Avizo 9.0.0 用户指南：专业软件操作手册

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"Avizo 9.0.0 用户指南" 《Avizo 9.0.0 用户指南》是为用户提供关于Avizo软件的详细操作和使用说明的文档。Avizo是一款强大的三维可视化和分析软件，尤其在科学成像领域有着广泛的应用。本指南由Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB) 和FEI SAS共同开发，旨在帮助用户充分利用该软件的各项功能。版权信息表明，该软件和用户指南的版权由1995年至2015年的ZIB和FEI SAS共同持有，所有权利均受法律保护。商标信息中提到，FEI、Amira、Avizo和OpenInventor等是FEI公司或其附属公司的注册商标，其他商标归各自所有者所有。 Avizo的开发不断进行，产品的性能可能会随时更新，因此用户在使用时应关注产品规格的最新变动。特别指出，Avizo X Earth Extension和Avizo XL Volume Extension这两个扩展功能包含了Landmark U.S. Patent Numbers 6,765,570的用户保护许可。此用户指南是专为FEI的许可用户准备的，与FEI提供的软件配套使用，并且根据书面许可协议提供。未经FEI的许可协议允许，用户不得复制、分发或部分使用本材料。同时，FEI保留不经通知即可修改产品规格的权利。用户指南中详细涵盖了Avizo 9.0.0的安装、界面介绍、基本操作、数据导入与导出、图像处理、三维建模、数据分析、结果可视化以及高级功能等内容。此外，还可能包括故障排除、系统需求和用户支持等章节，帮助用户解决在使用过程中可能遇到的问题。 Avizo软件适用于地质学、生物学、材料科学、物理学等多个领域的研究，其强大的图像处理和分析能力，如能面重构、体积渲染、测量计算等功能，使得用户可以深入探索和理解复杂的三维数据。通过学习和掌握《Avizo 9.0.0 用户指南》中的内容，用户能够熟练运用Avizo进行科学研究和数据分析，提升工作效率和研究质量。

12.3.2 Read Routines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 663

12.3.3 Write Routines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 671

12.3.4 Use the AmiraMesh API to read and write ﬁles in Avizo data format . . . . . 676

12.4 Writing Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 680

12.4.1 A Compute Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 680

12.4.2 A Display Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 688

12.4.3 A Module With Plot Output . . . . . . . . . . . . . . . . . . . . . . . . . . . 696

12.4.4 A Compute Module on GPU . . . . . . . . . . . . . . . . . . . . . . . . . . 701

12.5 Data Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 719

12.5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 720

12.5.2 Data on Regular Grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723

12.5.3 Unstructured Tetrahedral Data . . . . . . . . . . . . . . . . . . . . . . . . . 729

12.5.4 Unstructured Hexahedral Data . . . . . . . . . . . . . . . . . . . . . . . . . 731

12.5.5 Unstructured Mixed Models . . . . . . . . . . . . . . . . . . . . . . . . . . . 733

12.5.6 Other Issues Related to Data Classes . . . . . . . . . . . . . . . . . . . . . . 735

12.6 Documentation of Modules in Avizo XPand Extension . . . . . . . . . . . . . . . . . 739

12.6.1 The documentation ﬁle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 739

12.6.2 Generating the documentation . . . . . . . . . . . . . . . . . . . . . . . . . 740

12.7 Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 740

12.7.1 Time-Dependent Data And Animations . . . . . . . . . . . . . . . . . . . . . 741

12.7.2 Important Global Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . 743

12.7.3 Save-Project Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 745

12.7.4 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 746

xiv CONTENTS

Section 1.6 (First steps) provides hints about tutorials included in this guide.

Section 1.7 (Contact and Support) provides contact information for your technical support, license

administrator, or sales representative.

1.1 Overview

Avizo is a modular and object-oriented software system. Its basic system components are modules and

data objects. Modules are used to visualize data objects or to perform some computational operations

on them. The components are represented by little icons in the Project View. Icons are connected

by lines indicating processing dependencies between the components, i.e., which modules are to be

applied to which data objects. Alternatively, modules and data objects can be displayed in a Project

Tree View. Modules from data objects of speciﬁc types are created automatically from ﬁle input data

when reading or as output of module computations. Modules matching an existing data object are

created as instances of particular module types via a context-sensitive popup menu. Projects can be

created with a minimal amount of user interaction. Parameters of data objects and modules can be

modiﬁed in Avizo’s interaction area.

For some data objects such as surfaces or colormaps, there exist special-purpose interactive editors

that allow the user to modify the objects. All Avizo components can be controlled via a Tcl command

interface. Commands can be read from a script ﬁle or issued manually in a separate console window.

The biggest part of the screen is occupied by a 3D graphics window. Additional 3D views can be

created if necessary. Avizo is based on the latest release of Open Inventor by FEI, SAS. In addition,

several modules apply direct OpenGL rendering to achieve special rendering effects or to maximize

performance. In total, there are more than 270 data object and module types. They allow the system

to be used for a broad range of applications. Scripting can be used for customization and automation.

