Change Segmentation timestamp from UTC to local time (#15)
* Change timestamp from UTC to local time * 🚨 Fix flake8 warnings * 📝 Add comments and documentation
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40
README.md
40
README.md
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@ -1,32 +1,34 @@
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# Introduction
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# Introduction
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InnerEye-DICOM-RT contains tools to convert medical datasets in NIFTI format to DICOM-RT. Datasets converted using
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InnerEye-DICOM-RT contains tools to convert medical datasets in NIFTI format to DICOM-RT. Datasets converted using
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this tool can be consumed directly by [InnerEye-DeepLearning](https://github.com/microsoft/InnerEye-DeepLearning).
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Most of the work is done by a .NET Core 2.1 project in RTConvert, written in C#. There is a very lightweight wrapper
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around this so that it can be consumed from Python. The wrapper relies on the PyPI package https://pypi.org/project/dotnetcore2/ which wraps up .NET Core 2.1.
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# Installing
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## Installing
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## Git for Windows
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### Git for Windows
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Get the installer from [Git for Windows](https://git-scm.com/download/win)
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||||
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The installer will prompt you to "Select Components". Make sure that you tick
|
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The installer will prompt you to "Select Components". Make sure that you tick
|
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* Git LFS (Large File Support)
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* Git Credential Manager for Windows
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After the installation, open a command prompt or the Git Bash:
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- Run `git lfs install` to set up the hooks in git
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- Run `git config --global core.autocrlf true` to ensure that line endings are working as expected
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* Run `git lfs install` to set up the hooks in git
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* Run `git config --global core.autocrlf true` to ensure that line endings are working as expected
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Clone the InnerEye-DICOM-RT repository on your machine: Run `git lfs clone --recursive https://github.com/microsoft/InnerEye-DICOM-RT`
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## Visual Studio / .NET Core
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### Visual Studio / .NET Core
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The C# components can be built with the .NET Core SDK. We use version 2.1 for compatibility with the PyPI package `dotnetcore2`.
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Installation instructions are here: https://docs.microsoft.com/en-us/dotnet/core/install/.
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Visual Studio is not required to build, but if you wish to use it then for .Net Core 2.1 you need at least:
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Installation instructions are here: https://docs.microsoft.com/en-us/dotnet/core/install/.
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Visual Studio is not required to build, but if you wish to use it then for .Net Core 2.1 you need at least:
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[Visual Studio 2017 version 15.7](https://visualstudio.microsoft.com/vs/?utm_medium=microsoft&utm_source=docs.microsoft.com&utm_campaign=inline+link).
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### RTConvert
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@ -55,12 +57,12 @@ Finally, for consumption by the Python wrapper, this solution must be published:
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dotnet publish RTConvert --configuration Release -p:Platform=x64
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```
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This should create a folder with all the requirements for RTConvert at:
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This should create a folder with all the requirements for RTConvert at:
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`RTConvert/Microsoft.RTConvert.Console/bin/x64/Release/netcoreapp2.1/publish/*`
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### Echo
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Echo is a very simple application that takes 1 or 2 arguments. The first is echoed to `stdout`, and if a
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Echo is a very simple application that takes 1 or 2 arguments. The first is echoed to `stdout`, and if a
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second argument is supplied then it is echoed to `stderr`. This is only required for units tests to establish
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that a .NET Core application can be called.
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@ -95,6 +97,7 @@ The Python package is created with:
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```bash
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python setup.py sdist bdist_wheel
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```
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which builds a source distribution and wheel to the `dist` folder.
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To run the Python tests:
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@ -132,6 +135,7 @@ To call RTConvert:
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```
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where:
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* `in_file` is the path to the input Nifti file. This file is a 3D volume in [Nifti format](https://nifti.nimh.nih.gov/).
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* `reference_series` is the path to the input folder containing the reference DICOM series;
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* `out_file` is the path to the output DICOM-RT file;
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@ -153,6 +157,12 @@ where:
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* `interpreter` Interpreter for the DICOM-RT (check DICOM-RT documentation)
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* `roi_interpreted_types` is a list of ROIInterpretedType. Possible values (None, CTV, ORGAN, EXTERNAL).
