Avizo 6.1.1 Release notes

Introduction

Release Notes Avizo 6.1.1
Release Date: September 2009

This document describes the improvements and new features in version 6.1.1 of Avizo, the 3D Visualization Framework.

Supported platforms

• Windows XP/Vista, 32-bit code
• Windows XP/Vista (Intel 64/AMD64 architecture) 64-bit code
• Linux x86 (Red Hat Enterprise Linux 5) 32-bit code
• Linux x86_64 (Red Hat Enterprise Linux 5, Intel 64/AMD64 architecture) 64-bit code
• Mac OS 10.5, 32-bit code
  

For other platforms including Sun Solaris, Linux IA64, ... visit http://www.vsg3d.com.

Further details about software and hardware configuration are listed in the section "System Requirements" of the User's Guide included in this distribution and also available at http://www.vsg3d.com.

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 Pand Pack User's Guide.

• Windows XP/Vista: Visual Studio 2005
• Windows XP/Vista x64-Edition: Visual Studio 2005
• Linux: gcc 4.1.x

Avizo 6 is the last major version which will support the following platforms/compilers:

• Redhat EL4 32/64bits
• Mac PowerPc
• Visual Studio 2005 (i.e. non-SP1) , only Visual Studio 2005 SP1 will be supported

Avizo 6.1.1 Changes - Improvements and new features

Avizo 6.1 Changes - Improvements and new features

Avizo Standard Edition - Improvements and new features

• New subscription license which gives access to all Avizo editions and extension packages.
  
• The selection color in the segmentation editor can now be changed using a color editor.
  
• A new CSV (Comma Separated Value) wizard enables the user to import ASCII uniform scalar field 2D/3D data like 2D or 3D images.
  
• In the plot window associated with the LineProbe or the SplineProbe, it is now possible to choose the variable to use on the X-axis, which can be the line/spline length, the probe X, Y or Z coordinate. A new port 'offset' has been also added in order to translate the X-axis coordinates of the probe.
  
• SelectROI now displays the memory size of the selected region which is very usefull with an out of core dataset.
  
• Bounding box module enhancements including making accessible some tcl commands as new ports.
  
• Many bug fixes

Avizo Wind Edition - Improvements and new features

• New CFD/FEA file writers for the following formats: ANSYS, ABAQUS, ENSIGHT, CGNS, IDEAS, TECPLOT and NASTRAN.
  It is possible to export to these formats:
  • Tetrahedral grids (HxTetraGrid) with associated boundaries which could be issued for instance from a TetraGen after a surface reconstruction.
  • Any surfaces (HxSurface) composed of triangles or quadrangles.
    
• New compute module SecondaryVariables.
  This new module enables you to compute more than 50 secondary variables which are functions of several primary variables.
  This module makes the former compute module VorticityIdentification obsolete (but integrates its functionality).
  The variables computed can be classified into several categories: Density, Pressure, Temperature, Energy, Velocity, Vorticity, Turbulence.
  The main secondary variables which can be computed are:
  • total pressure
  • stagnation pressure
  • dynamic pressure
  • shock variable
  • temperature
  • stagnation temperature
  • kinetic energy
  • internal energy
  • stagnation energy
  • total energy
  • enthalpy
  • entropy
  • momentum
  • vorticity
  • helicity
  • lambda2
  • second invariant
  • gradient
  • newtonian fluid stress tensor
  • ...
    
• New Abaqus ODB reader (Windows only).
  
• New FLUENT/Fidap Neutral file reader.
  
• Arithmetic compute module can now also compute on boundaries if they exist (previously, it could only be done on 3D cells).
  
• Better retreival of CFD/CAE file format information (parts/boundaries names, boundaries types)
  

Avizo Fire Edition - Improvements and new features

• New specific crop editor for IM6 "on-disk" files in order to specify the calibration.

Avizo Earth Edition - Improvements and new features

• Extended support for the Log ASCII Standard (LAS) file format:
  • The version 2.1 is now also supported (only 2.0 before)
    
  • The tags XCOORD and YCOORD are now interpreted, which enables you to import well logs without importing well heads or well path.
    
• New horizon reader for X Y Z ascii file format.

