=============================================
Cell Maps ImmunoFluorescent Image Embedder
=============================================
|a| |b| |c| |d|
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:target: https://pypi.python.org/pypi/cellmaps_image_embedding
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:target: https://app.travis-ci.com/idekerlab/cellmaps_image_embedding
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:target: https://cellmaps-image-embedding.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. |d| image:: https://zenodo.org/badge/618547854.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10607452
:alt: Zenodo DOI badge
Generate embeddings from ImmunoFluorescent image data from `Human Protein Atlas <https://www.proteinatlas.org/>`__
* Free software: MIT license
* Documentation: https://cellmaps-image-embedding.readthedocs.io.
Dependencies
------------
* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__
* `tqdm <https://pypi.org/project/tqdm>`__
* `numpy <https://pypi.org/project/numpy>`__
* `pandas>=0.23.1 <https://pypi.org/project/pandas>`__
* `torch <https://pypi.org/project/torch>`__
* `torchvision <https://pypi.org/project/torchvision>`__
* `opencv-python <https://pypi.org/project/opencv-python>`__
* `mlcrate <https://pypi.org/project/mlcrate>`__
* `scikit-image <https://pypi.org/project/scikit-image>`__
* `scikit-learn>=0.19.0 <https://pypi.org/project/scikit-learn>`__
* `Pillow <https://pypi.org/project/Pillow>`__
Compatibility
-------------
* Python 3.8+
Installation
------------
.. code-block::
git clone https://github.com/idekerlab/cellmaps_image_embedding
cd cellmaps_image_embedding
make dist
pip install dist/cellmaps_image_embedding*whl
Run **make** command with no arguments to see other build/deploy options including creation of Docker image
.. code-block::
make
Output:
.. code-block::
clean remove all build, test, coverage and Python artifacts
clean-build remove build artifacts
clean-pyc remove Python file artifacts
clean-test remove test and coverage artifacts
lint check style with flake8
test run tests quickly with the default Python
test-all run tests on every Python version with tox
coverage check code coverage quickly with the default Python
docs generate Sphinx HTML documentation, including API docs
servedocs compile the docs watching for changes
testrelease package and upload a TEST release
release package and upload a release
dist builds source and wheel package
install install the package to the active Python's site-packages
dockerbuild build docker image and store in local repository
dockerpush push image to dockerhub
Before running tests, please install: ``pip install -r requirements_dev.txt``.
For developers
-------------------------------------------
To deploy development versions of this package
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Below are steps to make changes to this code base, deploy, and then run
against those changes.
#. Make changes
Modify code in this repo as desired
#. Build and deploy
.. code-block::
# From base directory of this repo cellmaps_image_embedding
pip uninstall cellmaps_image_embedding -y ; make clean dist; pip install dist/cellmaps_image_embedding*whl
Needed files
------------
The output directory for the image downloads is required (see `Cell Maps Image Downloader <https://github.com/idekerlab/cellmaps_imagedownloader/>`__). Optionally, a path to the image embedding model can be provided.
Usage
-----
For information invoke :code:`cellmaps_image_embeddingcmd.py -h`
**Example usage**
.. code-block::
cellmaps_image_embeddingcmd.py ./cellmaps_image_embedding_outdir --inputdir ./cellmaps_imagedownloader_outdir
Via Docker
~~~~~~~~~~~~~~~~~~~~~~
**Example usage**
.. code-block::
Coming soon...
Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _NDEx: http://www.ndexbio.org
=======
History
=======
0.2.1 (2024-09-06)
-------------------
* Bug fix in ``--inputdir`` argument.
0.2.0 (2024-08-29)
-------------------
* Added ``--provenance`` flag to pass a path to json file with provenance information. This removes the
necessity of input directory to be an RO-Crate.
* Bug fixes
* Resolved an issue in embedding generation process where images associated with multiple genes were not correctly
handled (ambiguous antibodies).
0.1.0 (2024-02-01)
------------------
* First release on PyPI.