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### Segmentation Timestamps
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In the process of converting from NIFTI masks to DICOM, InnerEye-DICOM-RT adds a timestamp tag to the series. This timestamp will be set to the ***local time of the compute resource that `rtconvert()` is run on***. This is as some DICOM readers do not handle timezones / UTC offsets from these tags and will result in erroneous times being displayed. Therefore, if your compute resource is running in a different timezone to the timezone you are viewing the DICOM files in, the timestamps may not be what you are expecting.
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## License
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[MIT License](LICENSE)
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**You are responsible for the performance, the necessary testing, and if needed any regulatory clearance for
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@ -162,7 +172,7 @@ where:
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|||
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This project welcomes contributions and suggestions. Most contributions require you to agree to a
|
||||
Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us
|
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the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
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the rights to use your contribution. For details, visit the [Micrsoft CLA page](https://cla.opensource.microsoft.com).
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||||
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When you submit a pull request, a CLA bot will automatically determine whether you need to provide
|
||||
a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions
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@ -174,8 +184,8 @@ contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with any additio
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## Trademarks
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This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft
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trademarks or logos is subject to and must follow
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This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft
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trademarks or logos is subject to and must follow
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[Microsoft's Trademark & Brand Guidelines](https://www.microsoft.com/en-us/legal/intellectualproperty/trademarks/usage/general).
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Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship.
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Any use of third-party trademarks or logos are subject to those third-party's policies.
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@ -55,7 +55,9 @@ namespace Microsoft.RTConvert.MedIO.RT
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ds.Add(DicomTag.SeriesNumber, string.Empty);
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// Type 3 tags - optional but useful
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var now = DateTime.UtcNow;
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// Using DateTime.Now as some DICOM readers do not handle UTC offests. Local time is best guess.
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var now = DateTime.Now;
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var date = now.ToString("yyyyMMdd", CultureInfo.InvariantCulture);
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var time = now.ToString("HHmmss", CultureInfo.InvariantCulture);
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ds.Add(DicomTag.SeriesDate, date);
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@ -63,4 +65,4 @@ namespace Microsoft.RTConvert.MedIO.RT
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}
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}
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}
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}
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@ -1,5 +1,5 @@
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dotnetcore2==2.1.23
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flake8==3.8.4
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flake8==5.0.4
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mypy==0.800
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pydicom==2.1.2
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pytest-cov==2.11.1
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@ -1,183 +1,179 @@
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# ------------------------------------------------------------------------------------------
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# Copyright (c) Microsoft Corporation. All rights reserved.
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# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
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# ------------------------------------------------------------------------------------------
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"""
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Tests for nifti_to_dicom_rt_converter.
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"""
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import logging
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from pathlib import Path
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from typing import List
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from pydicom import dcmread
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try:
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from InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
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except ImportError:
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logging.info("using local src")
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from src.InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
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logger = logging.getLogger('test_rtconvert')
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logger.setLevel(logging.DEBUG)
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def test_get_version() -> None:
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"""
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Test that .dotnet core can be called --info and that it is
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running version 2.1.
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"""
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(stdout, stderr) = get_version()
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert 'Microsoft.NETCore.App 2.1.' in stdout
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def test_echo() -> None:
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"""
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Test that the test Echo dll can be called and returns the test string and no error.
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"""
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test_string = "hello world2!"
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(stdout, stderr) = echo(test_string)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert stdout == test_string + '\n'
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def test_echo_err() -> None:
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"""
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Test that the test Echo dll can be called and returns the test and error strings.
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"""
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test_string = "hello world2!"
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test_error = "Test error."
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(stdout, stderr) = echo(test_string, test_error)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == test_error + '\n'
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assert stdout == test_string + '\n'
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# The directory containing this file.
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THIS_DIR: Path = Path(__file__).parent.resolve()
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# The TestData directory.