Avizo 6.0 Changes - Improvements and new features

All Avizo Editions:

• Avizo Standard Edition for Scientific Visualization,
• Avizo Wind Edition for CFD/FEA, Simulation Post-processing,
• Avizo Earth edition for Geosciences,
• Avizo Fire Edition for Material Science and NDT
• Avizo Green Edition for Environmental and Climate Data

are now supplied as separate applications with tailored user interface, specific feature-set and dedicated workflow.
Accordingly, Avizo network files (.hx) are now tagged with the edition that saved them in order to have a file association between Avizo editions and network files.

From version 6.0, the number of instances of Avizo which could run simultaneously on a same computer is limited to 2.

New Avizo Wind Edition

The new Avizo Wind edition is a high-end application for advanced post-processing of simulation data, including flow, thermal and stress data. Avizo Wind brings an extensive array of advanced visualization and analysis tools to CFD and multiphysics, mechanical and thermal engineering, manufacturing simulation and microstructural prediction, non linear structural and geotechnical problems.

Summary of features in Avizo Wind Edition:

• Extensive data support
  • Wide range of formats: Abaqus, Ansys, CGNS, Ensight, Fluent, Ideas, Nasa/Plot3D, Nastran, Star-CCM, Tecplot,...
  • Mixed polyhedral 3D grids composed of Hexahedrons, Tetrahedrons, Wedges, and Pyramids.
  • Scalar, vector and tensor fields
  • Multiphysics data support which allows mixing the result of simulations coming from different solvers.
  • Transient and stationary data support
  • On the fly load/unload datasets to optimize memory usage.
    
    
• Advanced visualization
  • High-end 2D/3D visualization techniques on 3D scalar fields
    • Contours on 3D grid skin
    • Cross sections
    • Boundaries visualisation
    • Isosurfaces
    • Isolines
    • Volume Rendering techniques
    • Per node and per cell data display
    • ...
      
      
  • Effective and innovative flow visualization on 3D vector fields
    • ISL (Illuminated Stream Lines)
    • Flow textures (Line Integral Convolution)
    • Particle animation
    • Stream ribbons
    • Vectors on cross section and vectors in the 3D volume
    • Flexible data mapping
    • ...
      
      
• Powerful analysis features
  • Surface/volume statistics (surface and volume integrals, mean value, flow rate, flux, force, standard deviation, etc) with spreadsheet/csv export.
  • Arithmetic computation module for scalar and vector fields. This module is optimized for multi-core CPUs for maximum performance.
  • Matlab® connection.
    
    
• High end vortex identification on 3D vector fields
  • Secondary variable computation including enstropy, vorticity, lambda2, helicity, Q factor, etc
  • Topological analysis of 3D vector fields:
    • Vortex core line extraction: Line passing through the center of vortices
    • Critical point extraction: Points around which different flow patterns can be identified (outflow, inflow, mixture of both)
      
      
• Measurement and inspection tools
  • 3D cell inspection for any 3D visualization tto retreive with a mouse click the cell topology, material, region, volume, data, etc.
  • Length and angle measurements
  • Histogram representation
  • Point, Line and spline probing.
    
    
• Major legend improvements
  • Variable name as title
  • Identification and display of the unit associated with the variable
    

New Avizo Green Edition

• The former XGreen pack dedicated to the visualization and analysis of climate, oceanography, environmental or earth-mapped data, has been repackaged as a new edition called the Green Edition.

Avizo Standard Edition - Improvements and new features

• New template networks mechanism
  Template networks can be used to ease repetitive tasks on a set of similar data.
  A template network consists of a backup of an original network that can be replicated on another data set of the same type.
  
  
• Measurement tools enhancements
  • Using the measure tool's drop down multi tool button immediately activates the chosen tool instead of choosing and activating it as before.
    
  • The measure tool now has the ability to toggle between any measure tool and the last given navigation tool (e.g. rotate, move, zoom) by pressing the ESC key.
    
  • Drawing more than one measurement of a certain type in a row.
    
  • Activating the last used measure tool by selecting a measurement of the list view, in order to immediately manipulate the measurement (drag etc.).
    
    
• Preferences enhancements
  • Preferences can be now saved into a separate file which can later be reloaded.
    
  • Preferences are automatically saved per-edition which means that the preferences for an edition can be different from the preferences for another one.
    
    
• New TreeView mode
  A new tree view mode is available:
  • Classifies Display/Compute and Data module into separate folders,
    
  • Displays a Green arrow icon followed by the input data name for all input connections,
    
  • Displays a Red arrow followed by the output data name icon for all output results generated by compute modules.
    
