BraTS integration with MLCube [WIP]

brats/.env

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+# author info
+AUTHOR_NAME = "Chuck Norris"
+AUTHOR_EMAIL = "[email protected]"
+# put your app name here
+APPLICATION_NAME = "AMAZING APPLICATION"
+# specify version here, if possible use semantic versioning
+APPLICATION_VERSION = "0.0.1"
+
+INPUT_FOLDER ="workspace/data/"
+OUTPUT_FOLDER ="workspace/data/results/"
+
+INPUT_FOLDER_DOCKER="/app/data/"
+OUTPUT_FOLDER_DOCKER ="/app/data/results/"

brats/.gitignore

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+__pycache__/

brats/Dockerfile_CPU

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+# for a CPU app use this Dockerfile, delete the Dockerfile_CUDA then.
+FROM python:3.8-buster
+
+# fill in your info here
+LABEL author="[email protected]"
+LABEL application="your application name"
+LABEL maintainer="[email protected]"
+LABEL version="0.0.1"
+LABEL status="beta"
+
+# basic
+RUN apt-get -y update && apt -y full-upgrade && apt-get -y install apt-utils wget git tar build-essential curl nano
+
+# install all python requirements
+WORKDIR /app
+COPY ./requirements.txt ./requirements.txt
+RUN pip3 install -r requirements.txt
+
+# copy all files
+COPY ./ ./
+
+ENTRYPOINT [ "python3","-u", "run.py"]

brats/Dockerfile_CUDA

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+# for a GPU app use this Dockerfile, delete the Dockerfile_CPU then.
+FROM nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04
+
+# fill in your info here
+LABEL author="[email protected]"
+LABEL application="your application name"
+LABEL maintainer="[email protected]"
+# specify version here, if possible use semantic versioning
+LABEL version="0.0.1"
+LABEL status="beta"
+
+# basic
+RUN apt-get -y update && apt -y full-upgrade && apt-get -y install apt-utils wget git tar build-essential curl nano
+
+# install python 3.6.9
+RUN apt-get update -y && apt-get install -y python3-pip python3-dev
+
+# install all python requirements
+WORKDIR /app
+COPY ./requirements.txt ./requirements.txt
+RUN pip3 install -r requirements.txt
+
+# copy all files
+COPY ./ ./
+RUN pip3 install -U python-dotenv
+
+ENTRYPOINT [ "python3","-u", "run.py"]

brats/README.md

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+# BraTS Challenge 2020 - MLCube integration
+
+Original implementation: ["BraTS Instructions Repo"](https://github.com/BraTS/Instructions)
+
+## Dataset
+
+Please refer to the [BraTS challenge page](http://braintumorsegmentation.org/) and follow the instructions in the data section.
+
+## Project setup
+
+```bash
+# Create Python environment and install MLCube Docker runner 
+virtualenv -p python3 ./env && source ./env/bin/activate && pip install mlcube-docker
+
+# Fetch the boston housing example from GitHub
+git clone https://github.com/mlcommons/mlcube_examples && cd ./mlcube_examples
+git fetch origin pull/39/head:feature/brats && git checkout feature/brats
+cd ./brats
+```
+
+## Tasks execution
+
+```bash
+# Run implementation with CPU support.
+mlcube run --mlcube=mlcube_cpu.yaml --task=run
+
+# Run implementation with GPU support.
+mlcube run --mlcube=mlcube_gpu.yaml --task=run
+```
+
+We are targeting pull-type installation, so MLCube images should be available on Docker Hub. If not, try this:
+
+```Bash
+mlcube run ... -Pdocker.build_strategy=always
+```

brats/mlcube_cpu.yaml

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+name: MLCommons Brats
+description: MLCommons Brats integration
+authors: 
+ - {name: "MLCommons Best Practices Working Group"}
+
+platform:
+  accelerator_count: 0
+
+docker:
+  # Image name.
+  image: mlcommons/brats_cpu:0.0.1
+  # Docker build context relative to $MLCUBE_ROOT. Default is `build`.
+  build_context: "."
+  # Docker file name within docker build context, default is `Dockerfile`.
+  build_file: "Dockerfile_CPU"
+
+tasks:
+  run:
+  # Run implementation
+    parameters:
+      inputs: {data_dir: data/}
+      outputs: {results_dir: data/results/}

