Metadata-Version: 2.1
Name: cellmaps-image-embedding
Version: 0.1.0a12
Summary: A tool to generate embeddings from HPA IF images
Home-page: https://github.com/idekerlab/cellmaps_image_embedding
Author: Ideker Cell Maps team
Author-email: tools@cm4ai.org
License: MIT license
Keywords: cellmaps_image_embedding
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Description-Content-Type: text/x-rst
Requires-Dist: cellmaps-utils
Requires-Dist: requests
Requires-Dist: tqdm
Requires-Dist: numpy
Requires-Dist: pandas (>0.23.1)
Requires-Dist: torch
Requires-Dist: torchvision
Requires-Dist: opencv-python
Requires-Dist: mlcrate
Requires-Dist: scikit-image
Requires-Dist: scikit-learn (>=0.19.0)
Requires-Dist: Pillow

=============================================
Cell Maps ImmunoFluorescent Image Embedder
=============================================


.. image:: https://img.shields.io/pypi/v/cellmaps_image_embedding.svg
        :target: https://pypi.python.org/pypi/cellmaps_image_embedding

.. image:: https://app.travis-ci.com/idekerlab/cellmaps_image_embedding.svg?branch=main
        :target: https://app.travis-ci.com/idekerlab/cellmaps_image_embedding

.. image:: https://readthedocs.org/projects/cellmaps-image-embedding/badge/?version=latest
        :target: https://cellmaps-image-embedding.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status


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

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::

   docker run -v `pwd`:`pwd` -w `pwd` idekerlab/cellmaps_image_embedding:0.1.0 cellmaps_image_embeddingcmd.py ./cellmaps_image_embedding_outdir --inputdir ./cellmaps_imagedownloader_outdir 


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
=======

0.1.0 (2023-05-18)
------------------

* First release on PyPI.


