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Merge pull request #47 from BrainLesion/43-add-2024-inpainting-algorithms
43 add 2024 inpainting algorithms
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‎README.md

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@@ -26,7 +26,7 @@ pip install brats
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> [!IMPORTANT]
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> To run `brats` you require a Docker installation. <br>
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> Many algorithms also require GPU support (NVIDIA Docker). <br>
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> In case you do not have access to a Cuda-capable GPU, the overview tables in the [Algorithms](#algorithms) section indicate which algorithms are CPU compatible.
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> In case you do not have access to a Cuda-capable GPU, the overview tables in the [Available Algorithms and Usage](#available-algorithms-and-Usage) section indicate which algorithms are CPU compatible.
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- **Docker**: Installation instructions on the official [website](https://docs.docker.com/get-docker/)
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- **NVIDIA Container Toolkit**: Refer to the [NVIDIA install guide](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html) and the official [GitHub page](https://github.com/NVIDIA/nvidia-container-toolkit)
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## Use Cases and Tutorials
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A minimal example to create a segmentation could look like this:
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## Available Algorithms and Usage
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### Segmentation
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<details open>
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<summary> <strong> Adult Glioma Segmentation </strong> </summary>
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<br>
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```python
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from brats import AdultGliomaSegmenter
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from brats.utils.constants import AdultGliomaAlgorithms
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from brats.constants import AdultGliomaAlgorithms
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segmenter = AdultGliomaSegmenter(algorithm=AdultGliomaAlgorithms.BraTS23_1, cuda_devices="0")
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# these parameters are optional, by default the winning algorithm will be used on cuda:0
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)
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```
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For more examples and details please refer to our extensive Notebook tutorials here [NBViewer](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/BraTS/tutorial.ipynb) ([GitHub](https://github.com/BrainLesion/tutorials/blob/main/BraTS/tutorial.ipynb)). For the best experience open the notebook in Colab.
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## Algorithms
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<details open>
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<summary> <strong> Adult Glioma Segmentation </strong> </summary>
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<br>
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**Class:** `brats.AdultGliomaSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.AdultGliomaSegmenter))
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | --------------------------------- | ------------------------------------------ | ----------- | ------------------------------------------------------------------------------------------------------------------------ |
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | --------------------------------- | ------------------------------------------ | ----------- | -------------------------------------------------------------------------------------------------------------------------- |
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| 2023 | 1st | _André Ferreira, et al._ | [Link](https://arxiv.org/abs/2402.17317v1) | &#x274C; | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AdultGliomaAlgorithms.BraTS23_1) |
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| 2023 | 2nd | _Andriy Myronenko, et al._ | N/A | &#x274C; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AdultGliomaAlgorithms.BraTS23_2) |
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| 2023 | 3rd | _Fadillah Adamsyah Maani, et al._ | N/A | &#x274C; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AdultGliomaAlgorithms.BraTS23_3) |
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<summary> <strong> BraTS-Africa Segmentation </strong> </summary>
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<br>
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```python
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from brats import AfricaSegmenter
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from brats.constants import AfricaAlgorithms
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segmenter = AfricaSegmenter(algorithm=AfricaAlgorithms.BraTS23_1, cuda_devices="0")
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# these parameters are optional, by default the winning algorithm will be used on cuda:0
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segmenter.infer_single(
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t1c="path/to/t1c.nii.gz",
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t1n="path/to/t1n.nii.gz",
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t2f="path/to/t2f.nii.gz",
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t2w="path/to/t2w.nii.gz",
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output_file="segmentation.nii.gz",
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)
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```
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**Class:** `brats.AfricaSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.AfricaSegmenter))
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------- |
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | --------------------------------------------------------------------------------------------------------------------- |
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| 2023 | 1st | _Andriy Myronenko, et al._ | TODO | &#x274C; | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AfricaAlgorithms.BraTS23_1) |
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| 2023 | 2nd | _Alyssa R Amod, et al._ | N/A | &#x274C; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AfricaAlgorithms.BraTS23_2) |
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| 2023 | 3rd | _Ziyan Huang, et al._ | N/A | &#x2705; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AfricaAlgorithms.BraTS23_3) |
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<summary> <strong> Meningioma Segmentation </strong> </summary>
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<br>
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```python
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from brats import MeningiomaSegmenter
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from brats.constants import MeningiomaAlgorithms
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segmenter = MeningiomaSegmenter(algorithm=MeningiomaAlgorithms.BraTS23_1, cuda_devices="0")
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# these parameters are optional, by default the winning algorithm will be used on cuda:0
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segmenter.infer_single(
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t1c="path/to/t1c.nii.gz",
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t1n="path/to/t1n.nii.gz",
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t2f="path/to/t2f.nii.gz",
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t2w="path/to/t2w.nii.gz",
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output_file="segmentation.nii.gz",
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)
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```
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**Class:** `brats.MeningiomaSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.MeningiomaSegmenter))
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | ----------------------------------------------------------------------------------------------------------------------- |
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------- |
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| 2023 | 1st | _Andriy Myronenko, et al._ | N/A | &#x274C; | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MeningiomaAlgorithms.BraTS23_1) |