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"description": "=============================================\nCell Maps ImmunoFluorescent Image Embedder\n=============================================\n|a| |b| |c| |d|\n\n.. |a| image:: https://img.shields.io/pypi/v/cellmaps_image_embedding.svg\n :target: https://pypi.python.org/pypi/cellmaps_image_embedding\n\n\n.. |b| image:: https://app.travis-ci.com/idekerlab/cellmaps_image_embedding.svg?branch=main\n :target: https://app.travis-ci.com/idekerlab/cellmaps_image_embedding\n\n\n.. |c| image:: https://readthedocs.org/projects/cellmaps-image-embedding/badge/?version=latest\n :target: https://cellmaps-image-embedding.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n\n.. |d| image:: https://zenodo.org/badge/618547854.svg\n :target: https://zenodo.org/doi/10.5281/zenodo.10607452\n :alt: Zenodo DOI badge\n\n\nGenerate embeddings from ImmunoFluorescent image data from `Human Protein Atlas <https://www.proteinatlas.org/>`__\n\n* Free software: MIT license\n* Documentation: https://cellmaps-image-embedding.readthedocs.io.\n\nDependencies\n------------\n\n* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__\n* `tqdm <https://pypi.org/project/tqdm>`__\n* `numpy <https://pypi.org/project/numpy>`__\n* `pandas>=0.23.1 <https://pypi.org/project/pandas>`__\n* `torch <https://pypi.org/project/torch>`__\n* `torchvision <https://pypi.org/project/torchvision>`__\n* `opencv-python <https://pypi.org/project/opencv-python>`__\n* `mlcrate <https://pypi.org/project/mlcrate>`__\n* `scikit-image <https://pypi.org/project/scikit-image>`__\n* `scikit-learn>=0.19.0 <https://pypi.org/project/scikit-learn>`__\n* `Pillow <https://pypi.org/project/Pillow>`__\n\nCompatibility\n-------------\n\n* Python 3.8+\n\nInstallation\n------------\n\n.. code-block::\n\n git clone https://github.com/idekerlab/cellmaps_image_embedding\n cd cellmaps_image_embedding\n make dist\n pip install dist/cellmaps_image_embedding*whl\n\n\nRun **make** command with no arguments to see other build/deploy options including creation of Docker image\n\n.. code-block::\n\n make\n\nOutput:\n\n.. code-block::\n\n clean remove all build, test, coverage and Python artifacts\n clean-build remove build artifacts\n clean-pyc remove Python file artifacts\n clean-test remove test and coverage artifacts\n lint check style with flake8\n test run tests quickly with the default Python\n test-all run tests on every Python version with tox\n coverage check code coverage quickly with the default Python\n docs generate Sphinx HTML documentation, including API docs\n servedocs compile the docs watching for changes\n testrelease package and upload a TEST release\n release package and upload a release\n dist builds source and wheel package\n install install the package to the active Python's site-packages\n dockerbuild build docker image and store in local repository\n dockerpush push image to dockerhub\n\n\nBefore running tests, please install: ``pip install -r requirements_dev.txt``.\n\nFor developers\n-------------------------------------------\n\n\nTo deploy development versions of this package\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nBelow are steps to make changes to this code base, deploy, and then run\nagainst those changes.\n\n#. Make changes\n\n Modify code in this repo as desired\n\n#. Build and deploy\n\n.. code-block::\n\n # From base directory of this repo cellmaps_image_embedding\n pip uninstall cellmaps_image_embedding -y ; make clean dist; pip install dist/cellmaps_image_embedding*whl\n\n\n\nNeeded files\n------------\n\nThe output directory for the image downloads is required (see `Cell Maps Image Downloader <https://github.com/idekerlab/cellmaps_imagedownloader/>`__). Optionally, a path to the image embedding model can be provided.\n\nUsage\n-----\n\nFor information invoke :code:`cellmaps_image_embeddingcmd.py -h`\n\n\n**Example usage**\n\n.. code-block::\n\n cellmaps_image_embeddingcmd.py ./cellmaps_image_embedding_outdir --inputdir ./cellmaps_imagedownloader_outdir\n\n\nVia Docker\n~~~~~~~~~~~~~~~~~~~~~~\n\n**Example usage**\n\n\n.. code-block::\n\n Coming soon...\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _NDEx: http://www.ndexbio.org\n\n\n=======\nHistory\n=======\n\n0.2.1 (2024-09-06)\n-------------------\n\n* Bug fix in ``--inputdir`` argument.\n\n0.2.0 (2024-08-29)\n-------------------\n\n* Added ``--provenance`` flag to pass a path to json file with provenance information. This removes the\n necessity of input directory to be an RO-Crate.\n\n* Bug fixes\n * Resolved an issue in embedding generation process where images associated with multiple genes were not correctly\n handled (ambiguous antibodies).\n\n0.1.0 (2024-02-01)\n------------------\n\n* First release on PyPI.\n",
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