Thermo Fisher Scientific Avizo Software Industrial Inspection 9.5 User guide

Thermo ScientiﬁcTM AvizoTM Software 9

User’s Guide

Copyright Information

ur Informationstechnik Berlin (ZIB), Germany

Trademark Information:

All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

Avizo is being jointly developed by Konrad-Zuse-Zentrum f¨

ur Informationstechnik Berlin (ZIB) and FEI SAS, a part of Thermo

Fisher Scientiﬁc.

The Avizo XEarth Extension and the Avizo XLVolume Extension include user protection under license for

Landmark U.S. Patent Numbers 6,765,570.

This manual has been prepared for Thermo Fisher Scientiﬁc licensees solely

for use in connection with software supplied by Thermo Fisher Scientiﬁc and

is furnished under a written license agreement. This material may not be used, reproduced

or disclosed, in whole or in part, except as permitted in the license agreement or by prior

written authorization of Thermo Fisher Scientiﬁc. Users are cautioned that

Thermo Fisher Scientiﬁc reserves the right to make changes without notice to the

speciﬁcations and materials contained herein and shall not be responsible for any

damages (including consequential) caused by reliance on the materials presented,

including but not limited to typographical, arithmetic or listing errors.

Contents

1 Introduction 1

1.1 Overview ......................................... 2

1.2 Features overview .................................... 2

1.2.1 Data import ................................... 3

1.2.2 Viewing, navigation, interactivity ........................ 3

1.2.3 Visualization of 3D Image Data ......................... 3

1.2.4 Image processing ................................ 4

1.2.5 Model reconstruction .............................. 5

1.2.6 Visualization of 3D models and numerical data ................. 6

1.2.7 General Data Processing and Data Analysis .................. 7

1.2.8 MATLAB integration .............................. 8

1.2.9 High Performance Visualization ........................ 8

1.2.10 Automation, Customization, Extensibility ................... 8

1.3 Editions and Extensions ................................. 9

1.3.1 Editions ..................................... 9

1.3.2 Optional Extensions ............................... 10

1.3.3 License keywords ................................ 12

1.4 System Requirements .................................. 12

1.4.1 Prioritizing hardware for Avizo ......................... 13

1.4.2 How hardware can help optimizing ....................... 17

1.4.3 Special considerations .............................. 18

1.5 Avizo License Manager ................................. 22

1.5.1 Contents ..................................... 22

1.5.2 About Avizo Licensing Management ...................... 22

1.5.3 License Manager Actions ............................ 23

1.5.4 Licensing Troubleshooting ........................... 42

1.5.5 Contacting the License Administrator ...................... 45

1.6 First steps in Avizo .................................... 45

1.7 Contact and Support ................................... 48

2 Getting Started 50

2.1 Start the program ..................................... 50

2.2 Loading Data ....................................... 52

2.3 Invoking Editors ..................................... 54

2.4 Visualizing Data ..................................... 54

2.5 Interaction with the Viewer ............................... 55

2.6 Data Import ....................................... 58

3 Tutorials: Visualizing and Processing 2D and 3D Images 60

3.1 How to load image data ................................. 60

3.1.1 The Avizo File Browser ............................. 61

3.1.2 Reading 3D Image Data from Multiple 2D Slices ............... 61

3.1.3 Setting the Bounding Box ............................ 63

3.1.4 The Stacked Slices ﬁle format .......................... 63

3.1.5 Working with Large Disk Data ......................... 64

3.1.6 Working with out-of-core data ﬁles (LDA) ................... 65

3.2 Visualizing 3D Images .................................. 71

3.2.1 Orthogonal Slices ................................ 72

3.2.2 Simple Data Analysis .............................. 74

3.2.3 Resampling the Data .............................. 74

3.2.4 Displaying an Isosurface ............................ 75

3.2.5 Cropping the Data ................................ 76

CONTENTS ii

3.2.6 Volume Rendering ................................ 78

3.3 Combined 3D and 2D views with Ortho Views (Avizo) ................. 84

3.3.1 Quick start .................................... 84

3.3.2 Manage combined 3D and 2D views with Ortho Views ............ 86

3.4 Intensity Range Partitioning ............................... 89

3.5 Segmentation of 3D Images ............................... 95

3.5.1 Interactive Image Segmentation ......................... 96

3.5.2 Volume and Statistics Measurement ....................... 98

3.5.3 Threshold Segmentation ............................. 98

3.5.4 Reﬁning Threshold Segmentation Results ................... 99

3.5.5 More Hints about Segmentation .........................100

3.6 Deconvolution for light microscopy ...........................102

3.6.1 General remarks about image deconvolution ..................102

