process-dcm


Nameprocess-dcm JSON
Version 0.10.0 PyPI version JSON
download
home_pagehttps://github.com/pontikos-lab/process-dcm
SummaryPython library and app to extract images from DCM in a JSON-based standard format
upload_time2025-07-09 08:24:36
maintainerNone
docs_urlNone
authorAlan Silva
requires_python<4.0,>=3.10
licenseMIT
keywords
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            # Process DCM

[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg?style=plastic)](https://github.com/pontikos-lab/process-dcm/graphs/commit-activity)
[![GitHub](https://img.shields.io/github/license/pontikos-lab/process-dcm?style=plastic)](https://github.com/pontikos-lab/process-dcm)
[![GitHub release (latest by date)](https://img.shields.io/github/v/release/pontikos-lab/process-dcm?display_name=tag&logo=github&style=plastic)](https://github.com/pontikos-lab/process-dcm)
[![GitHub Release](https://img.shields.io/github/release-date/pontikos-lab/process-dcm?style=plastic&logo=github)](https://github.com/pontikos-lab/process-dcm)
[![PyPI](https://img.shields.io/pypi/v/process-dcm?style=plastic&logo=pypi)](https://pypi.org/project/process-dcm/)
[![Poetry](https://img.shields.io/endpoint?style=plastic&url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
[![Ruff](https://img.shields.io/endpoint?style=plastic&url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=plastic)](https://github.com/pre-commit/pre-commit)

## About The Project

Python library and app to extract images from DCM files with metadata in a JSON-based standard format

## Installation and Usage

```bash
pip install process-dcm
```

```bash
 Usage: process-dcm [OPTIONS] INPUT_PATH

 Process DICOM files in subfolders, extract images and metadata.
 Version: 0.9.0

╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *    input_path      PATH  Input path to either a DCM file or a folder containing DICOM files. [default: None] [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --image_format        -f      TEXT     Image format for extracted images (png, jpg, webp). [default: png]                 │
│ --output_dir          -o      PATH     Output directory for extracted images and metadata. [default: exported_data]       │
│ --group               -g               Re-group DICOM files in a given folder by AcquisitionDateTime.                     │
│ --tol                 -t      FLOAT    Tolerance in seconds for grouping DICOM files by AcquisitionDateTime. Only used    │
│                                        when --group is set.                                                               │
│                                        [default: None]                                                                    │
│ --n_jobs              -j      INTEGER  Number of parallel jobs. [default: 1]                                              │
│ --mapping             -m      TEXT     Path to CSV containing patient_id to study_id mapping. If not provided and         │
│                                        patient_id is anonymised, a 'study_2_patient.csv' file will be generated.          │
│ --keep                -k      TEXT     Keep the specified fields (p: patient_key, n: names, d: date_of_birth, D:          │
│                                        year-only DOB, g: gender)                                                          │
│ --overwrite           -w               Overwrite existing images if found.                                                │
│ --reset               -r               Reset the output directory if it exists.                                           │
│ --quiet               -q               Silence verbosity.                                                                 │
│ --version             -V               Prints app version.                                                                │
│ --install-completion                   Install completion for the current shell.                                          │
│ --show-completion                      Show completion for the current shell, to copy it or customize the installation.   │
│ --help                -h               Show this message and exit.                                                        │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
```

## For Developers

To run this project locally, you will need to install the prerequisites and follow the installation section.

### Prerequisites

This Project depends on the [`poetry`](https://python-poetry.org/).

1. Install poetry, via `homebrew` or [`pipx`](https://github.com/pypa/pipx):

   ```bash
   brew install poetry
   ```

   or

   ```bash
   pipx install poetry
   ```

2. Don't forget to use the python environment you set before and, if using `VScode`, apply it there.

3. It's optional, but we strongly recommend [`commitizen`](https://github.com/commitizen-tools/commitizen), which follows [Conventional Commits](https://www.conventionalcommits.org/)

### Installation

1. Clone the repo

   ```sh
   git clone https://github.com/pontikos-lab/process-dcm
   cd process-dcm
   ```

## Bumping Version

We use [`commitizen`](https://github.com/commitizen-tools/commitizen), which follows [Conventional Commits](https://www.conventionalcommits.org/). The instructions below are only for exceptional cases.