  • This new behavior is activated by default with the Avizo Wind Edition and can be activated/deactivated in the preferences (i.e. Layout Tab/Group Pool).
    
    
• Help Window enhancements
  The help window's searching tool has been improved and the new behaviour is similar to Mozilla Firefox(TM).
  
  
• Avizo News display
  A new mechanism of web news display is available in order to let the user know when upgrades or new versions are available.
  
  
• New generic readers for ASCII valued point cluster files and any valued line set files
  A new CSV (Comma Separated Value) wizard enables the users to import ASCII valued point cluster files and any valued line set files.
  
  
• Emmergency saving of network
  In the rare case that Avizo encounters an error and cannot continue running, Avizo can now perform an emergency save of the current network in order to avoid lost work.
  
  
• Other minor enhancements
  • It is now possible to display a title with the DisplayColormap module.
    
  • The TensorDisplay module can now take a ROI as an input connection.
    
  • Adjust range support for the port colormap of LineSetView and ClusterView modules.
    
  • Fonts of Global and Local axis can now be changed with a font selector.
    
    
• Many bug fixes
  

Avizo XLVolume Pack - Improvements and new features

• New "Loading Priority" slider within the LDA tab preferences. This slider enables you to specify the priority for tile loading between slice display (OrthoSlice/ObliqueSlice) and volume display (Voltex).
  

Avizo Earth Edition - Improvements and new features

• Well Data import
  
  • New import for well heads.
    Well heads, which characterize the oil and gas well position in an oil field, can be imported using the CSV (Comma Separated Value) wizard.
    
    
  • New import for well path/trace.
    Well path, which is the depth measured along the wellbore, can be imported using the CSV (Comma Separated value) wizard.
    In order to make the Depth conversion, a checkshot file can be specified at the well path import.
    Once imported, the well path can be displayed as a pipe or line and this visualization can be mixed with seismic slice and volume visualizations.
    
    
  • New import for well tops.
    Well tops, which identify the depth of geological layers along a wellbore, cobe imported using the CSV (Comma Separated value) wizard.
    Once imported, well tops can be displayed as colored 3D markers.
    
    
  • New import of Log ASCII Standard (LAS) files which store well log information.
    Well logging, storing of one or more physical quantities in or around a well, is used to characterize subsurface stratigraphy in a wellbore.
    Once imported, well log curves can be displayed along the well path.
    

Avizo Fire Edition - Improvements and new features

• Huge Performance enhancements
  Most of the image processing commands have been parallelized in order to optimize the usage of multi-core CPUs. The performance gain is proportional to the number of cores. For instance for the mediafilter command applied to an 1800x1800 image on a typical multicore machine, the performance with 2 cores is 1.77 times faster than 1 core and the performance with 8 cores is 7.18 times faster.
  
  
• New Spread sheet export
  A new option (port) accessible in the property area of the Quantification modules enables you to export analyses to spread sheets.
  
  
• Calibration enhancements
  Before version 6.0, there were 2 ways to set the calibration within Avizo, one with the Crop Editor and another one with the Quantification-Calibration. These 2 ways were not uniform and not synchronized. In this new version, calibration can only be set with the Crop Editor.
  
  
• New Measurement commands:
  • The previous Measurements command group has been split into Measurement (2D images) and Measurement 3D.
    
    • New Measurement commands:
      • intercept: Gives the number of entries in an object along a given direction of a binary 2D image.
      • fractal: Measure the fractal dimension of a 2D images
      • locate: Gives the X and Y coordinates of all non-zero pixels of a binary 2D image.
      • number: Number of objects in a binary or labelled image.
      • perimeter: Measure the perimeter according to the Crofton formula.
      • rose: Characterize the directional structure of contours in a 2D image.
      • volume: Sum of pixel intensities in a 2D image.
        
        
    • New Measurement 3D commands:
      • euler3d: Euler-Poincare number to measure the connectivity of complex 3D stuctures.
      • fractal: Measure the fractal dimension of a 3D image.
      • integral_curvature: Integral of mean curvature and integral of total curvature in a binary image
        
        
• New Analysis commands
  • analyze_seg: Compute measurement directly.
  • filter_segment: Filter existing segment.
    
    
• New Thresholding commands:
  • hysteresis: Hysteresis thresholding.
    
