=========
dicom_wsi
=========
.. image:: https://img.shields.io/pypi/v/dicom_wsi.svg
:target: https://pypi.python.org/pypi/dicom_wsi
.. image:: https://img.shields.io/travis/Steven-N-Hart/dicom_wsi.svg
:target: https://travis-ci.com/Steven-N-Hart/dicom_wsi
.. image:: https://readthedocs.org/projects/dicom-wsi/badge/?version=latest
:target: https://dicom-wsi.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
----------
Package for converting whole slide image files to DICOM.
* Free software: MIT license
* Documentation: https://dicom-wsi.readthedocs.io.
=====
Usage
=====
First, you need to install dicom_wsi and its dependencies. See this link_ for details.
.. _link: https://dicom-wsi.readthedocs.io/en/latest/installation.html
To use dicom-wsi:
.. code-block:: console
python dicom_wsi.cli -w <WSI File path> -o <OutputDirectory> -p <output file prefix> -y yaml/base.yaml
or
.. code-block:: python
import dicom_wsi
dicom_wsi.dicom_wsi.create_dicom(cfg, pools=n_pools)
That's it! Most of the time you wan't need to change anything. But if you do, please see the example yaml_ file.
.. _yaml: https://github.com/Steven-N-Hart/dicom_wsi/blob/master/dicom_wsi/yaml/base.yaml
Features
--------
* Validate DICOM elements using pydicom_
* Output format DICOM formatted files (vetted with dciodvfy_)
TODO
--------
* Find out how to determine what `FileMetaInformationGroupLength` should be
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
.. _dciodvfy: https://www.dclunie.com/dicom3tools/dciodvfy.html
.. _`file type`: https://openslide.org/
.. _pydicom: https://pydicom.github.io/
=======
History
=======
1.0.5 (2025-10-09)
------------------
* Fixed AttributeError in cli.py by updating __init__.py.
1.0.4 (2023-10-27)
------------------
* Decreased dependencies for install
* Added tryCatch for Aperio data without expected metadata
0.1.0 (2021-1-22)
------------------
* First release on PyPI.
Raw data
{
"_id": null,
"home_page": "https://github.com/Steven-N-Hart/dicom_wsi",
"name": "dicom-wsi",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3",
"maintainer_email": null,
"keywords": "dicom_wsi",
"author": "Steven N. Hart",
"author_email": "hart.steven@mayo.edu",
"download_url": "https://files.pythonhosted.org/packages/62/0f/54be12f509d0a1e19ec9494372442338c870b2b0f9b609513978cd9ef7dc/dicom_wsi-1.0.5.tar.gz",
"platform": null,
"description": "=========\ndicom_wsi\n=========\n\n\n.. image:: https://img.shields.io/pypi/v/dicom_wsi.svg\n :target: https://pypi.python.org/pypi/dicom_wsi\n\n.. image:: https://img.shields.io/travis/Steven-N-Hart/dicom_wsi.svg\n :target: https://travis-ci.com/Steven-N-Hart/dicom_wsi\n\n.. image:: https://readthedocs.org/projects/dicom-wsi/badge/?version=latest\n :target: https://dicom-wsi.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n----------\n\nPackage for converting whole slide image files to DICOM.\n\n* Free software: MIT license\n* Documentation: https://dicom-wsi.readthedocs.io.\n\n=====\nUsage\n=====\n\nFirst, you need to install dicom_wsi and its dependencies. See this link_ for details.\n\n.. _link: https://dicom-wsi.readthedocs.io/en/latest/installation.html\n\nTo use dicom-wsi:\n.. code-block:: console\n\n python dicom_wsi.cli -w <WSI File path> -o <OutputDirectory> -p <output file prefix> -y yaml/base.yaml\n\nor\n\n.. code-block:: python\n\n import dicom_wsi\n dicom_wsi.dicom_wsi.create_dicom(cfg, pools=n_pools)\n\n\nThat's it! Most of the time you wan't need to change anything. But if you do, please see the example yaml_ file.