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vistools [2023/05/14 08:32] – [Ilastik] Ronell Sicatvistools [2026/09/07 11:01] (current) – James Kress
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 ====== Visualization Tools User Guides ====== ====== 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]]+ 
 +The KVL supports the following software at KAUST through user training, software installations on KAUST computing resources, and direct user support. For user support, email our ticketing system: [[help@vis.kaust.edu.sa]] 
 + 
 +<WRAP center round tip 100%> 
 +**Not sure which tool you need?** Ask us — or start here: 
 +{{tablelayout?tableSearch=0&tableSort=0&tablePrint=0&colwidth="120px,420px,300px"}} 
 +^ Tool ^ Best for ^ Where you can run it ^ 
 +| **Avizo / Amira** | Segmentation, 3D analysis and measurement of tomography and microscopy image stacks | IT Remote Workstations, local install, KVL workstations | 
 +| **ParaView** | Large-scale simulation data, tiled and immersive displays, Python scripting, in-situ via Catalyst | Ibex (interactive), Shaheen III (batch only), local install | 
 +| **VisIt** | 2D/3D structured and unstructured meshes, remote parallel rendering, Python/Java control | Ibex (interactive), Shaheen III (batch only), local install | 
 +| **Ilastik** | Machine-learning image segmentation, including large datasets | Ibex, IT Remote Workstations, local install | 
 +</WRAP> 
 + 
 +/* Tool headings are kept OUTSIDE the nicebox wraps on purpose: a heading placed 
 +   inside a WRAP loses its section-edit button, forcing whole-page edits. 
 +   Note also that <fs ...> takes a SPACE, not a colon: <fs 26px>text</fs>. */ 
 + 
 +----
  
 ===== Avizo ===== ===== 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. 
  
-<WRAP center round info 100%> <fs:26px>** Getting Help with Avizo** </fs>+<WRAP nicebox blue 100%> 
 +Avizo (also called Amira) is a software application which enables users to perform interactive visualization, automatic segmentation, analysis, and computation on 3D data sets such as tomography and microscopy image stacks. 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. 
 + 
 +<WRAP center round info 100%> 
 +<fs 26px>**Getting Help with Avizo**</fs>
  
-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.+The Avizo user guide is the best place to start when trying something new with Avizo or when searching for functionality. To access it, go to **Help → User's Guide** in the main menu bar.
 </WRAP> </WRAP>
  
-<WRAP center round box 100%> {{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <tab> <fs:26px>** KVL Training on Avizo **</fs>  +<WRAP center round box 100%> 
-  * KVL often runs training on Avizo, check out our current and past workshops for more: <wrap button>[[training:overview|Training Events]]</wrap> +{{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <fs 26px>**KVL Training on Avizo**</fs> 
-  * Here is a link to our recording of our <wrap button>[[https://www.youtube.com/watch?v=AjUAyhZEG5I|Introduction to Avizo Workshop]]</wrap>+  * KVL often runs training on Avizo — see our current and past workshops: <wrap button>[[training:overview|Training Events]]</wrap> 
 +  * Recording: <wrap button>[[https://www.youtube.com/watch?v=AjUAyhZEG5I|Introduction to Avizo Workshop]]</wrap>
 </WRAP> </WRAP>
  
 <WRAP center round important 100%> <WRAP center round important 100%>
-  * To use Avizo interactively on the IT Remote Workstations go [[http://myws.kaust.edu.sa|HERE]]. You have to request the service the first time you use it [[https://kaustforms.formstack.com/forms/remote_workstation_account|HERE]]. +<fs 26px>**Getting Access to Avizo**</fs> 
-  * To install Avizo locally, go [[https://it.kaust.edu.sa/software/avizo|HERE]].+  * **On the IT Remote Workstations:** open [[http://myws.kaust.edu.sa|myws.kaust.edu.sa]]. First time only, you must [[https://kaustforms.formstack.com/forms/remote_workstation_account|request the Remote Workstation service]]. 
 +  * **On your own machine:** [[https://it.kaust.edu.sa/software/avizo|download Avizo from KAUST IT]], then follow the [[https://softwaresolutions.kaust.edu.sa/AVIZO/Avizo_Installation_Instructions_Windows.pdf|Windows installation instructions (PDF)]]. 
 +</WRAP>
 </WRAP> </WRAP>
  
 +----
  
 ===== ParaView ===== ===== ParaView =====
 +
 +<WRAP nicebox green 100%>
 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. 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.
  
