Dataloader that serves MRI images from a mongodb
Project description
mongoslabs
Dataloader that serves MRI images from a mongodb.
The main idea is to keep MRI images and corresponding training labels
for segmentation tasks in a mongo database. However, each 2563 3D MRI
tensor even in 8 bit precision is 16Mb. mongo's records cannot be
larger than this limit and we need to also store the labels of the
same dimensions. mongoslabs fetches and aggregates each 2563
tensor stored across 8 records, together with corresponding labels
either for gray and white matter, 104 regions atlas, or a 50 region
atlas. (The scripts to populate such collection are upcoming.)
An example of maintaining a high utilization on 4 GPUs
installation
pip install mongoslabs
usage
A detailed example of how to create a dataloader using provided
dataset class and the corresponding tools is in
scripts/usage_example.py
Do not forget to move the batches to the GPU once obtained.
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