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TEST_DATA_DIR: Path = THIS_DIR / "TestData"
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# Test Nifti file.
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TestNiftiSegmentationLocation: Path = TEST_DATA_DIR / "hnsegmentation.nii.gz"
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# Test reference series.
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TestDicomVolumeLocation: Path = TEST_DATA_DIR / "HN"
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# Target test output file.
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TestOutputFile: Path = THIS_DIR / "test.dcm"
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# Test fill holes.
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FillHoles: List[bool] = \
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[
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True, True, True, True,
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False, False, True, True,
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True, True, False, True,
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True, True, True, False,
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True, False, True, True,
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False, True
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]
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# Test ROIInterpretedType.
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ROIInterpretedTypes: List[str] = \
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[
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None", "CTV", "EXTERNAL",
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"ORGAN", "None"
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]
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# Test structure colors.
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StructureColors: List[str] = \
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[
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"FF0001", "FF0002", "FF0003", "FF0004",
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"FF0101", "FF0102", "FF0103", "FF0103",
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"FF0201", "FF02FF", "FF0203", "FF0204",
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"FF0301", "FF0302", "01FF03", "FF0304",
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"FF0401", "00FFFF", "FF0403", "FF0404",
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"FF0501", "FF0502"
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]
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# Test structure names.
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StructureNames: List[str] = \
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[
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"External", "parotid_l", "parotid_r", "smg_l",
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"smg_r", "spinal_cord", "brainstem", "globe_l",
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"Globe_r", "mandible", "spc_muscle", "mpc_muscle",
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"Cochlea_l", "cochlea_r", "lens_l", "lens_r",
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"optic_chiasm", "optic_nerve_l", "optic_nerve_r", "pituitary_gland",
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"lacrimal_gland_l", "lacrimal_gland_r"
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]
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Manufacturer = "Contosos"
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Interpreter = "Ai"
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ModelId = "XYZ:12"
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def test_rtconvert() -> None:
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"""
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Test calling RTConvert for the test data.
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"""
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(stdout, stderr) = rtconvert(
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in_file=TestNiftiSegmentationLocation,
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reference_series=TestDicomVolumeLocation,
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out_file=TestOutputFile,
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struct_names=StructureNames,
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struct_colors=StructureColors,
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fill_holes=FillHoles,
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roi_interpreted_types=ROIInterpretedTypes,
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manufacturer=Manufacturer,
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interpreter=Interpreter,
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modelId=ModelId
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)
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logger.debug("stdout: %s", stdout)
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logger.debug("stderr: %s", stderr)
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assert stderr == ''
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assert "Successfully written" in stdout
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assert TestOutputFile.is_file()
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with open(TestOutputFile, 'rb') as infile:
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ds = dcmread(infile)
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assert ds is not None
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# Check the modality
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assert ds.Modality == 'RTSTRUCT'
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assert ds.Manufacturer == Manufacturer
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assert ds.SoftwareVersions == ModelId
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assert len(ds.StructureSetROISequence) == len(StructureNames)
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for i, item in enumerate(StructureNames):
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assert ds.StructureSetROISequence[i].ROINumber == i + 1
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assert ds.StructureSetROISequence[i].ROIName == item
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assert Interpreter in ds.RTROIObservationsSequence[i].ROIInterpreter
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assert ds.RTROIObservationsSequence[i].RTROIInterpretedType == ('' if ROIInterpretedTypes[i] == 'None' else ROIInterpretedTypes[i])
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assert len(ds.ROIContourSequence) == len(StructureNames)
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for i, item in enumerate(StructureNames):
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assert ds.ROIContourSequence[i].ReferencedROINumber == i + 1
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assert ds.ROIContourSequence[i].ROIDisplayColor == _parse_rgb(StructureColors[i])
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def _parse_rgb(rgb: str) -> List[int]:
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"""
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Convert the string representation of RGB color to an int list
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:param rgb: Color string
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:return: List of [R, G, B] components.
