Table of Contents

Visualization Tools User Guides

The KVL supports the following software at KAUST through user training, software installations on KAUST computing resources, and direct user support. For user support, please send an email to our ticketing system: help@vis.kaust.edu.sa

Avizo

Avizo is a software application which enables users to perform interactive visualization and computation on 3D data sets. The Avizo interface is modelled on visual programming. Users manipulate data and module components, organized in an interactive graph representation (called Pool), or in a Tree view. Data and modules can be interactively connected together, and controlled with several parameters, creating a visual processing network whose output is displayed in a 3D viewer. With this interface, complex data can be interactively explored and analyzed by applying a controlled sequence of computation and display processes resulting in a meaningful visual representation and associated derived data.

Getting Help with Avizo

The Avizo user guide is the best place to start when trying something new with Avizo or when searching for functionality. To access, go to Help → User's Guide in the main menu bar.

      KVL Training on Avizo

  • To use Avizo interactively on the IT Remote Workstations go HERE. You have to request the service the first time you use it HERE.
  • To install Avizo locally, go HERE. Installation instructions can be found HERE.

ParaView

ParaView is an open-source, multi-platform scientific data analysis and visualization tool that enables analysis and visualization of extremely large datasets. ParaView is both a general purpose, end-user application with a distributed architecture that can be seamlessly leveraged by your desktop or other remote parallel computing resources and an extensible framework with a collection of tools and libraries for various applications including scripting (using Python), web visualization (through ParaViewWeb), or in-situ analysis (with Catalyst). ParaView leverages parallel data processing and rendering to enable interactive visualization for extremely large datasets. It also includes support for large displays including tiled displays and immersive 3D displays with head tracking and wand control capabilities. ParaView also supports scripting and batch processing using Python. Using included Python modules, you can write scripts that can perform almost all the functionality exposed by the interactive application and much more.

Getting Help with ParaView

The ParaView user manual is the best place to start when trying something new with ParaView or when searching for functionality: ParaView User Manual

KVL Training on ParaView

  • For information on using ParaView on KAUST supercomputing resources or batch scripting, look at our extensive examples and instructions HERE.
  • To use ParaView interactively on Ibex go HERE.
  • Shaheen III does not support interactive ParaView use. Try batch scripting or use Ibex.

ParaView FAQ

  • NetCDF files and ParaView
    • To read a series of *.nc files as a time series:
      • Combine *_src.nc files into single out.nc file
      • ncrcat in_*.nc -O out.nc
    • Issues reading NetCDF files, may be due to time variables not being set as expected by ParaView:
      • ParaView imports *.nc files, but expects that Time is both a coordinate and a variable. The following Python code illustrates the process.
        • Note: Time units are in the format (where <time_units> are 'days', 'hours', etc.): <time_units> since <date>
        • Add Time / time variable (missing from wrfout_*.nc files):
          •     #!/usr/bin/env python
    import netCDF4 as nc
    import numpy as np
    import datetime as dt
 
    ncf = nc.Dataset('filename', 'a')
    t = ncf.createVariable('Time', 'i', ('Time',))
    t.units = "hours since 2009-11-24 00:00:00"
    t[:] = np.arange(t.size)
    ncf.close()

VisIt

VisIt is a free, open source, platform independent, distributed, parallel, visualization tool for visualizing data defined on two- and three-dimensional structured and unstructured meshes. VisIt’s distributed architecture allows it to leverage both the compute power of a large parallel computer and the graphics acceleration hardware of a local workstation. VisIt’s user interface is often run locally on a Windows, Linux, or macOS desktop computer while its compute engine component runs in parallel on a remote computer. VisIt’s distributed architecture allows VisIt to visualize simulation data where it was generated, eliminating the need to move the data to a visualization server. VisIt can be controlled by its Graphical User Interface (GUI), through the Python and Java programming languages, or from a custom user interface that you develop yourself. More information about VisIt can be found online at https://visit.llnl.gov/.

Getting Help with VisIt

The VisIt user manual is the best place to start when trying something new with VisIt or when searching for functionality: VisIt User Manual

KVL Training on VisIt

  • For information on using VisIt on KUAST supercomputing resources or batch scripting, look at our extensive examples and instructions HERE.
  • To use VisIt interactively on Ibex go HERE.
  • Shaheen III does not support interactive VisIt use. Try batch scripting or use Ibex.

Ilastik

Ilastik is a free and open-source tool for image segmentation. It allows users to easily leverage machine learning for segmentation. KVL supports running ilastik on the Ibex cluster in order to process large datasets (tutorial here).

Getting Help with Ilastik

The Ilastik user manual is the best place to start when trying something new with Ilastik or when searching for functionality: Ilastik User Manual

KVL Training on Avizo

  • To use Ilastik interactively on the IT Remote Workstations go HERE
  • To install Ilastik locally go HERE
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