Add ClearMLHandler to track all MONAI Experiments

docs/requirements.txt

@@ -22,6 +22,7 @@ pandas
 einops
 transformers<4.22  # https://github.com/Project-MONAI/MONAI/issues/5157
 mlflow>=1.28.0
+clearml >=1.9.1
 tensorboardX
 imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
 tifffile; platform_system == "Linux" or platform_system == "Darwin"

docs/source/handlers.rst

@@ -189,6 +189,17 @@ MLFlow handler
 .. autoclass:: MLFlowHandler
     :members:
 
+ClearML handlers
+----------------
+.. autoclass:: ClearMLHandler
+    :members:
+
+.. autoclass:: ClearMLStatsHandler
+    :members:
+
+.. autoclass:: ClearMLImageHandler
+    :members:
+
 NVTX Handlers
 -------------
 .. automodule:: monai.handlers.nvtx_handlers

docs/source/installation.md

@@ -1,18 +1,21 @@
 # Installation Guide
 
 ## Table of Contents
-1. [From PyPI](#from-pypi)
-	1. [Milestone release](#milestone-release)
-	2. [Weekly preview release](#weekly-preview-release)
-	3. [Uninstall the packages](#uninstall-the-packages)
-1. [From conda-forge](#from-conda-forge)
-2. [From GitHub](#from-github)
-	1. [System-wide](#milestone-release)
-	2. [Editable](#weekly-preview-release)
-3. [Validating the install](#validating-the-install)
-4. [MONAI version string](#monai-version-string)
-5. [From DockerHub](#from-dockerhub)
-6. [Installing the recommended dependencies](#installing-the-recommended-dependencies)
+
+- [Installation Guide](#installation-guide)
+	- [Table of Contents](#table-of-contents)
+	- [From PyPI](#from-pypi)
+		- [Milestone release](#milestone-release)
+		- [Weekly preview release](#weekly-preview-release)
+		- [Uninstall the packages](#uninstall-the-packages)
+	- [From conda-forge](#from-conda-forge)
+	- [From GitHub](#from-github)
+		- [Option 1 (as a part of your system-wide module)](#option-1-as-a-part-of-your-system-wide-module)
+		- [Option 2 (editable installation)](#option-2-editable-installation)
+	- [Validating the install](#validating-the-install)
+	- [MONAI version string](#monai-version-string)
+	- [From DockerHub](#from-dockerhub)
+	- [Installing the recommended dependencies](#installing-the-recommended-dependencies)
 
 ---
 
@@ -24,32 +27,39 @@ and the Python package index (PyPI). The pre-built Docker images are made availa
 To install optional features such as handling the NIfTI files using
 [Nibabel](https://nipy.org/nibabel/), or building workflows using [Pytorch
 Ignite](https://pytorch.org/ignite/), please follow the instructions:
+
 - [Installing the recommended dependencies](#installing-the-recommended-dependencies)
 
 The installation commands bellow usually end up installing CPU variant of PyTorch. To install GPU-enabled PyTorch:
+
 1. Install the latest NVIDIA driver.
 1. Check [PyTorch Official Guide](https://pytorch.org/get-started/locally/) for the recommended CUDA versions. For Pip package, the user needs to download the CUDA manually, install it on the system, and ensure CUDA_PATH is set properly.
 1. Continue to follow the guide and install PyTorch.
 1. Install MONAI using one the ways described below.
----
 
+---
 
 ## From PyPI
 
 ### Milestone release
+
 To install the [current milestone release](https://pypi.org/project/monai/):
+
 ```bash
 pip install monai
 ```
 
 ### Weekly preview release
+
 To install the [weekly preview release](https://pypi.org/project/monai-weekly/):
+
 ```bash
 pip install monai-weekly
 ```
 
 The weekly build is released to PyPI every Sunday with a pre-release build number `dev[%y%U]`.
 To report any issues on the weekly preview, please include the version and commit information:
+
 ```bash
 python -c "import monai; print(monai.__version__); print(monai.__commit_id__)"
 ```
@@ -61,7 +71,9 @@ without uninstalling the existing one first.
 To address this issue, please uninstall both packages, and retry the installation.
 