brats/mlcube_gpu.yaml

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+name: MLCommons Brats
+description: MLCommons Brats integration
+authors: 
+ - {name: "MLCommons Best Practices Working Group"}
+
+platform:
+  accelerator_count: 0
+
+docker:
+  # Image name.
+  image: mlcommons/brats_gpu:0.0.1
+  # Docker build context relative to $MLCUBE_ROOT. Default is `build`.
+  build_context: "."
+  # Docker file name within docker build context, default is `Dockerfile`.
+  build_file: "Dockerfile_CUDA"
+
+tasks:
+  run:
+  # Run implementation
+    parameters:
+      inputs: {data_dir: data/}
+      outputs: {results_dir: data/results/}

brats/requirements.txt

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+python-dotenv==0.12.0

brats/run.py

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+"""Load code"""
+import argparse
+from src.amazing_logic import run_code
+
+parser = argparse.ArgumentParser()
+parser.add_argument(
+    "--data_dir",
+    type=str,
+    default=None,
+    help="Path to dataset.",
+)
+parser.add_argument(
+    "--results_dir",
+    type=str,
+    default=None,
+    help="Path to output folder.",
+)
+args, _unkown = parser.parse_known_args()
+
+# execute
+run_code(args)

brats/src/amazing_logic.py

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+"""Logic file"""
+import os
+from shutil import copyfile
+from dotenv import dotenv_values
+from src.utils.utilities import helper
+
+config = dotenv_values(".env")
+APPLICATION_NAME = config["APPLICATION_NAME"]
+APPLICATION_VERSION = config["APPLICATION_VERSION"]
+INPUT_FOLDER = config["INPUT_FOLDER"]
+OUTPUT_FOLDER = config["OUTPUT_FOLDER"]
+
+
+def logic_wrapper(args):
+    """Edit your logic here"""
+    if args.data_dir is not None:
+        INPUT_FOLDER = args.data_dir
+    input_file = os.path.normpath(INPUT_FOLDER + "/something_t1.nii.gz")
+    # ... do the same for t1c, flair and t2 here
+    if args.results_dir is not None:
+        OUTPUT_FOLDER = args.results_dir
+    output_file = os.path.normpath(OUTPUT_FOLDER + "/something_seg.nii.gz")
+
+    # copy paste your amazing logic here
+    print("wrapper: I can feel the magic happening..it feels like a little sun rising inside me!")
+
+    # example logic
+    copyfile(input_file, output_file)
+    helper()
+
+
+def run_code(args):
+    """Main function"""
+    print("*** code execution started:",
+          APPLICATION_NAME, "version:", APPLICATION_VERSION, "! ***")
+    logic_wrapper(args)
+    print("*** code execution finished:",
+          APPLICATION_NAME, "version:", APPLICATION_VERSION, "! ***")

brats/src/utils/utilities.py

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+"""utility functions here"""
+def helper():
+    """helper function"""
+    print("helper: I am so useful it hurts.")

brats/workspace/data/results/.dockerignore

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+output.nii.gz

brats/workspace/data/results/.gitignore

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+*
+!.gitignore
+!.dockerignore

brats/workspace/data/something_flair.nii.gz

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+I am a standardized compressed nifti file!

brats/workspace/data/something_survival_metadata.csv

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+exam_id,age,resection_status
+something,NA,NA
+
+First column: exam name, string for the exam name
+Second Column: Age as a float or NA for missing
+Third Column: resection status as NA for missing, GTR/STR as a string
+
+ATTENTION: note the slightly changed column names in comparison to what you received for testing
+
+Example for a case without missing data:
+
+exam_id,age,resection_status
+BraTS20_Testing_015,51.449,GTR
+

brats/workspace/data/something_t1.nii.gz

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+I am a standardized compressed nifti file!

brats/workspace/data/something_t1ce.nii.gz

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+I am a standardized compressed nifti file!

brats/workspace/data/someting_t2.nii.gz

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+I am a standardized compressed nifti file!