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"""
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return [int(rgb[i:i+2], 16) for i in (0, 2, 4)]
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# ------------------------------------------------------------------------------------------
|
||||
# Copyright (c) Microsoft Corporation. All rights reserved.
|
||||
# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
|
||||
# ------------------------------------------------------------------------------------------
|
||||
|
||||
"""
|
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Tests for nifti_to_dicom_rt_converter.
|
||||
"""
|
||||
|
||||
import logging
|
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from pathlib import Path
|
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from typing import List
|
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from pydicom import dcmread
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|
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try:
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from InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
|
||||
except ImportError:
|
||||
logging.info("using local src")
|
||||
from src.InnerEye_DICOM_RT.nifti_to_dicom_rt_converter import echo, get_version, rtconvert # type: ignore
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||||
|
||||
logger = logging.getLogger('test_rtconvert')
|
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logger.setLevel(logging.DEBUG)
|
||||
|
||||
|
||||
def test_get_version() -> None:
|
||||
"""
|
||||
Test that .dotnet core can be called --info and that it is
|
||||
running version 2.1.
|
||||
"""
|
||||
(stdout, stderr) = get_version()
|
||||
|
||||
logger.debug("stdout: %s", stdout)
|
||||
logger.debug("stderr: %s", stderr)
|
||||
|
||||
assert stderr == ''
|
||||
assert 'Microsoft.NETCore.App 2.1.' in stdout
|
||||
|
||||
|
||||
def test_echo() -> None:
|
||||
"""
|
||||
Test that the test Echo dll can be called and returns the test string and no error.
|
||||
"""
|
||||
test_string = "hello world2!"
|
||||
(stdout, stderr) = echo(test_string)
|
||||
|
||||
logger.debug("stdout: %s", stdout)
|
||||
logger.debug("stderr: %s", stderr)
|
||||
|
||||
assert stderr == ''
|
||||
assert stdout == test_string + '\n'
|
||||
|
||||
|
||||
def test_echo_err() -> None:
|
||||
"""
|
||||
Test that the test Echo dll can be called and returns the test and error strings.
|
||||
"""
|
||||
test_string = "hello world2!"
|
||||
test_error = "Test error."
|
||||
(stdout, stderr) = echo(test_string, test_error)
|
||||
|
||||
logger.debug("stdout: %s", stdout)
|
||||
logger.debug("stderr: %s", stderr)
|
||||
|
||||
assert stderr == test_error + '\n'
|
||||
assert stdout == test_string + '\n'
|
||||
|
||||
|
||||
# The directory containing this file.
|
||||
THIS_DIR: Path = Path(__file__).parent.resolve()
|
||||
# The TestData directory.
|
||||
TEST_DATA_DIR: Path = THIS_DIR / "TestData"
|
||||
# Test Nifti file.
|
||||
TestNiftiSegmentationLocation: Path = TEST_DATA_DIR / "hnsegmentation.nii.gz"
|
||||
# Test reference series.
|
||||
TestDicomVolumeLocation: Path = TEST_DATA_DIR / "HN"
|
||||
# Target test output file.
|
||||
TestOutputFile: Path = THIS_DIR / "test.dcm"
|
||||
|
||||
# Test fill holes.
|
||||
FillHoles: List[bool] = [
|
||||
True, True, True, True,
|
||||
False, False, True, True,
|
||||
True, True, False, True,
|
||||
True, True, True, False,
|
||||
True, False, True, True,
|
||||
False, True
|
||||
]
|
||||
|
||||
# Test ROIInterpretedType.
|
||||
ROIInterpretedTypes: List[str] = [
|
||||
"ORGAN", "None", "CTV", "EXTERNAL",
|
||||
"ORGAN", "None", "CTV", "EXTERNAL",
|
||||
"ORGAN", "None", "CTV", "EXTERNAL",
|
||||
"ORGAN", "None", "CTV", "EXTERNAL",
|
||||
"ORGAN", "None", "CTV", "EXTERNAL",
|
||||
"ORGAN", "None"
|
||||
]