 +<WRAP center round info 100%>
 +<fs 26px>**Getting Help with ParaView**</fs>
  
-<WRAP center round info 100%> <fs:26px>** Getting Help with ParaView **</fs> +The ParaView user manual is the best place to start when trying something new with ParaView or when searching for functionality: [[https://docs.paraview.org/en/latest/|ParaView User Manual]]
- +
-The ParaView user manual is the best place to start when trying something new with ParaView or when searching for functionality: [[https://docs.paraview.org/en/latest/|ParaView User Manual ]]+
 </WRAP> </WRAP>
  
-<WRAP center round box 100%> {{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <fs:26px>** KVL Training on ParaView **</fs> +<WRAP center round box 100%> 
-  * KVL often runs training on ParaView, check out our current and past workshops for more: <wrap button>[[training:overview|Training Events]]</wrap> +{{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <fs 26px>**KVL Training on ParaView**</fs> 
-  * Here is a link to our recording of our <wrap button>[[https://www.youtube.com/watch?v=syp6Eu1dkpE&t=2605s|Introduction to ParaView Workshop]]</wrap> +  * KVL often runs training on ParaView — see our current and past workshops: <wrap button>[[training:overview|Training Events]]</wrap> 
-  * Here is a link to our recording of our <wrap button>[[https://www.youtube.com/watch?v=yhsTavGTVt4|Advanced ParaView Workshop]]</wrap>+  * Recording: <wrap button>[[https://www.youtube.com/watch?v=syp6Eu1dkpE&t=2605s|Introduction to ParaView Workshop]]</wrap> 
 +  * Recording: <wrap button>[[https://www.youtube.com/watch?v=yhsTavGTVt4|Advanced ParaView Workshop]]</wrap>
 </WRAP> </WRAP>
  
 <WRAP center round important 100%> <WRAP center round important 100%>
-  * For information on using ParaView on KAUST supercomputing resources or batch scripting, look at our extensive examples and instructions [[https://gitlab.kaust.edu.sa/kvl/KAUST_Visualization_Vignettes/-/tree/master/ParaView_Vignettes|HERE]]. +<fs 26px>**ParaView on KAUST Supercomputing Resources**</fs> 
-  * To use ParaView interactively on Ibex go [[https://gitlab.kaust.edu.sa/kvl/KAUST_Visualization_Vignettes/-/tree/master/ParaView_Vignettes#using-paraview-interactively-on-ibex|HERE]]. +  * **Examples and batch scripting:** see our [[https://gitlab.kitware.com/jameskress/KAUST_Visualization_Vignettes/-/tree/master/ParaView_Vignettes?ref_type=heads#paraview_vignettes|ParaView Vignettes]]. 
-  * Shaheen II does not support interactive ParaView use. Try batch scripting or use Ibex.+  * **Interactive use on Ibex:** follow [[https://gitlab.kitware.com/jameskress/KAUST_Visualization_Vignettes/-/tree/master/ParaView_Vignettes?ref_type=heads#using-paraview-interactively-on-ibex|Using ParaView interactively on Ibex]]. 
 +  * **Shaheen III does not support interactive ParaView use.** Use batch scripting, or use Ibex instead.
 </WRAP> </WRAP>
  
-<WRAP center round help 100%> <fs:26px>** ParaView FAQ **</fs> +<WRAP center round help 100%> 
-  * **//NetCDF files and ParaView//** +<fs 26px>**ParaView FAQ**</fs>
-    * **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): +
-          * <code python>  +
-    #!/usr/bin/env python +
-    import netCDF4 as nc +
-    import numpy as np +
-    import datetime as dt+
  
-    ncf = nc.Dataset('filename', 'a') +**Reading a series of ''*.nc'' (NetCDF) files as a time series**
-    t = ncf.createVariable('Time', 'i', ('Time',)) +
-    t.units = "hours since 2009-11-24 00:00:00" +
-    t[:] = np.arange(t.size) +
-    ncf.close() </code>+
  
 +Combine the individual ''in_*.nc'' files into a single ''out.nc'':
 +
 +<code bash>
 +ncrcat in_*.nc -O out.nc
 +</code>
 +
 +**ParaView won't read my NetCDF file correctly**
 +
 +This is usually because the time variables are not set the way ParaView expects. ParaView imports ''*.nc'' files but expects **Time** to be both a coordinate //and// a variable. Time units must be in the form ''<time_units> since <date>'', where ''<time_units>'' is ''days'', ''hours'', etc.
 +
 +The following adds the missing ''Time'' variable (absent from ''wrfout_*.nc'' files):
 +
 +<code python>
 +#!/usr/bin/env python
 +import netCDF4 as nc
 +import numpy as np
 +
 +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()
 +</code>
 +</WRAP>
 </WRAP> </WRAP>
 +
 +----
  
 ===== VisIt ===== ===== 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/]]. 
  
-<WRAP center round info 100%> <fs:26px>** Getting Help with VisIt**</fs>+<WRAP nicebox marine 100%> 
 +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/]]. 
 + 
 +<WRAP center round info 100%> 
 +<fs 26px>**Getting Help with VisIt**</fs>
  
-The VisIt user manual is the best place to start when trying something new with VisIt or when searching for functionality: [[https://visit-sphinx-github-user-manual.readthedocs.io/en/v3.3.2/index.html|VisIt User Manual ]]+The VisIt user manual is the best place to start when trying something new with VisIt or when searching for functionality: [[https://visit-sphinx-github-user-manual.readthedocs.io/en/stable/index.html|VisIt User Manual]]
 </WRAP> </WRAP>
  
