diff --git a/.codecov.yml b/.codecov.yml deleted file mode 100644 index c72cca6b3d..0000000000 --- a/.codecov.yml +++ /dev/null @@ -1,30 +0,0 @@ -coverage: - status: - project: - default: - target: 70% - threshold: 10 - base: parent - branches: null - if_no_uploads: error - if_not_found: success - if_ci_failed: error - only_pulls: false - flags: null - paths: null - patch: - default: - target: auto - # Allows PRs without tests, overall stats count - threshold: 100 - base: auto - branches: null - if_no_uploads: error - if_not_found: success - if_ci_failed: error - only_pulls: false - flags: null - paths: null - -# Disable comments on PR -comment: false diff --git a/examples/README.md b/examples/README.md index f723201500..61c3d7ecf9 100644 --- a/examples/README.md +++ b/examples/README.md @@ -1,3 +1,4 @@ +### 1. Requirements Most of the examples and tutorials require [matplotlib](https://matplotlib.org/) and [Jupyter Notebook](https://jupyter.org/). @@ -7,3 +8,39 @@ python -m pip install -U pip python -m pip install -U matplotlib python -m pip install -U notebook ``` + +### 2. List of examples +#### 1. [classification_3d](https://github.com/Project-MONAI/MONAI/tree/master/examples/classification_3d) +Training and evaluation examples of 3D classification based on DenseNet3D and [IXI dataset](https://brain-development.org/ixi-dataset): +The examples are standard PyTorch programs and have both dictionary-based and array-based transformation versions. +#### 2. [classification_3d_ignite](https://github.com/Project-MONAI/MONAI/tree/master/examples/classification_3d_ignite) +Training and evaluation examples of 3D classification based on DenseNet3D and [IXI dataset](https://brain-development.org/ixi-dataset): +The examples are PyTorch ignite programs and have both dictionary-based and array-based transformation versions. +#### 3. [notebooks/multi_gpu_test](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/multi_gpu_test.ipynb) +This notebook is a quick demo for devices, run the Ignite trainer engine on CPU, GPU and multiple GPUs. +#### 4. [notebooks/nifti_read_example](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/nifti_read_example.ipynb) +Illustrate reading NIfTI files and iterating over image patches of the volumes loaded from them. +#### 5. [notebooks/spleen_segmentation_3d](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/spleen_segmentation_3d.ipynb) +This notebook is an end-to-end training and evaluation example of 3D segmentation based on [MSD Spleen dataset](http://medicaldecathlon.com): +The example shows the flexibility of MONAI modules in a PyTorch-based program: +- Transforms for dictionary-based training data structure. +- Load NIfTI images with metadata. +- Scale medical image intensity with expected range. +- Crop out a batch of balanced image patch samples based on positive / negative label ratio. +- 3D UNet, Dice loss function, Mean Dice metric for 3D segmentation task. +- Sliding window inference. +- Deterministic training for reproducibility. +#### 6. [notebooks/transform_speed](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/transform_speed.ipynb) +Illustrate reading NIfTI files and test speed of different transforms on different devices. +#### 7. [notebooks/transforms_demo_2d](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/transforms_demo_2d.ipynb) +This notebook demonstrates the medical domain specific transforms on 2D medical images. +#### 8. [notebooks/unet_segmentation_3d_ignite](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/unet_segmentation_3d_ignite.ipynb) +This notebook is an end-to-end training & evaluation example of 3D segmentation based on synthetic dataset. +The example is a PyTorch Ignite program and shows several key features of MONAI, +especially with medical domain specific transforms and event handlers. +#### 9. [segmentation_3d](https://github.com/Project-MONAI/MONAI/tree/master/examples/segmentation_3d) +Training and evaluation examples of 3D segmentation based on UNet3D and synthetic dataset. +The examples are standard PyTorch programs and have both dictionary-based and array-based versions. +#### 10. [segmentation_3d_ignite](https://github.com/Project-MONAI/MONAI/tree/master/examples/segmentation_3d_ignite) +Training and evaluation examples of 3D segmentation based on UNet3D and synthetic dataset. +The examples are PyTorch Ignite programs and have both dictionary-base and array-based transformations.