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OpenViSUS Documentation

Table of contents

  1. OpenViSUS Visualization project
  2. Mission
  3. Installation
  4. Quick tour and Tutorials
  5. Run OpenVisus server
  6. Compilation
  7. IDX2
  8. Connecting to OpenViSUS Server Using a Proxy

OpenViSUS Visualization project

GitHub Actions Binder

Mission

The mission of ViSUS.org is to provide support for the scientific community with Big Data, management, analysis and visualization tools. In this website we provide access to open source software tools and libraries such as the ViSUS framework and the PIDX library. These softwares are distributed under the permissive BSD license (see LICENSE file).

Installation

For conda see docs/conda_installation.md.

Install OpenVisus:

python -m pip install --upgrade pip
python -m pip install --upgrade OpenVisus
python -m OpenVisus configure 
python -c "from OpenVisus import *"

Notes:

  • if you get permission denied error, use python -m pip install --user.
  • if you need a minimal installation without the GUI replace OpenVisus with OpenVisusNoGui
  • If you want to create an isolated virtual environment: 
      python -m pip install --upgrade virtualenv
  python -m venv ~/my-virtual-environment
  source ~/my-virtual-environment/bin/activate

Run the OpenVisus viewer:

python -m OpenVisus viewer

Quick tour and Tutorials

Start with quick_tour.ipynb Jupyter Notebook.

See Samples/jupyter directory.

To run the tutorials on the cloud click this binder link.

Run OpenVisus server

Run single Docker OpenVisus server:
docs/docker_modvisus.

Runload-balanced Kubernetes OpenVisus servers: docs/kubernetes.md.

Run load-balanced Docker Swarm OpenVisus servers: docs/docker_swarm_modvisus.md.

Compilation

See docs/compilation.md.

IDX2

Make sure you have the IDX submodule (check if IDX2/directory is in Libs/).

In cmake configure step enable VISUS_IDX2 checkbox and Build all.

You can download a test file from here https://github.com/sci-visus/OpenVisus/releases/download/files/MIRANDA-DENSITY-.384-384-256.-Float64.raw.

Create an idx2 file:

# under Windows
# set PATH=%PATH%;build\RelWithDebInfo\OpenVisus\bin

idx2 --encode --input MIRANDA-DENSITY-[384-384-256]-Float64.raw --accuracy 1e-16 --num_levels 2 --brick_size 64 64 64 --bricks_per_tile 512 --tiles_per_file 512 --files_per_dir 512 --out_dir tmp

To retrieve the data

idx2 --decode --input tmp/MIRANDA/DENSITY.idx2 --in_dir . --first 0 0 0 --last 383 383 255 --level 1 --mask 128 --accuracy 0.001 --out_dir tmp --out_file decode.raw

# CHECK the file

To test in OpenVisus viewer:

visusviewer tmp/MIRANDA/DENSITY.idx2

Connecting to OpenViSUS Server Using a Proxy

In your visus.config, you can specify a proxy scheme, ip, and port for the client (either the viewer or the python package) to use when connecting to an OpenViSUS server. This can be useful in accessing a server that is hosted on an internal network which is only accessible through SSH, for example.

An example visus.config file containing proxy information would look like this:

<visus>
	<Configuration>
		<NetService proxy="socks5://localhost" proxyport="55051"/>
	</Configuration>
	... (The rest of the config follows)
</visus>

The “proxy” variable above contains both the scheme (SOCKS5) and ip (localhost).

A user would need to start the SOCKS5 proxy connection using a client. This can be done using ssh on Linux/MacOS with the following command:

ssh -D 55051 user@server

On Windows, you can enable a SOCKS5 proxy by using PuTTY. More information on that can be found here.

Keep in mind that the port you open the connection with must match the one specified in the visus.config file.