|
||||
|
||||
# Test structure colors.
|
||||
StructureColors: List[str] = [
|
||||
"FF0001", "FF0002", "FF0003", "FF0004",
|
||||
"FF0101", "FF0102", "FF0103", "FF0103",
|
||||
"FF0201", "FF02FF", "FF0203", "FF0204",
|
||||
"FF0301", "FF0302", "01FF03", "FF0304",
|
||||
"FF0401", "00FFFF", "FF0403", "FF0404",
|
||||
"FF0501", "FF0502"
|
||||
]
|
||||
|
||||
# Test structure names.
|
||||
StructureNames: List[str] = [
|
||||
"External", "parotid_l", "parotid_r", "smg_l",
|
||||
"smg_r", "spinal_cord", "brainstem", "globe_l",
|
||||
"Globe_r", "mandible", "spc_muscle", "mpc_muscle",
|
||||
"Cochlea_l", "cochlea_r", "lens_l", "lens_r",
|
||||
"optic_chiasm", "optic_nerve_l", "optic_nerve_r", "pituitary_gland",
|
||||
"lacrimal_gland_l", "lacrimal_gland_r"
|
||||
]
|
||||
|
||||
Manufacturer = "Contosos"
|
||||
Interpreter = "Ai"
|
||||
ModelId = "XYZ:12"
|
||||
|
||||
def test_rtconvert() -> None:
|
||||
"""
|
||||
Test calling RTConvert for the test data.
|
||||
"""
|
||||
(stdout, stderr) = rtconvert(
|
||||
in_file=TestNiftiSegmentationLocation,
|
||||
reference_series=TestDicomVolumeLocation,
|
||||
out_file=TestOutputFile,
|
||||
struct_names=StructureNames,
|
||||
struct_colors=StructureColors,
|
||||
fill_holes=FillHoles,
|
||||
roi_interpreted_types=ROIInterpretedTypes,
|
||||
manufacturer=Manufacturer,
|
||||
interpreter=Interpreter,
|
||||
modelId=ModelId
|
||||
)
|
||||
|
||||
logger.debug("stdout: %s", stdout)
|
||||
logger.debug("stderr: %s", stderr)
|
||||
|
||||
assert stderr == ''
|
||||
assert "Successfully written" in stdout
|
||||
|
||||
assert TestOutputFile.is_file()
|
||||
|
||||
with open(TestOutputFile, 'rb') as infile:
|
||||
ds = dcmread(infile)
|
||||
|
||||
assert ds is not None
|
||||
|
||||
# Check the modality
|
||||
assert ds.Modality == 'RTSTRUCT'
|
||||
|
||||
assert ds.Manufacturer == Manufacturer
|
||||
assert ds.SoftwareVersions == ModelId
|
||||
|
||||
assert len(ds.StructureSetROISequence) == len(StructureNames)
|
||||
|
||||
for i, item in enumerate(StructureNames):
|
||||
assert ds.StructureSetROISequence[i].ROINumber == i + 1
|
||||
assert ds.StructureSetROISequence[i].ROIName == item
|
||||
assert Interpreter in ds.RTROIObservationsSequence[i].ROIInterpreter
|
||||
assert ds.RTROIObservationsSequence[i].RTROIInterpretedType == ('' if ROIInterpretedTypes[i] == 'None' else ROIInterpretedTypes[i])
|
||||
|
||||
assert len(ds.ROIContourSequence) == len(StructureNames)
|
||||
|
||||
for i, item in enumerate(StructureNames):
|
||||
assert ds.ROIContourSequence[i].ReferencedROINumber == i + 1
|
||||
assert ds.ROIContourSequence[i].ROIDisplayColor == _parse_rgb(StructureColors[i])
|
||||
|
||||
def _parse_rgb(rgb: str) -> List[int]:
|
||||
"""
|
||||
Convert the string representation of RGB color to an int list
|
||||
:param rgb: Color string
|
||||
:return: List of [R, G, B] components.
|
||||
"""
|
||||
return [int(rgb[i:i+2], 16) for i in (0, 2, 4)]
|
||||
|
|
|
|||
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