Avizo

Introduction

Release Notes Avizo 5.0
Release Date: November 20, 2007

This document describes changes and improvements in version 5.0 of Avizo, the 3D Visualization Framework.
Avizo 5 is the evolution of amira 4.1.1 for all application areas outside biomedical and life sciences.

Supported platforms

• Windows 2000/XP/Vista, 32-bit code
• Windows XP/Vista (AMD Opteron, Intel Xeon 64, etc.) 64-bit code
• Linux x86 (Red Hat Enterprise Linux 4.0/5.0) 32-bit code
• Linux AMD64 (Red Hat Enterprise Linux 4.0/5.0, AMD Opteron, Intel Xeon 64,
  etc.) 64-bit code

• Linux IA64 (Red Hat Enterprise Linux 3.0, Itanium 2) 64-bit code
• Mac OS X 10.4 Universal Binary
• Sun Solaris
• SGI Irix

Further details about software and hardware configuration are listed in the section "System Requirements" of the Avizo 5 User's Guide.

In order to add custom extensions to Avizo, a C++ compiler is also required. Details about the supported compilers and compiler versions can be found in the section "System Requirements" of the Avizo Developer Pack User's Guide.

• Windows 2000/XP: Visual Studio .NET 2005
• Windows XP 2003 x64 Edition: Visual Studio 2005
• Linux: gcc 3.4.x or 4.1.x
• More platforms to be supported soon

Avizo versus amira

amira grows and evolves. Initially known and widely used as the 3D visualization tool of choice in the Life Sciences research market, amira® has become a more and more sophisticated product, delivering powerful visualization and analysis capabilities in all visual simulation fields. Application areas such as Material sciences, Computer Aided Engineering post-processing, Virtual Reality and more, are becoming active adopters of the product.

To highlight our focus and commitment to these application areas, Mercury is introducing a new product name: Avizo. Using the same great core software plus domain specific extensions, amira® will continue to serve the Life Sciences market, while Avizo will address all other industries, such as Engineering & Manufacturing, Non-Destructive Testing, Material Sciences, Geosciences, Immersive VR and other industrial and scientific domains.

Editions and Packs

For former amira users, the former pack names has been renamed. For more information, see "About editions and extension package" chapter which is accessible from a link on the home page of the Avizo help browser.

Improvements and new features:

Avizo

* Pool -- Graph View/Tree View, Pool/Explorer

In previous versions of Avizo, the Pool displayed your data objects and modules and their connections in what could be called a "graph view". This feature is, of course, still available. However, it is now possible to select instead (via Edit/Preferences/Layout) a "tree view" of your data objects and modules. This can be useful when working with large numbers of objects as it allows you to organize them into folders.

Note: When in tree view mode, the Pool pane and the Pool menu are relabeled "Explorer".

Although the look of the tree view is quite different, the principles are the same. You select an object by clicking on it. A right click brings up its context menu. For data objects and modules, the list contains the list of available items that can be connected. For folders, the context menu allows you to rename or delete the folder, add a new folder below, and possibly import data.

For objects that have an associated colormap, e.g., an OrthoSlice with Mapping Type Colormap, a colormap icon is shown in the Explorer. A right click on the icon brings up the standard colormap context menu, a left click brings up the colormap editor.

For objects that have a slice number, e.g., OrthoSlice, the slice number is shown in the Explorer.

One important change in the GUI between the graph view and tree view is how input connections are handled. In the graph view, you could use the mouse to interactively change the connections between data objects and modules directly in the Pool. In the tree view, the input connections are handled as ports in the Properties Area.

Example: You have loaded motor.am and you connect an OrthoSlice to it. In the OrthoSlice control panel in the Properties Area, the first port is a Data port showing that motor.am is connected.

If there are other data objects in the Pool/Explorer that could be connected to the OrthoSlice, they will be listed in the data port's pulldown menu. You can select one of them to connect the OrthoSlice to a different data object.

Currently, there are two "templates" that control the organization of the tree view: a default template for most Avizo users, and a "seismic" template for users who have an AvizoEarth license for working with geoscience data. See the "Avizo Earth Edition" topic below for more details on the seismic template.

