Caterva2 demo data

This repository contains the data files (roots and datasets) used to deploy a Caterva2 demo site, but they may be used independently.

How data was generated

Note: These instructions are not needed to use the data, only to re-generate it.

First, make sure that the caterva2 submodule is cloned and up-to-date:

git submodule update --init --recursive caterva2

Then, install Caterva2 in a Python virtual environment:

test -d venv || python3 -m venv venv
(. venv/bin/activate && pip install -e ./caterva2[services,hdf5,blosc2-plugins] \
 && pip install pillow)

Note: If you want to update the version of Caterva2, update the caterva2 submodule, update the virtual environment (see above), re-generate data files and commit the changes.

Caterva2 directory root (root-example)

venv/bin/python -m caterva2.services.dirroot root-example.new \
&& (. venv/bin/activate && python scripts/lung_b2nd.py 10 root-example.new/lung-jpeg2000_10x.b2nd) \
&& mv root-example root-example.old && mv root-example.new root-example

Make sure to commit the changes to the root-example directory, while adding possible new files:

git add root-example
git commit -m "Update root-example"

HDF5 root (hdf5root-example.h5)

venv/bin/python -m caterva2.services.hdf5root hdf5root-example.new.h5 \
&& mv hdf5root-example.new.h5 hdf5root-example.h5

JPEG 2000 numbers HDF5 root (numbers-jpeg2000.h5)

(. venv/bin/activate && cd caterva2/test-images && python encode-grok-numbers.py) \
&& mv caterva2/test-images/numbers-jpeg2000.h5 numbers-jpeg2000.new.h5 \
&& mv numbers-jpeg2000.new.h5 numbers-jpeg2000.h5

JPEG 2000 lung tomography HDF5 root (lung-jpeg2000.h5)

(. venv/bin/activate && python scripts/lung_hdf5.py lung-jpeg2000.new.h5) \
&& mv lung-jpeg2000.new.h5 lung-jpeg2000.h5

Caterva2 directory root (root-blosc2-tests)

This root contains files used for testing blosc2, like the C2Array class.