 ### Uninstall the packages
+
 The packages installed using `pip install` could be removed by:
+
 ```bash
 pip uninstall -y monai
 pip uninstall -y monai-weekly
@@ -70,51 +82,64 @@ pip uninstall -y monai-weekly
 ## From conda-forge
 
 To install the [current milestone release](https://anaconda.org/conda-forge/monai):
+
 ```bash
 conda install -c conda-forge monai
 ```
 
 ## From GitHub
+
 (_If you have installed the
-PyPI release version using ``pip install monai``, please run ``pip uninstall
-monai`` before using the commands from this section. Because ``pip`` by
+PyPI release version using `pip install monai`, please run `pip uninstall
+monai` before using the commands from this section. Because `pip` by
 default prefers the milestone release_.)
 
-The milestone versions are currently planned and released every few months.  As the
+The milestone versions are currently planned and released every few months. As the
 codebase is under active development, you may want to install MONAI from GitHub
 for the latest features:
 
 ### Option 1 (as a part of your system-wide module):
+
 ```bash
 pip install git+https://github.com/Project-MONAI/MONAI#egg=monai
 ```
+
 or, to build with MONAI C++/CUDA extensions:
+
 ```bash
 BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=monai
 ```
 
 To build the extensions, if the system environment already has a version of Pytorch installed,
 `--no-build-isolation` might be preferred:
+
 ```bash
 BUILD_MONAI=1 pip install --no-build-isolation git+https://github.com/Project-MONAI/MONAI#egg=monai
 ```
+
 this command will download and install the current `dev` branch of [MONAI from
 GitHub](https://github.com/Project-MONAI/MONAI).
 
 This documentation website by default shows the information for the latest version.
 
 ### Option 2 (editable installation):
+
 To install an editable version of MONAI, it is recommended to clone the codebase directly:
+
 ```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 ```
-This command will create a ``MONAI/`` folder in your current directory.
+
+This command will create a `MONAI/` folder in your current directory.
 You can install it by running:
+
 ```bash
 cd MONAI/
 python setup.py develop
 ```
+
 or, to build with MONAI C++/CUDA extensions and install:
+
 ```bash
 cd MONAI/
 BUILD_MONAI=1 python setup.py develop
@@ -123,6 +148,7 @@ BUILD_MONAI=1 CC=clang CXX=clang++ python setup.py develop
 ```
 
 To uninstall the package please run:
+
 ```bash
 cd MONAI/
 python setup.py develop --uninstall
@@ -131,72 +157,82 @@ python setup.py develop --uninstall
 ./runtests.sh --clean
 ```
 
-Alternatively, simply adding the root directory of the cloned source code (e.g., ``/workspace/Documents/MONAI``) to your ``$PYTHONPATH``
+Alternatively, simply adding the root directory of the cloned source code (e.g., `/workspace/Documents/MONAI`) to your `$PYTHONPATH`
 and the codebase is ready to use (without the additional features of MONAI C++/CUDA extensions).
 
 > The C++/CUDA extension features are currently experimental, a pre-compiled version is made available via
 > [the recent docker image releases](https://hub.docker.com/r/projectmonai/monai).
 > Building the extensions from source may require [Ninja](https://ninja-build.org/) and [CUDA Toolkit](https://developer.nvidia.com/cuda-toolkit).
 > By default, CUDA extension is built if `torch.cuda.is_available()`. It's possible to force building by
-> setting ``FORCE_CUDA=1`` environment variable.
-
+> setting `FORCE_CUDA=1` environment variable.
 
 ## Validating the install
+
 You can verify the installation by:
+
 ```bash
 python -c "import monai; monai.config.print_config()"
 ```
+
 If the installation is successful, this command will print out the MONAI version information, and this confirms the core
 modules of MONAI are ready-to-use.
 