3.6.2 Data acquisition and sampling rates .......................103

3.6.3 Standard Deconvolution Tutorial ........................105

3.6.4 Blind Deconvolution Tutorial ..........................110

3.6.5 Bead Extraction Tutorial ............................112

3.6.6 Performance issues and multi-processing ....................119

4 Tutorials: Advanced Image Processing, Segmentation and Analysis 124

4.1 Getting Started with Advanced Image Processing and Quantitative Analysis . . . . . 124

4.1.1 Processing images ................................125

4.1.2 Interpretation as 3D image or 2D image stack .................127

4.1.3 Getting more help ................................127

4.1.4 Binarization ...................................127

4.1.5 More about binary images ............................129

4.1.6 More hints about binarization ..........................129

4.1.7 Separation ....................................130

4.1.8 Analysis .....................................131

4.1.9 Interactive selection ...............................133

4.1.10 Filtering based on measures ...........................134

CONTENTS iii

4.1.11 Classifying measures with sieves ........................136

4.1.12 Label images ..................................136

4.1.13 Processing data on disk .............................138

4.1.14 Scripting .....................................138

4.1.15 Conclusion ....................................138

4.2 Example 1: Measuring a Catalyst ............................139

4.2.1 Object Detection and Masks ..........................140

4.2.2 More about Region of Interest and Masks ...................144

4.2.3 Using Distance Map ...............................144

4.2.4 More about Distance Maps ...........................147

4.2.5 Measurement Distribution ............................148

4.3 Example 2: Separating, Measuring and Reconstructing .................148

4.3.1 Principle of the Watershed Algorithm ......................150

4.3.2 Prior Segmentation ...............................150

4.3.3 Separation using Watershed step by step ....................152

4.3.4 Separation Troubleshooting ...........................156

4.3.5 Filtering Individual Objects ...........................158

4.3.6 Geometry Reconstruction ............................160

4.4 Example 3: Further Image Analysis - Distribution of Pore Diameters in Foam . . . . 161

4.4.1 First step: pore detection ............................161

4.4.2 Second step: pore post-processing .......................162

4.4.3 Third step: custom measure group deﬁnition to determine the distribution of

pore diameters ..................................163

4.4.4 Fourth step: custom measure deﬁnition to compute the sphericity of pore . . . 166

4.5 Example 4: Further Image Analysis - Average Thickness of Material in Foam . . . . . 170

4.5.1 Porosity Detection ................................171

4.5.2 Detection of the Separation Surfaces ......................172

4.5.3 Distance Map of the Material ..........................173

4.5.4 Calculation of the Material Average Thickness .................176

4.6 Watershed Segmentation .................................176

4.6.1 Segmenting sand pack with watershed tool in the Segmentation Editor . . . . 177

CONTENTS iv

4.6.2 Segmenting multiphase using the Watershed Segmentation wizard ......180

4.7 More about Image Filtering ...............................191

4.7.1 Choosing image ﬁlters ..............................191

4.7.2 Tuning image ﬁlters ...............................193

4.7.3 Compositing image ﬁlters ............................196

4.8 More about label measures ...............................201

4.8.1 The Measures Group Selection dialog .....................201

4.8.2 User measures ..................................203

4.8.3 Conﬁgurable native measures ..........................203

4.8.4 About project backup ..............................205

4.8.5 Scripting tips ..................................206

5 Tutorials: Surfaces, meshes, skeletons, modeling geometry from 3D images 207

5.1 Surface Reconstruction from 3D Images ........................207

5.1.1 Extracting Surfaces from Segmentation Results ................208

5.1.2 Simplifying the Surface .............................208

5.2 Creating a Tetrahedral Grid from a Triangular Surface .................209

5.2.1 Editing the Surface ...............................210

5.2.2 Generation of a Tetrahedral Grid ........................212

5.3 Advanced Surface and Grid Generation .........................213

5.3.1 Getting started: a workﬂow from 3D images to surfaces and grids .......215

5.3.2 Adjusting segmentation for geometry extraction ................216

5.3.3 Generating surfaces with controlled smoothing .................219

5.3.4 Using the Simpliﬁcation Editor .........................221

5.3.5 Using the Surface Editor ............................223

5.3.6 Remeshing and exporting surfaces .......................227

5.3.7 Generating tetrahedral grid ...........................228

5.3.8 Assigning boundary conditions and exporting data ...............230

5.4 Visualization and Analysis of 3D Models and Numerical Data with Avizo .......233

5.4.1 Avizo features for surfaces ...........................234