    
• New Point Operation commands:
  • combdirimg: Combines two images following a symmetry axis or center.
    
    
• New Morphology commands:
  • lerode: Linear erosion on a binary or greyscale image.
  • colorerode: Erosion on a RGB image.
  • ldilate: Linear dilation on a binary or greyscale image.
  • colordilate: Erosion on a RGB image.
  • lopening: Linear opening on a binary or greyscale image.
  • unionlopening: Union of the opening in the four directions on a binary or greyscale image.
  • coloropen: Opening on a RGB image.
  • lclosing: Linear closing on a binary or greyscale image.
  • unionlclosing: Intersection of closing on a binary or greyscale image.
  • colorclose: Closing on a RGB image.
  • ultimate: Search the ultimate eroded set on a binary or label image.
  • interior_points: Hit-or-miss transforms on a binary image.
  • end_points: Hit-or-miss transform on a binary image.
  • triple_points: Hit-or-miss transform on a binary image.
  • isolated_points: Hit-or-miss transform on a binary image
  • convex_hull: Fill the concavities of particles in a binary image without connecting the particles.
  • hitormiss: Hit-or-miss transform on a binary image.
  • skeleton: Skeleton of a binary image.
  • prune: Eliminate artifacts after a skeleton on a binary image.
  • centroid: Centroids on a RGB image.
  • bissecto: Sets of erosion on a binary image.
  • thick_skel: Skeleton by successive thickenings of a binary image.
  • thick_prune: Eliminate artifacts after a thick_skel on a binary image.
  • fastskeleton: Skeleton based on distance function of a binary image.
  • fastprune: Eliminate artifacts after a thick_skel on a binary image.
    
    
• New Frequency commands:
  • topower2: Provide a square image
  • circular_profil: Calculate intensity value along circles centered on the image center.
    
    
• New Edge Detection commands:
  • compass_3x3: Edge detection and determination of the directions of the gradient of the input image.
  • gradient: Gradient computation of the input image.
  • mgradient: Morphological gradient of the input image.
  • gradient_mag: Gradient amplitude and orientation of the input image.
  • rgradient: Recursive algorithm for gradient computation of the input image.
  • zero_crossings: Remove noise. Zero-crossings are points where the Laplacian switches from positive to negative values, and vice versa.
  • lmaxima: Provides suppression of non-local maxima of the gradient amplitude.
  • crete: Provides the local maxima using an edge tracking process.
  • laplacian_3x3: 3x3 Laplacian on an image.
  • laplacian_5x5: 5x5 Laplacian on an image.
  • laplacian_7x7: 7x7 Laplacian on an image.
  • dob_filter: Calculates the difference between two local averages computed oversquare neighborhoods of different sizes (Difference Of Boxes) applied on the same image.
  • rlaplacian: Recursive Laplacian on an image
  • link_chains: Provides pixel linking from an edge image into chains.
  • link_oriented: Performs pixel linking from an edge image into oriented chains.
  • link_approx: Perform pixel linking from an edge image into chains, approximated by polygons of linear segments.
  • unlink_chain: Creates an image and plots linked chains on this output image.
  • I_extract_edge: Detects edges in a grey level image, converts those edges into a list of segments.
    
    
• New Edge Approximation commands:
  • seg_approx: Gives the outlines of the polygones in a binary image.
  • polyg_approx: Converts a chain object into a segment by approximating the polygons of linear segments.
  • unlink_seg: Create an image and plot linear segments in this output image.
  • link_cells: Joins adjacent CHAINS into a single CHAIN.
  • insidelength: Computes the diameter of the skeleton of every simple polygon.
  • segholefill: Destroys all interior chains of a segment object.
  • segtolabel: Creates a label image from a segment object.
  • segequidist: Modifies a segment object. The aim is to build a new polygon with same distance between all vertices.
  • segadjust: Modifies a segment object. The aim is to build a new polygon using gradient images to adjust vertices.
  • segcnvxhull: Modifies a segment object. It replaces all polygons by their convex hulls.
  • chain_extract: Extracts one polyline of a segment object.
  • segtocircle: For each polygon, this command computes the circle that minimizes the least square criteria.
  • segtorectangle: For each polygon of a segment object, this command computes the smallest enclosing rectangle.
  • ellipse: Computes the smoothing ellipse.
    