User-deﬁned extensions are facilitated by the Avizo developer version.

1.2 Features overview

Avizo provides a large number of data types and modules allowing you to visualize, analyze and model

various kinds of 3D data. The Avizo framework is ideal to integrate the data from multiple sources

into a single environment.

This section summarizes the main features of the Avizo software suite. For more complete informa-

tion, you may browse indexes for data types, ﬁle formats and modules in the Reference Guide. This is

accessible from the home page of the online help browser.

Section 1.3 describes the Avizo optional editions and extensions.

2 Chapter 1: Introduction

1.2.1 Data import

Avizo can load directly different types of data, including:

• 2D and 3D image and volume data

• Geometric models such as point sets, line sets, surfaces, grids

• Numerical simulation data

• Time series and animations

A large number of ﬁle formats are supported in Avizo or through speciﬁc optional readers. For an

introduction to data import, see section 3.1. For more details, see section 2.6.

1.2.2 Viewing, navigation, interactivity

All visualization techniques can be arbitrarily combined to produce a single scene. Moreover, multiple

data sets can be visualized simultaneously, either in several viewer windows or in a common one. Thus

you can display single or multiple data sets in a single or multiple viewer windows, and navigate freely

around or through those objects. Views can be synchronized to facilitate comparisons.

A built-in spatial transform editor makes it easy to register data sets with respect to each other or to

deal with different coordinate systems. Automatic alignment and registration of image or geometric

data is also possible.

Direct interaction with the 3D scene allows you to quickly control regions of interest, slices, probes

and more.

Combinations of data sets, representation and processing features can be deﬁned with minimal user

interaction for simple or complex tasks. See section 1.1.

1.2.3 Visualization of 3D Image Data

1.2.3.1 Slicing and Clipping

You can quickly explore 3D images looking at single or multiple orthographic or oblique sections.

Data sets can be superimposed on slices, displayed as height ﬁelds, or with isolines contouring. You

can cut away parts of your data to uncover hidden regions. Curved or cylinder slices are also available.

1.2.3.2 Volume Rendering

One of the most intuitive and most powerful techniques for visualizing 3D image data is direct volume

rendering. Light emission and light absorption parameters are assigned to each point of the volume.

Simulating the transmission of light through the volume makes it possible to display your data from any

view direction without constructing intermediate polygonal models. By exploiting modern graphics

hardware, Avizo is able to perform direct volume rendering in real time, even on very large data when

Features overview 3

using the Avizo XLVolume Extension. Thus volume rendering can instantly highlight relevant features

of your data. Volume rendered images can be combined with any type of polygonal display. This

improves the usefulness of this technique signiﬁcantly. Moreover, multiple data sets can be volume

rendered simultaneously – a unique feature of Avizo. Transfer functions with different characteristics

required for direct volume rendering can be either generated automatically or edited interactively using

an intuitive colormap editor. Avizo volume rendering can use the latest techniques for high quality

visualization effects such as lighting or shadows.

1.2.3.3 Isosurfaces

Isosurfaces are most commonly used for analyzing arbitrary scalar ﬁelds sampled on discrete grids.

Applied to 3D images, the method provides a very quick, yet sometimes sufﬁcient method for recon-

structing polygonal surface models. Beside standard algorithms, Avizo provides an improved method,

which generates signiﬁcantly fewer triangles with very little computational overhead. In this way, large

3D data sets can be displayed interactively even on smaller desktop graphics computers.

1.2.3.4 Large Volume Data

With the Avizo XLVolume Extension, even very large data sets that cannot be fully loaded in mem-

ory can be manipulated at interactive speed. Multi-resolution techniques can manage and visualize

extremely large amounts of volume data of up to hundreds of gigabytes. You can then, for instance,

quickly select a region of interest and extract down-sampled or partial data for further processing.

1.2.4 Image processing

1.2.4.1 Alignment of image slices

The image Align Slices enables you to build a consistent stack of images with manual or automatic

tools, if, for instance, physical cross sections have been shifted during image acquisition.

1.2.4.2 Image ﬁlters

Image features can be enhanced by applying a wide range of ﬁlters for controlling contrast, smoothing,

noise reduction and feature enhancement. See Section 4.8 More about Image Filtering.

1.2.4.3 Image segmentation

Segmentation means assigning labels to image voxels that identify and separate objects in a 3D image.

Avizo offers a large set of segmentation tools, ranging from purely manual to fully automatic: brush

(painting), lasso (contouring), magic wand (region growing), thresholding, intelligent scissors, contour

ﬁtting (snakes), contour interpolation and extrapolation, wrapping, smoothing and de-noising ﬁlters,

4 Chapter 1: Introduction

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