Initial commit

.github/workflows/test_and_deploy.yml

@@ -0,0 +1,73 @@
+# 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: tests
+
+on: push
+
+jobs:
+  ubuntu-latest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools tox tox-gh-actions
+      - name: Test with tox
+        run: tox
+      - name: Coverage
+        uses: codecov/codecov-action@v1
+
+  # minimizing matrix by only testing 3.6 on mac & windows
+  mac-win:
+    name: ${{ matrix.platform }} (3.6)
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [macos-latest, windows-latest]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.6
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools tox tox-gh-actions
+      - name: Test with tox
+        run: tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+  deploy:
+    needs: [ubuntu-latest, mac-win]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+        run: |
+          git tag
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

.gitignore

@@ -0,0 +1,79 @@
+# 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/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+*/_version.py

LICENSE

@@ -0,0 +1,28 @@
+
+Copyright (c) 2020, Draga Doncila Pop
+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 napari-nd2-reader 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.

MANIFEST.in

@@ -0,0 +1,6 @@
+include LICENSE
+include README.md
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

README.md

@@ -0,0 +1,57 @@
+# napari-nd2-reader
+
+[![License](https://img.shields.io/pypi/l/napari-nd2-reader.svg?color=green)](https://github.com/napari/napari-nd2-reader/raw/master/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-nd2-reader.svg?color=green)](https://pypi.org/project/napari-nd2-reader)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-nd2-reader.svg?color=green)](https://python.org)
+[![tests](https://github.com/DragaDoncila/napari-nd2-reader/workflows/tests/badge.svg)](https://github.com/DragaDoncila/napari-nd2-reader/actions)
+[![codecov](https://codecov.io/gh/DragaDoncila/napari-nd2-reader/branch/master/graph/badge.svg)](https://codecov.io/gh/DragaDoncila/napari-nd2-reader)
+
+Plugin to load nd2 data into napari
+
+----------------------------------
+
+This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/cookiecutter-napari-plugin#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/docs/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-nd2-reader` via [pip]:
+
+    pip install napari-nd2-reader
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [BSD-3] license,
+"napari-nd2-reader" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+[file an issue]: https://github.com/DragaDoncila/napari-nd2-reader/issues
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_nd2_reader/__init__.py

@@ -0,0 +1,10 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+# replace the asterisk with named imports
+from .nd2_reader import napari_get_reader
+
+
+__all__ = ["napari_get_reader"]

napari_nd2_reader/_tests/test_nd2_reader.py

@@ -0,0 +1,30 @@
+import numpy as np
+from napari_nd2_reader import napari_get_reader
+
+
+# tmp_path is a pytest fixture
+def test_reader(tmp_path):
+    """An example of how you might test your plugin."""
+
+    # write some fake data using your supported file format
+    my_test_file = str(tmp_path / "myfile.npy")
+    original_data = np.random.rand(20, 20)
+    np.save(my_test_file, original_data)
+
+    # try to read it back in
+    reader = napari_get_reader(my_test_file)
+    assert callable(reader)
+
+    # make sure we're delivering the right format
+    layer_data_list = reader(my_test_file)
+    assert isinstance(layer_data_list, list) and len(layer_data_list) > 0
+    layer_data_tuple = layer_data_list[0]
+    assert isinstance(layer_data_tuple, tuple) and len(layer_data_tuple) > 0
+
+    # make sure it's the same as it started
+    np.testing.assert_allclose(original_data, layer_data_tuple[0])
+
+
+def test_get_reader_pass():
+    reader = napari_get_reader("fake.file")
+    assert reader is None

napari_nd2_reader/nd2_reader.py

@@ -0,0 +1,79 @@
+"""
+This module is an example of a barebones numpy reader plugin for napari.
+
+It implements the ``napari_get_reader`` hook specification, (to create
+a reader plugin) but your plugin may choose to implement any of the hook
+specifications offered by napari.
+see: https://napari.org/docs/plugins/hook_specifications.html
+
+Replace code below accordingly.  For complete documentation see:
+https://napari.org/docs/plugins/for_plugin_developers.html
+"""
+import numpy as np
+from napari_plugin_engine import napari_hook_implementation
+
+
+@napari_hook_implementation
+def napari_get_reader(path):
+    """A basic implementation of the napari_get_reader hook specification.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    function or None
+        If the path is a recognized format, return a function that accepts the
+        same path or list of paths, and returns a list of layer data tuples.
+    """
+    if isinstance(path, list):
+        # reader plugins may be handed single path, or a list of paths.
+        # if it is a list, it is assumed to be an image stack...
+        # so we are only going to look at the first file.
+        path = path[0]
+
+    # if we know we cannot read the file, we immediately return None.
+    if not path.endswith(".npy"):
+        return None
+
+    # otherwise we return the *function* that can read ``path``.
+    return reader_function
+
+
+def reader_function(path):
+    """Take a path or list of paths and return a list of LayerData tuples.
+
+    Readers are expected to return data as a list of tuples, where each tuple
+    is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
+    both optional.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    layer_data : list of tuples
+        A list of LayerData tuples where each tuple in the list contains
+        (data, metadata, layer_type), where data is a numpy array, metadata is
+        a dict of keyword arguments for the corresponding viewer.add_* method
+        in napari, and layer_type is a lower-case string naming the type of layer.
+        Both "meta", and "layer_type" are optional. napari will default to
+        layer_type=="image" if not provided
+    """
+    # handle both a string and a list of strings
+    paths = [path] if isinstance(path, str) else path
+    # load all files into array
+    arrays = [np.load(_path) for _path in paths]
+    # stack arrays into single array
+    data = np.squeeze(np.stack(arrays))
+
+    # optional kwargs for the corresponding viewer.add_* method
+    # https://napari.org/docs/api/napari.components.html#module-napari.components.add_layers_mixin
+    add_kwargs = {}
+
+    layer_type = "image"  # optional, default is "image"
+    return [(data, add_kwargs, layer_type)]

requirements.txt

@@ -0,0 +1,2 @@
+napari-plugin-engine>=0.1.4
+numpy