* Pool -- The new "Duplicate mode" toggle is handy if you will be attaching multiple modules of the same type to a data object and you want the modules to have the same initial port values. If the toggle is on, the port values of the first module will be used to intialize the port values of subsequently attached modules.

Example: Attach an Orthoslice to your data object and set the Mapping type to "Colormap" and the colormap range to 0-3. If you attach another Orthoslice to the same data object, its Mapping type will be "Colormap" and the colormap range will be 0-3.

* Pool -- The new "Auto adjust range of colormaps" toggle allows you to request that Avizo automatically adjust the range of a colormap to correspond to the data range of the data set it is connected to. Note that this feature only applies to the geoscience modules: seismic slices Inline, Crossline, TimeSlice, etc., CroppedVolume, and SeismicSurfaceView.

* Segmentation Editor -- The Segmentation Editor has been enhanced with the following new features:

• Views can be zoomed individually.
  If the "Current viewer" button is checked, then the zoom buttons apply to the currently active viewer rather than to all views.
• Data windows can be adjusted individually.
  If the "Current viewer" button is checked, then the data window tool adjusts the window of the currently
  active viewer rather than all views.
• Colormap support.
  The colormap of the image can be changed from the default gray ramp to another colormap by pressing the "Select colormap" button.
• Square brush.
  The "Square brush" option will paint, as the name suggests, a square region instead of the default circular region. The other brush options will work with it as expected.
• Brush range can be limited.
  If the "Limited range only" option is selected, the brush will paint only pixels whose values fall between those in the range slider.
• Line tool (part of brush tool).
  It is possible to fence an area defined with line segments by pressing {\em Alt}, and clicking successively to points with the left mouse button (holding down the {\em Alt} key all the time).
  Successive points will be connected with straight line segments.
  To finish interaction, release the {\em Alt} key and click a last time. The contour is then closed, and the lines traced over with the brush.

* Colormap Editor Alpha Curve -- The Colormap Editor has been enhanced to allow editing of the colormap alpha values using an alpha curve that you can shape interactively with the mouse.
Previously the alpha values could only be edited using "keys".

This feature is accessed via the Edit->Show Alpha Curve item of the Colormap Editor dialog. Unlike most attribute settings in Avizo, this setting is persistent across Avizo sessions.

* CollectiveTCL -- This is a new module for executing a Tcl command on objects in the Pool. You can specify that it be applied to all visible objects (i.e., not hidden), all selected objects, or all objects of a specified type.

* ExtractSurface -- This new module allows you to extract surfaces displayed by one or more modules, e.g., SurfaceView, GridVolume, HexaView. In order to extract a surface, you will first select the parts of the object you are interested in using the selection mechanisms provided by the input modules. For example, in case of a SurfaceView module different parts can be selected via the materials menu, via the selection box (buffer show/hide), via 2D lasso selection (buffer draw), or by selecting or deselecting individual triangles with the mouse. All visible triangles will be extracted into a new
surface object when you press the Apply button.

* PlotSpreadSheet -- Some modules, such as MaterialStatistics, create a spreadsheet of values. The new PlotSpreadSheet module allows you to display the values as a plot in a separate window. You can select a single column of data to be used for the X axis values, and one or more columns to be plotted on the Y axis.

* ViewerPlot -- Some modules, such as Histogram and LineProbe, create a plot in a separate window. The new ViewerPlot module allows you to instead display the plot within the viewer window. You can control the placement, size, transparency, and other attributes of the plot within the viewer.

* Demo Framework -- The Demo Framework is a framework for organizing your demos. It incorporates four major parts:

• A directory and file structure containing the Avizo scripts to execute the demos, their description, and their data. The directory structure may realize a grouping and can also resemble a project structure of the demos.
• Several scripts to select demos from the demo collection, utilities to download data from remote servers, helper scripts for demo steering, etc.
• Demo GUI, an editor for conveniently selecting and changing demo collections.
• DemoSequence, an Avizo script object for driving the selected demos.