    
• New Correlation commands:
  • bincorrel: Performs the logical correlation between a binary image and a binary kernel.
  • mcorrel: Performs a multiplication correlation between a grey level image and a grey level kernel, returning the correlation image.
  • dcorrel: Calculates the difference correlation between a grey level image, and a grey level kernel, returning the correlation image.
  • scorrel: Provides sign change criterion correlation between a grey level image and a grey level kernel.
  • formimage: Creates a binary image from an annotation selected in another image.
  • fastbincorrel: Provides a fast binary correlation between a binary image and a binary kernel.
  • fastmcorrel: An optimization of the standard multiplication correlation.
  • fastdcorrel: Provides a fast difference correlation between a grey level image and a grey level kernel.
  • fastscorrel: A fast sign change criterion correlation between a grey level image and a grey level kernel.
    
    
• New Fast Morphology commands:
  • greyseparate: Compute watershed lines on the grey-level image for black objects or on the inverted image for white objects.
    
    
• New Segmentation commands:
  • mean: Gives each pixel the mean value in its neighbourhood.
  • variance: Gives each pixel the variance value in its neighbourhood.
  • skewness: Gives each pixel the skewness value in its neighbourhood.
  • kurtosis: Gives each pixel the kurtosis value in its neighbourhood.
  • contrast: Gives each pixel the contrast value in its neighbourhood.
  • variation: Gives each pixel the variation value in its neighbourhood.
  • statorder2: Gives some information concerning the texture thanks to statistics of order 2.
  • energy: Gives each pixel the energy value in its neighbourhood in the reduced image.
  • entropy: Gives each pixel the entropy of its neighbourhood in the reduced image.
  • gaborfiltering: Makes filtered images using Gabor filters, which are well known for localisation in frequency and space.
  • lawfiltering: Creates energy images using linear filters
  • crosscorrel: Computes the cross correlation of an image in a given window size.
  • statnormalize: Performs the statistical normalization of a sequence of images.
  • karhunenloeve: Performs the reduction of the number of images in a sequence, keeping the main informations of it.
  • auto_classification: Segments the input image into regions which have the same caracteristics.
  • lab_classification: Creates a classification using a label image in which each object corresponds to a class.
  • last_classification: Same as lab_classification but for several images.
  • regionsimplify: Makes a simplification of a region image, based on the filtering method.
  • regiongrowing: Makes a segmentation of an image, based on the region growing method.
  • regiongrowinggrad: Makes a segmentation of an image using the growing region method, but only with the Gradient criterion.
  • getcriterionparam: Gives the different parameters of a criterion for region growing segmentation.
  • setcriterionparam: Allows changing the different parameters of a criterion for region growing segmentation.
    
    
• New Materials analysis commands
  • extractjoints: Extracts joints between cells.
  • astm_intercept: Gives the mean size of the grain using the metric system.
  • astm_planimetric: Gives the mean size of the grain using english units.
    
    
• Other commands:
  • The previous command group Image Editing has been split into two groups: Image Editing and Image Editing3D.
  • avi2im6: Converts a avi file to a Visilog image (memory or file).
  • mergefield: Merges two images, considered as even and odd frames, to produce an interlaced image.
  • mergefieldseq: Performs a MERGEFIELD command from a Visilog sequence to a Visilog sequence.
  • splitfield: Separates even and odd frames from an interlaced image.
  • splitfieldseq: Performs a SPLITFIELD command from a Visilog sequence to a Visilog sequence.
  • buildsepar: Creates a rectangular construction of an image from two different arrays.
  • buildcirc: Creates a circular construction of an image from a single array.
  • random: Creates an image with random values following a uniform distribution.
  • randomgauss: Creates an image with random values following a gaussian distribution.
  • bayer2rgb: Creates an RGB image from a Bayer image.
  • decorrelstrech: Maximizes (stretch) the difference between different bands of data, by trying to remove the inter-band correlation found in the input pixels.
  • zstack: Create an image with the best pixels of a Visilog sequence.
  • seq2color: Convert a Visilog sequence to Visilog Multi-Sources.
    
    
• Many bugs fixed.

Avizo 5.1 Changes - Improvements and new features

Introduction

Release Notes Avizo 5.1
Release Date: September 2008

This document describes the improvements and new features delivered by the version 5.1 of Avizo, the 3D Visualization Framework.

