python.org)
+[![tests](https://github.com/multiview-stitcher/napari-stitcher/actions/workflows/test_and_deploy.yml/badge.svg)](https://github.com/multiview-stitcher/napari-stitcher/actions)
+[![codecov](https://codecov.io/gh/multiview-stitcher/napari-stitcher/branch/main/graph/badge.svg)](https://codecov.io/gh/multiview-stitcher/napari-stitcher)
+[![DOI](https://zenodo.org/badge/697999800.svg)](https://zenodo.org/doi/10.5281/zenodo.13151252)
+
+
+# napari-stitcher
+
+A napari plugin for stitching large multi-positioning datasets in 2/3D+t using [`multiview-stitcher`](https://github.com/multiview-stitcher/multiview-stitcher).
+
+![](docs/images/napari-stitcher-loaded-mosaic-annotated.png)
+<small>Image data by Arthur Michaut @ Jérôme Gros Lab @ Institut Pasteur.</small>
+
+#### Quick guide:
+
+1. Directly stitch napari layers: Use napari to load, visualize and [preposition](prearrangement.md) the tiles to be stitched.
+2. When working with multi-channel data, stick to the following [naming convention](naming_convention.md): `{tile} :: {channel}`.
+3. Load either all or just a subset of the layers into the plugin.
+4. Choose registration options: registration channel, binning and more.
+5. Stitching = registration (refining the positions, optional) + fusion (joining the tiles into a single image).
+6. The registration result is shown in the viewer and the fused channels are added as new layers.
+
+## Demo
+
+https://github.com/user-attachments/assets/8773e49f-af18-4ff3-ab2f-2a5f1b1cadf2
+
+<small>This demo uses the awesome [`napari-threedee`](https://github.com/napari-threedee/napari-threedee) for prepositioning the tiles. Image data: [BigStitcher](https://imagej.net/plugins/bigstitcher/).</small>
+
+## Documentation
+
+Head over to the [user guide](https://multiview-stitcher.github.io/napari-stitcher/main/) for more details.
+
+## Installation
+
+You can install `napari-stitcher` via `pip`:
+
+```bash
+pip install napari-stitcher
+```
+
+For more installation options, see the [installation docs](https://multiview-stitcher.github.io/napari-stitcher/main/installation/).
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with `tox`.
+
+## License
+
+Distributed under the terms of the [BSD-3] license, "napari-stitcher" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue](https://github.com/multiview-stitcher/napari-stitcher/issues) along with a detailed description.

napari_stitcher-0.1.0/docs/contributing.md

@@ -0,0 +1,3 @@
+# Contributing
+
+Contributions are very welcome.

napari_stitcher-0.1.0/docs/docs_requirements.txt

@@ -0,0 +1,84 @@
+appnope==0.1.4
+asttokens==2.4.1
+attrs==24.2.0
+babel==2.16.0
+backcall==0.2.0
+beautifulsoup4==4.12.3
+bleach==6.1.0
+certifi==2024.8.30
+charset-normalizer==3.4.0
+click==8.1.7
+colorama==0.4.6
+decorator==5.1.1
+defusedxml==0.7.1
+docopt==0.6.2
+EditorConfig==0.12.4
+executing==2.1.0
+fastjsonschema==2.20.0
+ghp-import==2.1.0
+griffe==1.4.1
+idna==3.10
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
+ipython==8.12.3
+jedi==0.19.1
+Jinja2==3.1.4
+jsbeautifier==1.15.1
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter_client==8.6.3
+jupyter_core==5.7.2
+jupyterlab_pygments==0.3.0
+Markdown==3.7
+MarkupSafe==3.0.1
+matplotlib-inline==0.1.7
+mergedeep==1.3.4
+mike==2.1.3
+mistune==3.0.2
+mkdocs==1.6.1
+mkdocs-autorefs==1.2.0
+mkdocs-get-deps==0.2.0
+mkdocs-material==9.5.41
+mkdocs-material-extensions==1.3.1
+mkdocs-mermaid2-plugin==1.1.1
+mkdocstrings==0.26.2
+mkdocstrings-python==1.12.1
+nbclient==0.10.0
+nbconvert==7.16.4
+nbformat==5.10.4
+packaging==24.1
+paginate==0.5.7
+pandocfilters==1.5.1
+parso==0.8.4
+pathspec==0.12.1
+pexpect==4.9.0
+pickleshare==0.7.5
+pipreqs==0.5.0
+platformdirs==4.3.6
+prompt_toolkit==3.0.48
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