5.4.2 Supported grids in Avizo XMesh Extension ..................234

CONTENTS v

5.4.3 Avizo XMesh Extension features for 3D grids .................235

5.4.4 Scalar ﬁelds visualization ............................236

5.4.5 Vector ﬁelds visualization ............................237

5.4.6 Time dependent data visualization .......................238

5.4.7 Compute modules ................................239

5.5 Skeletonization ......................................239

5.5.1 Getting started with Skeletonization: the Auto Skeleton module ........240

5.5.2 Displaying and exporting skeletonization results ................242

5.5.3 Skeletonization step-by-step ..........................252

5.5.4 Skeletonization with large data .........................256

6 Registration, Alignment and Data Fusion 262

6.1 Getting started with spatial data registration using the Transform Editor ........263

6.1.1 Using the Transform Editor ...........................263

6.1.2 Applying Transforms ..............................266

6.1.3 Numerical input, console and script commands .................270

6.1.4 Transform Manipulators .............................272

6.2 Data fusion, comparing and merging data ........................274

6.2.1 Color Wash ...................................275

6.2.2 Ortho Views ...................................276

6.2.3 Mapping a 3D volume overlaid on a surface ..................278

6.2.4 Side-by-side viewers, synchronized views and objects .............279

6.2.5 More about Data Fusion .............................282

6.3 Registration with landmarks, warping surfaces and image ...............283

6.3.1 Creating landmark sets .............................284

6.3.2 Registration with Rigid Transformation .....................287

6.3.3 Warping surfaces ................................289

6.3.4 Warping volumes (3D images) .........................290

6.3.5 Retrieving and copying registration transformation using Tcl command . . . . 291

6.4 Registration of 3D image data sets ............................292

6.4.1 Getting started with Register Images module ..................292

CONTENTS vi

6.4.2 Register Images guidelines ...........................297

6.4.3 Using the Image Registration Wizard - example with partially overlapping

images ......................................299

6.4.4 More about the Register Images module ....................304

6.5 Registration of 2D image and 3D image data sets ....................309

6.5.1 Guidelines ....................................310

6.5.2 Pre-alignment: Searching for a 2D slice (needle) in a 3D volume (haystack) . 310

6.5.3 Reﬁned alignment ................................312

6.6 Alignment of 2D images stacks .............................313

6.6.1 Basic manual alignment .............................314

6.6.2 Automatic alignment ..............................316

6.6.3 Alignment via landmarks ............................316

6.6.4 Optimizing the least-squares quality function ..................318

6.6.5 Resampling the input data into result ......................319

6.6.6 2D alignment guidelines, more about Align Slices ...............320

6.7 Alignment and pre-processing of FIB/SEM images stacks using the FIB Stack Wizard 322

6.7.1 Images import, voxel size and foreshortening correction ............324

6.7.2 Geometric corrections overview .........................327

6.7.3 Getting started with FIB Stack Wizard .....................329

6.7.4 Selecting what to align using masks ......................336

6.7.5 Further processing of FIB Stacks ........................338

6.8 Registration of 3D surfaces ...............................338

6.8.1 Getting started with Align Surfaces module ..................338

6.8.2 Align Surfaces guidelines ............................343

6.8.3 Alignment of surface subsets ..........................344

6.8.4 Measure and visualize surface distance .....................346

6.9 Registration of 3D image and surface, nominal-actual analysis .............348

6.9.1 A simple workﬂow for nominal-actual analysis .................349

6.9.2 Advanced - Image/surface registration step by step ...............353

7 Animations and Movies 355

CONTENTS vii

7.1 Creating animations ...................................355

7.1.1 Creating a project ................................356

7.1.2 Animating an Ortho Slice module ........................356

7.1.3 Activating a module in the viewer window ...................359

7.1.4 Using a camera rotation .............................361

7.1.5 Removing one or more events ..........................362

7.1.6 Overlaying the inside surfaces with outer surface ................362

7.1.7 Using clipping to add the outer surface gradually ................362

7.1.8 More comments on clipping ...........................365

7.1.9 Breaks and function keys ............................366

7.1.10 Loops and Goto .................................367

7.1.11 Storing and replaying the animation sequence .................369

7.2 Creating movie ﬁles ...................................369

7.2.1 Attaching Movie Maker to a Camera-Path ...................370

7.2.2 Creating a movie from an animated demonstration ...............372

8 User Interface Components, General Concepts, Start-Up 374

8.1 User Interface Components ...............................374