Supported platforms

• Windows XP/Vista, 32-bit code
• Windows XP/Vista (Intel 64/AMD64 architecture) 64-bit code
• Linux x86 (Red Hat Enterprise Linux 4.0/5.0) 32-bit code
• Linux x86_64 (Red Hat Enterprise Linux 4.0/5.0, Intel 64/AMD64 architecture) 64-bit code
  
• MAC OS 10.5
• Sun Solaris 8 - In Progress
  
• Linux Suse 10 IA64 - On Demand
• IRIX 32 - On Demand

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 XPand Pack User's Guide.

• Windows XP/Vista: Visual Studio 2005
• Windows XP/Vista x64-Edition: Visual Studio 2005
• Linux: gcc 4.1.x

Avizo 5.1 Changes - Improvements and new features

Avizo Standard Edition

• New Display Modules:
  
  • New AnnotatedIsoline display module. Displays isolines with annotations on 3D scalar fields.
    
  • New BumpSlice display module. Displays ortho-slice with embossed mapping on any regular scalar field.
    
  • New CityPlot display module. This module displays a scalar data field as a 3D histogram.
    
  • New DisplayParticle display module. This module displays a HxVectorField3 as a set of particles.
    
  • New DisplayDate display module. This module displays the date.
    
  • New ClusterStringLabels display module. This module visualizes string labels associated with data objects of type Cluster.
    
    
• Voltex improvements:
  
  • The high quality volume rendering features (Voltex) of the XLVolume Pack are now available for any uniform scalar field.
    
  • Volume rendering (Voltex) of data on rectilinear grids is now supported. Rectilinear grids allow non-uniform voxel spacing on each axis of the volume.
    
    
• Unicode support in Annotation module.
  The Annotation module now supports Unicode character strings allowing correct display in any language and character set.
  
  
• New license manager dialog to simplify the import of license strings.
  
  
• Matlab improvements:
  
  • The CalculusMatlab module is now available on Windows 64.
    
  • Improved Matlab engine connection. The CalculusMatlab module now transfers all native Avizo data types to and from Matlab. The previous solution only supported a single data type (double) connection.
    

• Avizo was previously based on Trolltech Qt 3 for the graphical user interface. Avizo 5.1 now uses Trolltech Qt 4 for better stability and better performances.
  
  
• New Nifti reader. Nifti is a file format for the exchange of neuro imaging data.
  
  
• Image filtering improvements:
  • New FilteredOblique slice module which applies filters and visualizes data from an arbitrary slice.
    
  • Image filters have been renamed using more explicit names.
    
  • All 3D image filters have now a 2D equivalent filter.
    
    
• New Projection module defining a projection.
  This module allows, for example, correctly rendering data defined on a grid of latitude and longitude coordinates. Some display nodes now have a projection port which can be connected to a Projection module.
  
  
• New option to move an oblique slice with low resolution.
  
  
• DemoMaker script improved for handling complex sequences:
  
  • Search in event list.
    
  • Save and load a file containing the event list, using internal format. In some cases, it can be convenient to export, import or edit this event list file.
    
    
• New transparency types available in viewers.
  Sorted Layers and Sorted Layers Delayed transparency algorithms are the best known real-time rendering techniques to correctly display transparent objects.
  
  
• The DisplayISL display module now allows you to specify the seed points using a HxVertexSet data object.
  
  
• The DisplayLineSet display module now allows you to specify the complexity for spheres and circles.
  
  
• Colormap management improvements:
  
  • Each scalar data set now has a colormap port. By default it is disabled. When enabled (using the edit popup menu), each display module attached to this data set will automatically use this colormap. Assigning a colormap is thus much easier than before.
    
  • Colormaps appear in a specific color in the pool as soon as they are used by a display module or a data set. Colormap now are visible when used. They can be easily identified in the pool by their specific color.
    
  • A new edit button has been added to the colormap port to replace the old right button click. Editing colormaps is much more natural this way.
    
  • Each colormap now has a help button (question mark button) in the property window.
    
    
• A help button has been added to all data objects in the property window. It is now easier to find out the data type.
  
  
• Mesh quality testing improved:
  
  • The TetraQuality module has been improved to support more quality check. It can be connected directly to a data set.
    
  • A new HexaQuality module has been added for Hexahedron mesh.
    
    
• Histogram module now handles line sets as inputs.
  