\n\n.. _yaml: https://github.com/Steven-N-Hart/dicom_wsi/blob/master/dicom_wsi/yaml/base.yaml\n\nFeatures\n--------\n* Validate DICOM elements using pydicom_\n* Output format DICOM formatted files (vetted with dciodvfy_)\n\nTODO\n--------\n* Find out how to determine what `FileMetaInformationGroupLength` should be\n\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.. _dciodvfy: https://www.dclunie.com/dicom3tools/dciodvfy.html\n.. _`file type`: https://openslide.org/\n.. _pydicom: https://pydicom.github.io/\n\n\n=======\nHistory\n=======\n\n1.0.5 (2025-10-09)\n------------------\n\n* Fixed AttributeError in cli.py by updating __init__.py.\n\n1.0.4 (2023-10-27)\n------------------\n\n* Decreased dependencies for install\n* Added tryCatch for Aperio data without expected metadata\n\n\n\n0.1.0 (2021-1-22)\n------------------\n\n* First release on PyPI.\n",
"bugtrack_url": null,
"license": "MIT license",
"summary": "Package for converting whole slide image files to dicom.",
"version": "1.0.5",
"project_urls": {
"Homepage": "https://github.com/Steven-N-Hart/dicom_wsi"
},
"split_keywords": [
"dicom_wsi"
],
"urls": [
{
"comment_text": null,
"digests": {
"blake2b_256": "2e05db1b38e830110cd9e06740b6037006d84aaab19b3e6425a85fe6ee35a43a",
"md5": "3d8afdd4dacc7d88f3ef01ae5a6f0b95",
"sha256": "db738f5d532cd125bac95028e79acec33ae2ca8116ef3dfe33fbcbac25c94594"
},
"downloads": -1,
"filename": "dicom_wsi-1.0.5-py3-none-any.whl",
"has_sig": false,
"md5_digest": "3d8afdd4dacc7d88f3ef01ae5a6f0b95",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3",
"size": 48861,
"upload_time": "2025-10-09T13:44:38",
"upload_time_iso_8601": "2025-10-09T13:44:38.319668Z",
"url": "https://files.pythonhosted.org/packages/2e/05/db1b38e830110cd9e06740b6037006d84aaab19b3e6425a85fe6ee35a43a/dicom_wsi-1.0.5-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": null,
"digests": {
"blake2b_256": "620f54be12f509d0a1e19ec9494372442338c870b2b0f9b609513978cd9ef7dc",
"md5": "9c61c03b8f2c53fcb680c480ab988aec",
"sha256": "add737572fdc0415927932aff43db0e1370747cc3cb4573ab8f00c3b95fa9ec1"
},
"downloads": -1,
"filename": "dicom_wsi-1.0.5.tar.gz",
"has_sig": false,
"md5_digest": "9c61c03b8f2c53fcb680c480ab988aec",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3",
"size": 324791,
"upload_time": "2025-10-09T13:44:39",
"upload_time_iso_8601": "2025-10-09T13:44:39.659633Z",
"url": "https://files.pythonhosted.org/packages/62/0f/54be12f509d0a1e19ec9494372442338c870b2b0f9b609513978cd9ef7dc/dicom_wsi-1.0.5.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-10-09 13:44:39",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "Steven-N-Hart",
"github_project": "dicom_wsi",
"travis_ci": true,
"coveralls": false,
"github_actions": true,
"requirements": [
{
"name": "pyvips",
"specs": []
},
{
"name": "pydicom",
"specs": []
},
{
"name": "PyYAML",
"specs": []
},
{
"name": "numpy",
"specs": []
},
{
"name": "Pillow",
"specs": []
},
{
"name": "tifffile",
"specs": []
},
{
"name": "tiffile",
"specs": []
},
{
"name": "datetime",
"specs": []
},
{
"name": "openslide-python",
"specs": []
},
{
"name": "cython",
"specs": []
},
{
"name": "pylibjpeg",
"specs": []
},
{
"name": "pylibjpeg-libjpeg",
"specs": []
},
{
"name": "pylibjpeg-openjpeg",
"specs": []
},
{
"name": "pytest",
"specs": []
}
],
"lcname": "dicom-wsi"
}
JSON
