├── .dockerignore ├── .github ├── FUNDING.yml ├── PULL_REQUEST_TEMPLATE.md ├── codespell_ignore_words.txt ├── dev-requirements.txt └── workflows │ ├── codespell.yaml │ ├── docs.yaml │ └── main.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .pylintrc ├── .travis.yml ├── AUTHORS.md ├── CHANGELOG.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── deid ├── __init__.py ├── config │ ├── __init__.py │ ├── standards.py │ └── utils.py ├── data │ ├── __init__.py │ ├── deid.dicom │ ├── deid.dicom.ultrasound │ └── deid.dicom.xray.chest ├── dicom │ ├── __init__.py │ ├── actions │ │ ├── __init__.py │ │ ├── jitter.py │ │ └── uids.py │ ├── config.json │ ├── fields.py │ ├── filter.py │ ├── groups.py │ ├── header.py │ ├── parser.py │ ├── pixels │ │ ├── __init__.py │ │ ├── clean.py │ │ └── detect.py │ ├── tags.py │ ├── utils.py │ └── validate.py ├── logger │ ├── __init__.py │ ├── message.py │ └── progress.py ├── main │ ├── __init__.py │ ├── identifiers.py │ └── inspect.py ├── tests │ ├── Xtest_dicom_header.py │ ├── __init__.py │ ├── common.py │ ├── resources │ │ ├── filter_multiple_first_filter_match.dicom │ │ ├── filter_multiple_rule_innerop_false.dicom │ │ ├── filter_multiple_rule_innerop_true.dicom │ │ ├── filter_multiple_second_filter_match.dicom │ │ ├── filter_multiple_two_filter_match.dicom │ │ ├── filter_multiple_zero_filter_match.dicom │ │ ├── filter_single_rule_false.dicom │ │ ├── filter_single_rule_innerop_false.dicom │ │ ├── filter_single_rule_innerop_true.dicom │ │ ├── filter_single_rule_true.dicom │ │ ├── filter_tag_number.dicom │ │ ├── keepcoordinates.dicom │ │ ├── keepcoordinates_from.dicom │ │ ├── keepcoordinates_noaction.dicom │ │ ├── remove_all.dicom │ │ ├── remove_coordinates.dicom │ │ ├── remove_coordinates_groups.dicom │ │ ├── remove_coordinates_multiple.dicom │ │ ├── remove_coordinates_multiple_filters.dicom │ │ ├── remove_coordinates_us.dicom │ │ └── remove_coordinates_us_all.dicom │ ├── test_action_interaction.py │ ├── test_blank_action.py │ ├── test_clean.py │ ├── test_clean_pixel_dimensions.py │ ├── test_cli.py │ ├── test_config.py │ ├── test_data.py │ ├── test_deid_recipe.py │ ├── test_dicom_fields.py │ ├── test_dicom_funcs.py │ ├── test_dicom_groups.py │ ├── test_dicom_pixels.py │ ├── test_dicom_tags.py │ ├── test_dicom_utils.py │ ├── test_file_meta.py │ ├── test_filter_detect.py │ ├── test_nested_dicom_fields.py │ ├── test_remove_action.py │ ├── test_replace_action.py │ ├── test_replace_identifiers.py │ ├── test_sequence_blank.py │ ├── test_sequence_jitter.py │ ├── test_sequence_remove.py │ ├── test_sequence_replace.py │ ├── test_utils.py │ └── test_utils_files.py ├── utils │ ├── __init__.py │ ├── actions.py │ └── fileio.py └── version.py ├── docs ├── .gitignore ├── Gemfile ├── README.md ├── _config.yml ├── _data │ └── links.yml ├── _docs │ ├── _defaults.md │ ├── contributing │ │ ├── code.md │ │ └── docs.md │ ├── development │ │ ├── image-format.md │ │ ├── index.md │ │ └── linting-format.md │ ├── examples │ │ ├── client.md │ │ ├── deid-dataset.md │ │ ├── func-replace.md │ │ ├── func-sequence-replace.md │ │ ├── header-expanders.md │ │ ├── index.md │ │ └── recipe.md │ ├── getting-started │ │ ├── dicom-config.md │ │ ├── dicom-get.md │ │ ├── dicom-loading.md │ │ ├── dicom-pixels.md │ │ ├── dicom-put.md │ │ └── index.md │ ├── install │ │ ├── docker.md │ │ ├── index.md │ │ └── local.md │ └── user-docs │ │ ├── client.md │ │ ├── index.md │ │ ├── recipe-filters.md │ │ ├── recipe-funcs.md │ │ ├── recipe-groups.md │ │ ├── recipe-headers.md │ │ ├── recipe-labels.md │ │ └── tags.md ├── _includes │ ├── head.html │ └── navigation.html ├── _layouts │ └── default.html ├── _posts │ ├── 2018-12-09-docs.md │ └── _defaults.md ├── api_docs │ ├── .nojekyll │ ├── Makefile │ ├── _static │ │ └── theme.css │ ├── _templates │ │ ├── class.rst │ │ └── function.rst │ ├── assets │ │ ├── favicon.ico │ │ └── logo.png │ ├── conf.py │ ├── docs-requirements.txt │ ├── index.rst │ ├── requirements.txt │ └── source │ │ ├── deid.config.rst │ │ ├── deid.data.rst │ │ ├── deid.dicom.actions.rst │ │ ├── deid.dicom.pixels.rst │ │ ├── deid.dicom.rst │ │ ├── deid.logger.rst │ │ ├── deid.main.rst │ │ ├── deid.rst │ │ ├── deid.tests.rst │ │ ├── deid.utils.rst │ │ └── modules.rst ├── apidoc.sh ├── assets │ ├── css │ │ └── deid.css │ ├── fonts │ │ ├── helveticaneueout-webfont.woff │ │ └── helveticaneueout-webfont.woff2 │ ├── img │ │ ├── apple-touch-icon.png │ │ ├── emblem.svg │ │ ├── favicon.ico │ │ ├── favicon.png │ │ ├── interaction-grid.png │ │ ├── logo.png │ │ ├── menu.svg │ │ ├── open-source-halloween-2021.png │ │ ├── siteicon.png │ │ └── touch-icon.png │ └── js │ │ ├── lunr.min.js │ │ └── search.js └── pages │ ├── 404.md │ ├── changelog.html │ ├── index.md │ ├── robots.txt │ └── search.html ├── examples ├── README.md ├── deid │ ├── README.md │ ├── deid.dicom │ ├── deid.dicom-groups │ ├── deid.dicom-private-creator-syntax │ └── deid.dicom-pusheen └── dicom │ ├── README.md │ ├── dicom-extract │ ├── README.md │ └── create-dicom-csv.py │ ├── header-manipulation │ ├── README.md │ ├── deid.dicom │ ├── file-meta │ │ ├── deid.dicom │ │ └── example.py │ ├── func-replacement.py │ └── func-sequence-replace │ │ ├── MR.dcm │ │ ├── cleaned.dcm │ │ ├── deid.dicom │ │ └── example.py │ ├── pixels │ ├── run-cleaner-client.py │ └── run-inspect-pixels.py │ └── recipe │ ├── deid-dicom-example.py │ ├── deid.dicom │ └── private-tags-demo.py ├── pyproject.toml ├── setup.cfg └── setup.py /.dockerignore: -------------------------------------------------------------------------------- 1 | deid.egg-info 2 | .build 3 | -------------------------------------------------------------------------------- /.github/FUNDING.yml: -------------------------------------------------------------------------------- 1 | github: vsoch 2 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: 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