  
• The editor's capability for handling bad tetras has been improved.
  
  
• The VolumePro 500 and VolumePro 1000 volume rendering boards are no longer supported.
  
  
• Many bugs fixed.
  
  

Avizo XLVolume Pack

• New multi-sample option on LDA ortho and oblique slices.
  New interpolation type which provides much higher quality images than linear interpolation.
  
  
• New volume rendering (Voltex) quality and performance options:
  
  • Edge coloring option: Enables to color edges based on the gradient direction.
    
  • 2D edge detection option: A 2D edge detection algorithm is used to highlight edges of the rendered volume image.
    
  • Boundary opacity option: Increases the opacity of boundaries based on the magnitude of the gradient.
    
  • Illumination quality option: Provides different methods for computing the gradient (normal) used when the rendering is lighted.
    
  • Less ringing artefacts option: Decreases slice edge artefacts when few slices are displayed.
    
  • Cubic interpolation option to get a smooth rendering.
    
  • New performances options: Exposed different techniques in order to improve performance.
    
    
• New LDA conversion options on LDA data:
  
  • Data Compression: Compressed data uses less disk space and can be loaded faster (fewer bytes to move). Currently gzip and jpeg compressions are available.
    
  • Border size option: In order to avoid discontinuity artifacts with lighted volume rendering or with embossed mapped slices, a border size of 3 should be specified.
    
    
• New Arithmetic compute module on LDA Data. This new module performs calculations on up to three input LDA data objects according to a user-defined expression.
  
  

Avizo XLMicroscopy Pack

The Leica Image Format (LIF) reader now supports the LIF version 2 file format.

Avizo Earth Edition - Improvements and new features

• Enhancements of the SEGY-Wizard to support SEGY-2D file.
  The following display modules will be accessible once the SEGY-2D file has been read:
  
  • Bounding Box
    
  • Seismic 2D line which is similar to a fence slice display with SEGY-3D data set.
    
    
• Attribute computation on 3D seismic volume:
  Attribute computation on 3D seismic volume enables to make appear some particular features useful for the geologist analysis. An attributes computation is a real-valuated function applied to each seismic trace.
  The following instantaneous seismic attributes could be computed:
  
  • Instantaneous Amplitude
  • Instantaneous Phase
  • Instantaneous Frequency
  • Instantaneous Cosine Phase
  • Instantaneous Amplitude 1st Derivative
  • Instantaneous Amplitude 2nd Derivative
  • Instantaneous Envelope Weighted Phase
  • Instantaneous Envelope Weighted Frequency
  • Instantaneous Phase Acceleration
    
    
  Avizo proposes two methods to compute seismic attributes:
  
  • On the fly computation: From an inline, crossline, or time slice, you can choose the attribute to compute and it is computed instantly.
    
  • Global computation: Generation of a 3D seimic volume with a seismic attribute computed.
    

Avizo XQuant Pack - Improvements and new features

• Graphical User Interface improvement providing better integration within Avizo.
  
  
• The performance of the binseparate morphologic tool has been improved.

New Avizo XGreen Pack

The new, separately licensed Avizo XGreen Pack, can be used to visualize weather and climate data
from Simulations with numerical Earth System Models.

With its powerful NetCDF-CF1 file interface, the Green Pack allows you to read and visualize the
typical long time series of multivariate 3D data produced by weather and climate models by using
the most commonly used native file formats. Depending on the local hardware configuration, large
files can be cached in memory in order to accelerate the interactive access. Very large time dependent
files can be visualized right away from the hard disks.
A topography and map module, complemented by a geographic projection module with user definable
exaggeration of the vertical axis allows to interactively explore the data in the correct geographic
context.

Avizo XGreen Pack offers a wide range of state of the art visualization methods as well as some
advanced methods and features like Line Integral Convolution (LIC), Illuminated Streamlines (ISL) or
Particle Advection for visualizing vector fields like wind and ocean currents.

Avizo 5.0 Changes - Improvements and new features

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

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

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

It indicates from which direction you're viewing the survey data.

Viewer toolbar buttons

They allow you to view your data from north, south, east, or west.

New options in the Layout tab of the Preferences dialog

They allow you to select tree view or graph view, geoscience template or default template, and the position of the compass.

The SEG-Y Wizard

It 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.

Avizo Earth Edition User's Guide

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.