The documentation for the Demo Framework is accessible from the home page of the Avizo help browser.

New Avizo XTeam Pack

The new, separately licensed AvizoXTeam enables remote users to work efficiently together by sharing a common Avizo session.

Avizo XTeam pack is based on a client/server architecture. The server handles the list of opened collaborative sessions. When a user connects to the server, he can create his own session and join
as the initial operator. Or he can join an existing session as a spectator.

The collaborative session is directed by a single operator who can create new modules in the Pool, change ports, and interact with draggers in the 3D view. The other collaborators are spectators that watch what the operator is doing. They can be allowed by the operator to choose their own viewpoint. Once the operator has finished his work, he can close the session or give his operator privileges to another collaborator. When the operator transfers his privileges, he becomes just another spectator.

For more information, see the Avizo XTeam User's Guide which is accessible from a link on the home page of the Avizo help browser.

Avizo Earth Edition

Mercury is proud to announce Avizo Earth Edition, which includes a much expanded feature set for the geosciences.

For your convenience, this new edition is unlocked by a single license, AvizoEarth, which unlocks the following packs:

• XLVolume Pack,
• XReadSEGY Pack

and which also enables the geoscience GUI. The new features and enhancements, including the geoscience GUI, are highlighted below.

* Pool -- Tree view display of objects in the Pool. This provides a more familiar user interface to those in the Oil & Gas field, and can be more convenient when working with large numbers of data sets and modules. Its new features are described in further detail above in the Avizo section.

In tree view mode, the Pool pane and the Pool menu are relabeled "Explorer".

A geoscience "template" for tree view includes predefined folders for 3D surveys, horizons, faults, etc.

Note: A folder for wells is shown in the geoscience template, but import of well data is not yet implemented.

* On-screen compass indicates from which direction you're viewing the survey data.

* Viewer toolbar buttons allow you to view your data from north, south, east, or west.

* New options in the Layout tab of the Preferences dialog allow you to select tree view or graph view, geoscience template or default template, and the position of the compass.

* The SEG-Y Wizard now has a help button for easy access of its corresponding help topic.

* FenceSlice -- new module for drawing fence slices.

* FaultSticks and FaultSticksView -- FaultSticks is a new kind of data object created when you load fault stick data. It can be viewed with the new FaultSticksView module, which allows you to specify a line width scale factor and line color for the fault sticks.

* SeismicSurfaceView -- new module for drawing seismic surfaces using a specified draw style and specified colormap.

* SeismicSettings -- This module allows you to set global seismic attributes, including the coordinate system (UTM or crossline/inline/time), a time (Z) scale factor, a default seismic colormap, and a default surfaces color map. This module is always present in the Pool if an XReadSEGY license is found.

Note 1: Previously the global time (Z) scale factor was specified in a port of the LDA seismic object, e.g., your_data.lda.
Note 2: This global scale factor applies to *all* visualizations in the viewer, not just seismic visualizations. Normally seismic and non-seismic data sets are not visualized together so normally this should not cause a problem.

* Shared Colormap -- Seismic data objects, e.g., your_data.lda, now have a new port, Shared colormap, which specifies the colormap to be associated by default with all of the visualization modules attached to the data object.

* Pool/Explorer -- The new "Auto adjust range of colormaps" toggle allows you to request that Avizo automatically adjust the range of a colormap to correspond to the data range of the data set it is connected to. Note that this feature only applies to the geoscience modules: seismic slices Inline, Crossline, TimeSlice, etc., CroppedVolume, and SeismicSurfaceView.

* Geoscience GUI -- The geoscience GUI is enabled by default if you have an AvizoEarth license. Components of the geoscience GUI include the following:

• Tree view display with the geoscience template selected
• Display of compass in viewer
• Viewer toolbar buttons for selecting view from north, south, etc.
• Colormap editor configured to use alpha curve for editing
  transparency

Each of these items can be reset to their non-geoscience state if desired.

* The new "Avizo Earth Edition" User's Guide introduces you to many of the geoscience features. Its link appears on the home page of the Avizo help browser.