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| 2023 | 2nd | _Ziyan Huang, et al._ | N/A | &#x2705; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MeningiomaAlgorithms.BraTS23_2) |
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| 2023 | 3rd | _Zhifan Jiang et al._ | N/A | &#x274C; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MeningiomaAlgorithms.BraTS23_3) |
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<summary> <strong> Brain Metastases Segmentation </strong> </summary>
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<br>
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```python
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from brats import MetastasesSegmenter
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from brats.constants import MetastasesAlgorithms
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segmenter = MetastasesSegmenter(algorithm=MetastasesAlgorithms.BraTS23_1, cuda_devices="0")
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# these parameters are optional, by default the winning algorithm will be used on cuda:0
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segmenter.infer_single(
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t1c="path/to/t1c.nii.gz",
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t1n="path/to/t1n.nii.gz",
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t2f="path/to/t2f.nii.gz",
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t2w="path/to/t2w.nii.gz",
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output_file="segmentation.nii.gz",
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)
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```
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**Class:** `brats.MetastasesSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.MetastasesSegmenter))
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | ----------------------------------------------------------------------------------------------------------------------- |
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------- |
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| 2023 | 1st | _Andriy Myronenko, et al._ | N/A | &#x274C; | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MetastasesAlgorithms.BraTS23_1) |
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| 2023 | 2nd | _Siwei Yang, et al._ | N/A | &#x274C; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MetastasesAlgorithms.BraTS23_2) |
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| 2023 | 3rd | _Ziyan Huang, et al._ | N/A | &#x2705; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MetastasesAlgorithms.BraTS23_3) |
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<summary> <strong> Pediatric Segmentation </strong> </summary>
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<br>
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```python
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from brats import PediatricSegmenter
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from brats.constants import PediatricAlgorithms
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segmenter = PediatricSegmenter(algorithm=PediatricAlgorithms.BraTS23_1, cuda_devices="0")
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# these parameters are optional, by default the winning algorithm will be used on cuda:0
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segmenter.infer_single(
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t1c="path/to/t1c.nii.gz",
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t1n="path/to/t1n.nii.gz",
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t2f="path/to/t2f.nii.gz",
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t2w="path/to/t2w.nii.gz",
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output_file="segmentation.nii.gz",
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)
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```
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**Class:** `brats.PediatricSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.PediatricSegmenter))
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | ---------------------------------------------------------------------------------------------------------------------- |
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------ |
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| 2023 | 1st | _Zhifan Jiang et al._ | N/A | &#x274C; | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_1) |
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| 2023 | 2nd | _Andriy Myronenko, et al._ | N/A | &#x274C; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_2) |
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| 2023 | 3rd | _Yubo Zhou_ | N/A | &#x274C; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_3) |
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</details>
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---
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### Inpainting
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<details>
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<summary> <strong> Inpainting </strong> </summary>
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<br>
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```python
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from brats import Inpainter
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from brats.constants import InpaintingAlgorithms
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inpainter = Inpainter(algorithm=InpaintingAlgorithms.BraTS24_1, cuda_devices="0")
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inpainter.infer_single(
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t1n="path/to/voided_t1n.nii.gz",
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mask="path/to/mask.nii.gz",
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output_file="inpainting.nii.gz",
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)
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```
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**Class:** `brats.Inpainter` ([Docs](https://brats.readthedocs.io/en/latest/core/inpainting_algorithms.html#brats.core.inpainting_algorithms.Inpainter))
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | ----------------------- | ----- | ----------- | ----------------------------------------------------------------------------------------------------------------------- |
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| 2023 | 1st | _Juexin Zhang, et al._ | N/A | &#x2705; | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_1) |
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| 2023 | 2nd | _Alicia Durrer, et al._ | N/A | &#x274C; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_2) |
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| 2023 | 3rd | _Jiayu Huo, et al._ | N/A | &#x2705; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_3) |
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| Year | Rank | Author | Paper | CPU Support | Key Enum |
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| ---- | ---- | ---------------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------- |
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| 2024 | 1st | _Ke Chen, Juexin Zhang, Ying Weng_ | N/A | &#x2705; | [BraTS24_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS24_1) |
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| 2024 | 2nd | _André Ferreira, et al._ | N/A | &#x274C; | [BraTS24_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS24_2) |
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| 2024 | 3rd | _Team SMINT_ | N/A | &#x274C; | [BraTS24_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS24_3) |
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| 2023 | 1st | _Juexin Zhang, et al._ | N/A | &#x2705; | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_1) |
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| 2023 | 2nd | _Alicia Durrer, et al._ | N/A | &#x274C; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_2) |
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| 2023 | 3rd | _Jiayu Huo, et al._ | N/A | &#x2705; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_3) |
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</details>
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>[!TIP]
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>For a full notebook example with more details please check here:
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> [![nbviewer](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/BraTS/tutorial.ipynb)
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## Citation
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If you use BraTS in your research, please cite it to support the development!