-<WRAP center round box 100%> {{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <fs:26px>** KVL Training on VisIt**</fs> +<WRAP center round box 100%> 
-  * KVL often runs training on VisIt, check out our current and past workshops for more: <wrap button>[[training:overview|Training Events]]</wrap> +{{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <fs 26px>**KVL Training on VisIt**</fs> 
-  * Here is a link to our recording of our <wrap button>[[https://www.youtube.com/watch?v=h9_Sg7CN5Cg|Introduction to VisIt Workshop]]</wrap>+  * KVL often runs training on VisIt — see our current and past workshops: <wrap button>[[training:overview|Training Events]]</wrap> 
 +  * Recording: <wrap button>[[https://www.youtube.com/watch?v=h9_Sg7CN5Cg|Introduction to VisIt Workshop]]</wrap>
 </WRAP> </WRAP>
  
 <WRAP center round important 100%> <WRAP center round important 100%>
-  * For information on using VisIt on KUAST supercomputing resources or batch scripting, look at our extensive examples and instructions [[https://gitlab.kaust.edu.sa/kvl/KAUST_Visualization_Vignettes/-/tree/master/VisIt_Vignettes|HERE]]. +<fs 26px>**VisIt on KAUST Supercomputing Resources**</fs> 
-  * To use VisIt interactively on Ibex go [[https://gitlab.kaust.edu.sa/kvl/KAUST_Visualization_Vignettes/-/tree/master/VisIt_Vignettes#using-visit-interactively-on-ibex|HERE]]. +  * **Examples and batch scripting:** see our [[https://gitlab.kitware.com/jameskress/KAUST_Visualization_Vignettes/-/tree/master/VisIt_Vignettes?ref_type=heads#visit-vignettes|VisIt Vignettes]]. 
-  * Shaheen II does not support interactive VisIt use. Try batch scripting or use Ibex.+  * **Interactive use on Ibex:** follow [[https://gitlab.kitware.com/jameskress/KAUST_Visualization_Vignettes/-/tree/master/VisIt_Vignettes?ref_type=heads#using-visit-interactively-on-ibex|Using VisIt interactively on Ibex]]. 
 +  * **Shaheen III does not support interactive VisIt use.** Use batch scripting, or use Ibex instead. 
 +</WRAP>
 </WRAP> </WRAP>
  
 +----
  
 ===== Ilastik ===== ===== 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 ([[https://www.youtube.com/watch?v=63k0fM_w_R8&t=7463s|tutorial here]]).+<WRAP nicebox purple 100%> 
 +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 ([[https://www.youtube.com/watch?v=63k0fM_w_R8&t=7463s|tutorial here]]).
  
-<WRAP center round info 100%> <fs:26px>** Getting Help with Ilastik**</fs>+<WRAP center round info 100%> 
 +<fs 26px>**Getting Help with Ilastik**</fs>
  
-The Ilastik user manual is the best place to start when trying something new with Ilastik or when searching for functionality: [[https://www.ilastik.org/documentation/index.html|Ilastik User Manual ]]+The Ilastik user manual is the best place to start when trying something new with Ilastik or when searching for functionality: [[https://www.ilastik.org/documentation/index.html|Ilastik User Manual]]
 </WRAP> </WRAP>
  
-<WRAP center round box 100%> {{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <fs:26px>** KVL Training on Avizo**</fs> +<WRAP center round box 100%> 
-  * KVL often runs training on Ilastik, check out our current and past workshops for more: <wrap button>[[training:overview|Training Events]]</wrap> +{{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} <fs 26px>**KVL Training on Ilastik**</fs> 
-  * Here is a link to our recording of our <wrap button>[[https://www.youtube.com/watch?v=63k0fM_w_R8|Introduction to Image Segmentation]]</wrap>+  * KVL often runs training on Ilastik — see our current and past workshops: <wrap button>[[training:overview|Training Events]]</wrap> 
 +  * Recording: <wrap button>[[https://www.youtube.com/watch?v=63k0fM_w_R8|Introduction to Image Segmentation]]</wrap>
 </WRAP> </WRAP>
  
 <WRAP center round important 100%> <WRAP center round important 100%>
-  * To use Ilastik interactively on the IT Remote Workstations go [[https://gitlab.kaust.edu.sa/kvl/ilastik-configs#user-workflows|HERE]] +<fs 26px>**Getting Access to Ilastik**</fs> 
-  * To install Ilastik locally go [[https://www.ilastik.org/|HERE]]+  * **On Ibex and the IT Remote Workstations:** see our [[https://gitlab.kaust.edu.sa/kvl/ilastik-configs#user-workflows|Ilastik configs and user workflows]]. 
 +  * **On your own machine:** [[https://www.ilastik.org/|download Ilastik]]. 
 +</WRAP>
 </WRAP> </WRAP>
 +
 +
  
 ---- ----
 +
 {{tag>visit avizo paraview help sciviz scientific_visualization software supercomputing ibex shaheen ilastik}} {{tag>visit avizo paraview help sciviz scientific_visualization software supercomputing ibex shaheen ilastik}}