-
 ## MONAI version string
+
 The MONAI version string shows the current status of your local installation. For example:
+
 ```
 MONAI version: 0.1.0+144.g52c763d.dirty
 ```
-- ``0.1.0`` indicates that your installation is based on the ``0.1.0`` milestone release.
-- ``+144`` indicates that your installation is 144 git commits ahead of the milestone release.
-- ``g52c763d`` indicates that your installation corresponds to the git commit hash ``52c763d``.
-- ``dirty`` indicates that you have modified the codebase locally, and the codebase is inconsistent with ``52c763d``.
 
+- `0.1.0` indicates that your installation is based on the `0.1.0` milestone release.
+- `+144` indicates that your installation is 144 git commits ahead of the milestone release.
+- `g52c763d` indicates that your installation corresponds to the git commit hash `52c763d`.
+- `dirty` indicates that you have modified the codebase locally, and the codebase is inconsistent with `52c763d`.
 
 ## From DockerHub
+
 Make sure you have installed the NVIDIA driver and Docker 19.03+ for your Linux distribution.
 Note that you do not need to install the CUDA toolkit on the host, but the driver needs to be installed.
 Please find out more information on [nvidia-docker](https://github.com/NVIDIA/nvidia-docker).
 
 Assuming that you have the Nvidia driver and Docker 19.03+ installed, running the following command will
 download and start a container with the latest version of MONAI. The latest `dev` branch of MONAI from GitHub
 is included in the image.
+
 ```bash
 docker run --gpus all --rm -ti --ipc=host projectmonai/monai:latest
 ```
 
 You can also run a milestone release docker image by specifying the image tag, for example:
+
 ```
 docker run --gpus all --rm -ti --ipc=host projectmonai/monai:0.1.0
 ```
 
 ## Installing the recommended dependencies
+
 By default, the installation steps will only download and install the minimal requirements of MONAI.
 Optional dependencies can be installed using [the extras syntax](https://packaging.python.org/tutorials/installing-packages/#installing-setuptools-extras) to support additional features.
 
 For example, to install MONAI with Nibabel and Scikit-image support:
+
 ```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 cd MONAI/
 pip install -e '.[nibabel,skimage]'
 ```
 
 Alternatively, to install all optional dependencies:
+
 ```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 cd MONAI/
 pip install -e '.[all]'
 ```
 
 To install all optional dependencies with `pip` based on MONAI development environment settings:
+
 ```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 cd MONAI/
@@ -205,6 +241,7 @@ pip install -r requirements-dev.txt
 
 To install all optional dependencies with `conda` based on MONAI development environment settings (`environment-dev.yml`;
 this will install PyTorch as well as `pytorch-cuda`, please follow https://pytorch.org/get-started/locally/#start-locally for more details about installing PyTorch):
+
 ```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 cd MONAI/
@@ -215,10 +252,12 @@ conda env update -n <name> -f environment-dev.yml
 Since MONAI v0.2.0, the extras syntax such as `pip install 'monai[nibabel]'` is available via PyPI.
 
 - The options are
+
 ```
-[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna]
+[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, clearml, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna]
 ```
+
 which correspond to `nibabel`, `scikit-image`, `pillow`, `tensorboard`,
-`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, respectively.
+`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `clearml`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, respectively.
 
 - `pip install 'monai[all]'` installs all the optional dependencies.

monai/handlers/__init__.py

@@ -14,6 +14,7 @@
 from .checkpoint_loader import CheckpointLoader
 from .checkpoint_saver import CheckpointSaver
 from .classification_saver import ClassificationSaver
+from .clearml_handlers import ClearMLHandler, ClearMLImageHandler, ClearMLStatsHandler
 from .confusion_matrix import ConfusionMatrix
 from .decollate_batch import DecollateBatch
 from .earlystop_handler import EarlyStopHandler