1. Using [poetry-bumpversion](https://github.com/monim67/poetry-bumpversion). Bump the version number by running `poetry version [part] [--dry-run]` where `[part]` is `major`, `minor`, or `patch`, depending on which part of the version number you want to bump.

   Use `--dry-run` option to check it in advance.

1. Push the tagged commit created above and the tag itself, i.e.:

   ```bash
   ver_tag=$(poetry version | cut -d ' ' -f2)
   git tag -a v"$ver_tag" -m "Tagged version $ver_tag"
   git push
   git push --tags
   ```

Raw data

            {
    "_id": null,
    "home_page": "https://github.com/pontikos-lab/process-dcm",
    "name": "process-dcm",
    "maintainer": null,
    "docs_url": null,
    "requires_python": "<4.0,>=3.10",
    "maintainer_email": null,
    "keywords": null,
    "author": "Alan Silva",
    "author_email": "3899850+alanwilter@users.noreply.github.com",
    "download_url": "https://files.pythonhosted.org/packages/10/84/6635056c030bef62523240f689b5dd40451d44f0c8ad8bc63e6bdae08600/process_dcm-0.10.0.tar.gz",
    "platform": null,
    "description": "# Process DCM\n\n[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg?style=plastic)](https://github.com/pontikos-lab/process-dcm/graphs/commit-activity)\n[![GitHub](https://img.shields.io/github/license/pontikos-lab/process-dcm?style=plastic)](https://github.com/pontikos-lab/process-dcm)\n[![GitHub release (latest by date)](https://img.shields.io/github/v/release/pontikos-lab/process-dcm?display_name=tag&logo=github&style=plastic)](https://github.com/pontikos-lab/process-dcm)\n[![GitHub Release](https://img.shields.io/github/release-date/pontikos-lab/process-dcm?style=plastic&logo=github)](https://github.com/pontikos-lab/process-dcm)\n[![PyPI](https://img.shields.io/pypi/v/process-dcm?style=plastic&logo=pypi)](https://pypi.org/project/process-dcm/)\n[![Poetry](https://img.shields.io/endpoint?style=plastic&url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)\n[![Ruff](https://img.shields.io/endpoint?style=plastic&url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)\n[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=plastic)](https://github.com/pre-commit/pre-commit)\n\n## About The Project\n\nPython library and app to extract images from DCM files with metadata in a JSON-based standard format\n\n## Installation and Usage\n\n```bash\npip install process-dcm\n```\n\n```bash\n Usage: process-dcm [OPTIONS] INPUT_PATH\n\n Process DICOM files in subfolders, extract images and metadata.\n Version: 0.9.0\n\n\u256d\u2500 Arguments \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 *    input_path      PATH  Input path to either a DCM file or a folder containing DICOM files. [default: None] [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --image_format        -f      TEXT     Image format for extracted images (png, jpg, webp). [default: png]                 \u2502\n\u2502 --output_dir          -o      PATH     Output directory for extracted images and metadata. [default: exported_data]       \u2502\n\u2502 --group               -g               Re-group DICOM files in a given folder by AcquisitionDateTime.                     \u2502\n\u2502 --tol                 -t      FLOAT    Tolerance in seconds for grouping DICOM files by AcquisitionDateTime. Only used    \u2502\n\u2502                                        when --group is set.                                                               \u2502\n\u2502                                        [default: None]                                                                    \u2502\n\u2502 --n_jobs              -j      INTEGER  Number of parallel jobs. [default: 1]                                              \u2502\n\u2502 --mapping             -m      TEXT     Path to CSV containing patient_id to study_id mapping. If not provided and         \u2502\n\u2502                                        patient_id is anonymised, a 'study_2_patient.csv' file will be generated.          \u2502\n\u2502 --keep                -k      TEXT     Keep the specified fields (p: patient_key, n: names, d: date_of_birth, D:          \u2502\n\u2502                                        year-only DOB, g: gender)                                                          \u2502\n\u2502 --overwrite           -w               Overwrite existing images if found.                                                \u2502\n\u2502 --reset               -r               Reset the output directory if it exists.                                           \u2502\n\u2502 --quiet               -q               Silence verbosity.                                                                 \u2502\n\u2502 --version             -V               Prints app version.                                                                \u2502\n\u2502 --install-completion                   Install completion for the current shell.                                          \u2502\n\u2502 --show-completion                      Show completion for the current shell, to copy it or customize the installation.   \u2502\n\u2502 --help                -h               Show this message and exit.                                                        \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n## For Developers\n\nTo run this project locally, you will need to install the prerequisites and follow the installation section.\n\n### Prerequisites\n\nThis Project depends on the [`poetry`](https://python-poetry.org/).\n\n1. Install poetry, via `homebrew` or [`pipx`](https://github.com/pypa/pipx):\n\n   ```bash\n   brew install poetry\n   ```\n\n   or\n\n   ```bash\n   pipx install poetry\n   ```\n\n2. Don't forget to use the python environment you set before and, if using `VScode`, apply it there.\n\n3. It's optional, but we strongly recommend [`commitizen`](https://github.com/commitizen-tools/commitizen), which follows [Conventional Commits](https://www.conventionalcommits.org/)\n\n### Installation\n\n1. Clone the repo\n\n   ```sh\n   git clone https://github.com/pontikos-lab/process-dcm\n   cd process-dcm\n   ```\n\n## Bumping Version\n\nWe use [`commitizen`](https://github.com/commitizen-tools/commitizen), which follows [Conventional Commits](https://www.conventionalcommits.org/). The instructions below are only for exceptional cases.\n\n1. Using [poetry-bumpversion](https://github.com/monim67/poetry-bumpversion). Bump the version number by running `poetry version [part] [--dry-run]` where `[part]` is `major`, `minor`, or `patch`, depending on which part of the version number you want to bump.\n\n   Use `--dry-run` option to check it in advance.\n\n1. Push the tagged commit created above and the tag itself, i.e.:\n\n   ```bash\n   ver_tag=$(poetry version | cut -d ' ' -f2)\n   git tag -a v\"$ver_tag\" -m \"Tagged version $ver_tag\"\n   git push\n   git push --tags\n   ```\n",
    "bugtrack_url": null,
    "license": "MIT",
    "summary": "Python library and app to extract images from DCM in a JSON-based standard format",
    "version": "0.10.0",
    "project_urls": {
        "Homepage": "https://github.com/pontikos-lab/process-dcm",
        "Repository": "https://github.com/pontikos-lab/process-dcm"
    },
    "split_keywords": [],
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "1a1d482833b9c71bac7c9c7d495b6ad39428e49ca3f3000cb716868f603d741e",
                "md5": "3db8e3cae531440825d3e46ad55e946f",
                "sha256": "51fec359f4c0d703c92fdc675a2fb7564c4f359162be21f915b43d4e2c80e316"
            },
            "downloads": -1,
            "filename": "process_dcm-0.10.0-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "3db8e3cae531440825d3e46ad55e946f",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": "<4.0,>=3.10",
            "size": 17967,
            "upload_time": "2025-07-09T08:24:35",
            "upload_time_iso_8601": "2025-07-09T08:24:35.504130Z",
            "url": "https://files.pythonhosted.org/packages/1a/1d/482833b9c71bac7c9c7d495b6ad39428e49ca3f3000cb716868f603d741e/process_dcm-0.10.0-py3-none-any.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "10846635056c030bef62523240f689b5dd40451d44f0c8ad8bc63e6bdae08600",
                "md5": "118c91d24c11fdebd2d5f58c00befa0c",
                "sha256": "2296a31c5bb33aeee3453380a666e6df63ed247c96e27d7a4ff8f7352179299d"
            },
            "downloads": -1,
            "filename": "process_dcm-0.10.0.tar.gz",
            "has_sig": false,
            "md5_digest": "118c91d24c11fdebd2d5f58c00befa0c",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": "<4.0,>=3.10",
            "size": 17843,
            "upload_time": "2025-07-09T08:24:36",
            "upload_time_iso_8601": "2025-07-09T08:24:36.485383Z",
            "url": "https://files.pythonhosted.org/packages/10/84/6635056c030bef62523240f689b5dd40451d44f0c8ad8bc63e6bdae08600/process_dcm-0.10.0.tar.gz",
            "yanked": false,
            "yanked_reason": null
        }
    ],
    "upload_time": "2025-07-09 08:24:36",
    "github": true,
    "gitlab": false,
    "bitbucket": false,
    "codeberg": false,
    "github_user": "pontikos-lab",
    "github_project": "process-dcm",
    "travis_ci": false,
    "coveralls": false,
    "github_actions": true,
    "lcname": "process-dcm"
}
Alan Silva
Elapsed time: 0.66981s