‎brats/utils/constants.py renamed to ‎brats/constants.py

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class InpaintingAlgorithms(Algorithms):
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"""Constants for the available BraTS Inpainting algorithms."""
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BraTS24_1 = "BraTS24_1"
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""" BraTS24 Inpainting 1st place """
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BraTS24_2 = "BraTS24_2"
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""" BraTS24 Inpainting 2nd place """
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BraTS24_3 = "BraTS24_3"
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""" BraTS24 Inpainting 3rd place """
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BraTS23_1 = "BraTS23_1"
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"""BraTS23 Inpainting 1st place (GPU only)"""
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""" BraTS23 Inpainting 1st place """
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BraTS23_2 = "BraTS23_2"
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"""BraTS23 Inpainting 2nd place (GPU only) (Very Slow)"""
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""" BraTS23 Inpainting 2nd place (Very Slow) """
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BraTS23_3 = "BraTS23_3"
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"""BraTS23 Inpainting 3rd place (GPU only)"""
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""" BraTS23 Inpainting 3rd place """
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# DIRECTORIES
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DATA_DIR = Path(__file__).parent.parent / "data"
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DATA_DIR = Path(__file__).parent / "data"
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META_DIR = DATA_DIR / "meta"
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PARAMETERS_DIR = DATA_DIR / "parameters"
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ADDITIONAL_FILES_FOLDER = DATA_DIR / "additional_files"

‎brats/core/brats_algorithm.py

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from brats.core.docker import run_container
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from brats.utils.algorithm_config import load_algorithms
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from brats.utils.constants import OUTPUT_NAME_SCHEMA, Algorithms, Task
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from brats.constants import OUTPUT_NAME_SCHEMA, Algorithms, Task
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from brats.utils.data_handling import InferenceSetup
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# Remove the default logger and add one with level INFO

‎brats/core/docker.py

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from rich.progress import Progress
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from brats.utils.algorithm_config import AlgorithmData
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from brats.utils.constants import DUMMY_PARAMETERS, PARAMETERS_DIR
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from brats.constants import DUMMY_PARAMETERS, PARAMETERS_DIR
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from brats.utils.exceptions import (
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AlgorithmNotCPUCompatibleException,
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BraTSContainerException,
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# Wait for the container to finish
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exit_code = container.wait()
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container_output = "\n\r".join(
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[line.decode("utf-8") for line in container_output]
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[line.decode("utf-8", errors="replace") for line in container_output]
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)
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# Check if the container exited with an error
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if exit_code["StatusCode"] != 0:

‎brats/core/inpainting_algorithms.py

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from loguru import logger
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from brats.core.brats_algorithm import BraTSAlgorithm
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from brats.utils.constants import INPAINTING_ALGORITHMS, InpaintingAlgorithms, Task
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from brats.constants import INPAINTING_ALGORITHMS, InpaintingAlgorithms, Task
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from brats.utils.data_handling import input_sanity_check
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‎brats/core/segmentation_algorithms.py

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from loguru import logger
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from brats.core.brats_algorithm import BraTSAlgorithm
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from brats.utils.constants import (
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from brats.constants import (
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ADULT_GLIOMA_SEGMENTATION_ALGORITHMS,
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AFRICA_SEGMENTATION_ALGORITHMS,
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MENINGIOMA_SEGMENTATION_ALGORITHMS,

‎brats/data/meta/inpainting.yml

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algorithms:
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######## 2024 Algorithms ########
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BraTS24_1:
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meta:
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authors: Ke Chen, Juexin Zhang, Ying Weng
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paper: N/A
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challenge: BraTS24 Inpainting
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rank: 1st
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year: 2024
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run_args:
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docker_image: brainles/brats24_inpainting_ying_weng:latest
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input_name_schema: "BraTS-GLI-{id:05d}-000"
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requires_root: false
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parameters_file: true
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cpu_compatible: true
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weights:
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record_id: "14230865"
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param_name: "checkpoint_path"
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BraTS24_2:
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meta:
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authors: André Ferreira, et al.
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paper: N/A
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challenge: BraTS24 Inpainting
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rank: 2nd
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year: 2024
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run_args:
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docker_image: brainles/brats24_inpainting_faking_it:latest
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input_name_schema: "BraTS-GLI-{id:05d}-000"
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requires_root: false
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parameters_file: false
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shm_size: "4gb"
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BraTS24_3:
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meta:
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authors: Team SMINT
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paper: N/A
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challenge: BraTS24 Inpainting
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rank: 3rd
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year: 2024
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run_args:
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docker_image: brainles/brats24_inpainting_smint:latest
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input_name_schema: "BraTS-GLI-{id:05d}-000"
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requires_root: false
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parameters_file: true
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weights:
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record_id: "14231079"
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param_name: "weights"
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checkpoint_path: "savedmodel395000.pt"
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######## 2023 Algorithms ########
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BraTS23_1:
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meta:
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authors: Juexin Zhang, et al.
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run_args:
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docker_image: brainles/brats23_inpainting_ying_weng:latest
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input_name_schema: "BraTS-GLI-{id:05d}-000"
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requires_root: true
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requires_root: false
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parameters_file: true
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cpu_compatible: true
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weights:

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