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Release Notes 3.0

Introduction

This document describes changes and improvements in version 3.0 of the Visualization and 3D Reconstruction system Amira and of the expandable version AmiraDev 3.0.

We are pleased to announce the release of Amira 3.0. It offers expanded functionality and increased performance.
Some of the new features and benefits include:

Easy creation of animation sequences, direct MPEG export
New features in the Image Segmentation Editor
Significantly extended documentation, new scripting guide.
New file formats for data import and export (e.g. DICOM 3 export)
New module for modifying 3d image volumes with 3d drawing tools
New features for Finite Element post processing and CFD visualization, like Stream Ribbons
and more...

Supported Platforms

Microsoft Windows 98/ME/NT4/2000/XP (Recommended: Windows 2000 or XP)
HP-UX 11.0 with OpenGL support
SGI Irix 6.5.x (all SGI graphics cards)
SUN Solaris 8 with OpenGL support
Linux with OpenGL support (RedHat 8.0)

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.amiravis.com.

In order to add custom extensions to amira also a C++ compiler is also required. Details about the supported compilers and compiler versions can be found in the section "System Requirements" of the Programmer's Guide included in the amira developer version.

Changes Since amira 2.3

Slice aligner: reduced memory consumption, new option to align images with respect to a fixed slice.
New module HxDisplace for applying displacement vector fields to geometric models.
Support for TeraRecon's VolumePro 1000 volume rendering hardware including combined geometry and volume rendering and volume rendering of large 3D image stacked (images must not reside in main memory).
Point probe module: new option for computing an averaged data value inside a sphere.
Line probe module: option for converting a line probe into a line set.
New module for displaying a test pattern for passive stereo projection.
Improved annotation module (multiple lines).
New scripting guide. Revised Tcl commands for all data objects and modules. Better documentation of the Tcl commands. In order to get the help text for a command or for a port just type in the command in the console window and press the F1 key.
Better Tcl error messages.
New DICOM 3.0 export, improved DICOM 3.0 import (image preview).
New image segmentation editor features, including improved region growing, translation and rotation of selected areas, option for rotated or flipped views, new wrapping tool, new selection replace option in addition to add and subtract, way to create template label fields with predefined materials.
New option tile in the snapshot dialog, which allows generating snapshots with arbitrary high resolution.
Creation of snapshots with an alpha channel for later image compositing (viewer 0 snapshot -alpha <imagefile>). With this option two snapshots are taken, one with a black and one with a white background. From these images the correct color and alpha values are computed.
Possibility to write snapshots in DICOM 3.0 format.
Renamed the GMC module for surface generation to SurfaceGen.
Improved smoothing of label fields: new algorithm guarantees that no label is changed by the smoothing operation. The new option is available as an option in the SurfaceGen module. This is a major enhancement allowing to reconstruct much better surfaces in many situations. The old smoothing in the image segmentation editor (smooth labels 3D) is still available.
New features for dealing with large disk data (LDD concept). Very large regular 3D data stored on disk can be quickly accessed in parts or in low resolution. For fastest access a new distributed disk data file format is provided. Big raw data file, AmiraMesh files, and stacks of 2D images can be accessed via the LDD interface too.
New Region-of-interest concept. ROI's can be defined either using the new SelectROI module or implicitly using an LDD-Access module. Standard modules such as LineSetView or all module derived from HxViewBase (Isosurface, SurfaceView, GridVolume, HexaView, ...), can be connected to a ROI provider. Then the view will be automatically restricted to the ROI.
New module for displaying boundary faces in a hexahedral grid.
Support for the the Leica TIFF image format.
New -proc option for the module or dataClass Tcl commands used to register objects in Amira .rc-files. With this option a Tcl procedure can be defined which is called right after the object is created. This allows e.g. to modify the default settings of an existing module. It also allows to create popup menu entries for virtual objects (just omit the -class statement). When selecting such an entry no object is created but just the Tcl procedure will be executed. With the same mechanism ScriptObjects can be added to the popup menu.
New module for creating MPEG files directly from Amira (MovieMaker).
New CameraRotate object for producing simple animations. The MovieMaker module can be directly connected to this object.
New module VolumeEdit for modifying a 3D image with 3D drawing tools. Useful for 3D image segmentation and background/noise removal.
Improved TissueStatistics module. New options area per slice and volume per VOI.
New Grouping module allowing to define arbitrary groups of elements in all modules derived from HxViewBase (SurfaceView, GridVolume, HexaView, etc.). The grouping module is connected to one or more of these display modules. It allows to define and select groups. The groups can be stored in AmiraMesh files or in network scripts.
Improved time series control module. The module now optionally allows to interpolate between different time steps (surfaces and surface fields, tetrahedral and hexahedral grids and associated data fields, any other data type derived from HxVertexSet).
New module CuttingPlane. The module defines cutting plane (via an Inventor dragger). It then cuts all geometry in the scene with this plane and produces a line set. Connected line segments are identified.
New module SurfDistance. Computes the Hausdorff distance between two arbitrary surface.
New module AlignSurfaces. Aligns two arbitrary surfaces so that the Hausdorff distance is minimized. The surfaces need not to have corresponding points.
New module AlignPrincipalAxes. Aligns two arbitrary data objects derived from HxVertexSet (e.g. surfaces, grids, or point clusters) so that the center and the principal axes of both inputs match.
New module SurfaceNormals for visualizing the normals of a surface.
VertexMorph module replaced by new Interpolate module. The new module optionally also interpolates data fields connected to a grid or to a surface, or it optionally interpolates the grid or surface if connected to a field defined on such objects.
New module TetraVectors. Visualizes the vectors of a vector field defined on a tetrahedral grid. Can be connected to GridVolume or GridBoundary. Vectors are displayed on the elements selected by these modules.
New module StreamRibbons. Computes ribbons in a vector field.
New module Animate. Allows to animate standard Amira ports (sliders and numerical text fields) using a single Time object.
Significantly improved Arithmetic module. Now operates on all fields on regular, tetrahedral, and hexahedral grids, as well as on surface fields. Can compute n-component result instead of only a scalar one.
New module Merge. Combines an arbitrary number of possibly transformed 3D images into one big resampled image using distance based interpolation. Useful for reconstructing 3D models from objects which are scanned in in different parts.
Colormap icons are shown in the popup menu of PortColormap. Colormaps can be loaded and edited directly from the popup menu. Better representation of transparent colormap in the user interface.
Improved color map editor. New menu 'Extras' allowing to set predefined colormaps. Smaller brush for interactive editing of a channel function.
New local range feature for PortColormap. Previously the colormap range was always taken from the colormap object itself. Now it is possible to define a module-specific range in PortColormap.
Before quitting Amira now it is checked if any data object or the current network need to be saved. These checks can be disabled or enabled in the preferences dialog.
Transformed data sets are shown in Italics in the object pool. Modified data sets are marked with an asterisk.
Significantly improved transform editor. The editor now provides an optional dialog allowing to define absolute or relative transformations exactly using text input field. For vertex set objects the editor now also provides an 'Apply Transform' button. Transformations can be copied into and pasted from an internal buffer. This makes it possible to copy a transformation from one data object to another very easily.
Improved Curvature module. Now allows to compute the mean curvature, the Gaussian curvature, the maximum curvature, or both main curvature values or their inverse values.
New module LegoSurface. This module reconstructs a surface from a label field like SurfaceGen, but the surface exactly matches the voxel boundaries.
Improved online help. Module and editor indices contain short explanation now.
Better support for color fields with stacked coordinates. In particular, the modules CastField, OrthoSlice, and ObliqueSlice now support such input.
Many bug fixes and minor improvements.