Algorithms

What is an algorithm?

An algorithm is a container image that is executed on a set of inputs, producing a set of outputs. The inputs and outputs can be text, numbers, booleans, medical images or annotations.

Algorithm Inputs

Inputs to an algorithm are available in the container in the /input directory. You can specify component interfaces that will provide the inputs to your algorithm in the “Inputs” field on the create/update algorithm form. You can find a list of the currently available interfaces on grand challenge.

The relative_path property on the ComponentInterface is used to determine where the input value will be placed inside the container.

Most types get written to a json file, located in /input/{relative_path} in the container. You can read and parse these with

import json

with open("/input/{relative_path}") as f:
    val = json.loads(f.read())

When creating a new experiment for an algorithm, you can provide values for all ComponentInterfaces using the form provided.

Image files

Grand Challenge works with two image formats that will need to be read or written by your algorithm container image .mha and .tif.

Execution

A container will be created from the container image whenever you create an experiment for your algorithm.

Any output for both stdout and stderr is captured. The output for stderr gets marked as a warning in the experiment’s result.

If an algorithm does not properly run, it should exit with a non zero exit code. The job for the algorithm then gets marked as failed.

Algorithm Outputs

Outputs of an algorithm must be stored in the directory /output/. As with the inputs, a ComponentInterface needs to be defined for each of the expected outputs in the “Outputs” field on the create/update algorithm form. You can find a list of the currently available interfaces on grand challenge.

results.json

If one of the defined outputs for the algorithms is a results.json file, the contents of this file will be parsed and shown on the algorithm’s result page. You can provide a jinja template to an algorithm for the rendering of these results.

Frequently Asked Questions

What resources are available?

Currently algorithms are run with 1 NVidia T4 GPU with CUDA 10 and 16GB GPU memory. Algorithms are allowed to use 200% CPU, 24GB system memory and 512 threads. The algorithms are run without any access to the network. All container privileges are dropped.

Where can I write data?

The container filesystem and output directories are writable, the input directory is read only.

Time limit exceeded errors with PyTorch

Algorithms have a wall time limit of 2 hours. Sometimes, the algorithm will produce little to no output in the logs. Often, this is due to using PyTorch DataLoaders. These require using shared memory, which is not enabled on grand-challenge.org. To resolve this, set num_workers to 0 when initialising your DataLoader.

pthread_setaffinity_np failed errors with ONNX Runtime

Algorithms are limited to a select number of CPUs. Because of that ONNX Runtime does not have the permissions to automatically set the CPU affinities. To solve this create an InferenceSession by explicitly providing the number of threads via a SessionOptions instance. E.g.:

import onnxruntime

so = onnxruntime.SessionOptions()
so.inter_op_num_threads = 4
so.intra_op_num_threads = 2

session = onnxruntime.InferenceSession(model_file, sess_options=so)

Output overlay not visible or incorrectly placed on input image

It is important to specify the correct voxel spacing, origin, and direction for image outputs that should be shown as overlays on the input images. When using output_sitk_img = SimpleITK.GetImageFromArray(numpy_array) SimpleITK will set default values that might not correspond with the input image resulting in an incorrectly placed overlay. Use output_sitk_img.CopyInformation(input_sitk_img) to copy the origin, spacing and direction values from the input image to the output image to ensure they correspond.