8.1.1 File Menu ....................................374

8.1.2 Edit Menu ....................................378

8.1.3 Project Menu ..................................379

8.1.4 View Menu ...................................382

8.1.5 Window Menu ..................................385

8.1.6 Help Menu ....................................387

8.1.7 Standard Toolbar ................................388

8.1.8 Workrooms Toolbar ...............................388

8.1.9 Project View ...................................388

8.1.10 Properties Area .................................395

8.1.11 Progress Bar ...................................397

8.1.12 Viewer Window .................................398

8.1.13 Consoles Panel .................................405

CONTENTS viii

8.1.14 Online Help ...................................406

8.1.15 Histogram Panel .................................409

8.1.16 Correlation Panel ................................413

8.1.17 File Dialog ....................................416

8.1.18 Job Dialog ....................................416

8.1.19 Preferences Dialog ...............................419

8.1.20 Snapshot Dialog .................................429

8.1.21 System Information Dialog ...........................432

8.1.22 Object Popup ..................................432

8.1.23 Create Object Popup ...............................439

8.2 General Concepts ....................................440

8.2.1 Class Structure ..................................440

8.2.2 Scalar Field and Vector Fields ..........................441

8.2.3 Coordinates and Grids ..............................442

8.2.4 Surface Data ...................................443

8.2.5 Vertex Set ....................................444

8.2.6 Transformations .................................444

8.2.7 Data parameters .................................444

8.2.8 Shadowing ....................................445

8.2.9 Units in Avizo ..................................446

8.2.10 Automatic Display in Avizo ...........................453

8.2.11 Workroom Concept ...............................456

9 Automating, Customizing, Extending 457

9.1 Template Projects ....................................457

9.1.1 Template Projects Description ..........................457

9.2 Recipes ..........................................459

9.3 Avizo Start-Up ......................................459

9.3.1 Command Line Options .............................460

9.3.2 Environment Variables .............................461

9.3.3 User-deﬁned start-up script ...........................463

CONTENTS ix

9.4 TCL Scripting ......................................464

9.4.1 Scripting Introduction ..............................464

9.4.2 Introduction to Tcl ................................465

9.4.3 Avizo Script Interface ..............................471

9.4.4 Global Commands ................................473

9.4.5 Avizo Script Files ................................487

9.4.6 Conﬁguring Popup Menus ...........................488

9.4.7 Registering pick callbacks ............................491

9.4.8 File readers in Tcl ................................492

9.4.9 How to Create Recipe-Compliant Script-Object ................493

9.4.10 Versioning of Script Objects and backward compatibility ...........496

9.5 Python Scripting .....................................499

9.5.1 Python Documentation .............................499

9.5.2 Python Tutorials .................................523

9.6 Using MATLAB with Avizo ...............................528

9.6.1 Using MATLAB Scripts .............................528

10 Avizo XFiber Extension User’s Guide 529

10.1 Introduction to the Filament Editor ...........................529

10.1.1 Exploration of the Volume Data .........................530

10.1.2 Automatic Extraction of the Dendritic Tree ...................531

10.1.3 Filament Tracing ................................533

10.1.4 Visualize the Network ..............................534

10.1.5 Alternative Way to Extract a Network Using the Segmentation Editor . . . . . 535

10.2 Detecting Fibers or Tube-Like Structures ........................536

10.2.1 Computing Normalized Cross Correlation ...................536

10.2.2 Tracing the Centerlines .............................542

10.2.3 Computing Basic Statistics for Tracing Results .................544

10.2.4 References ....................................545

10.3 Computing Advanced Statistics .............................545

10.3.1 Analyzing Contact Points ............................547

CONTENTS x

10.3.2 Extracting Statistics about the Fibers’ Shape ..................551

10.3.3 Plotting the Distribution of Fibers ........................552

10.3.4 Removing Fibers that are touching the Bounding Box .............553

10.3.5 Filtering Fibers .................................555

10.3.6 Calculating and Visualizing Local Statistics ..................557

10.3.7 Plotting Orientations in 3D ...........................561

11 Avizo XWind Extension User’s Guide 564

11.1 Meshing Workroom ...................................565

11.1.1 First Steps ....................................566

11.1.2 Inspecting the Generated Mesh .........................568

11.1.3 Fast Meshing versus Precise Meshing ......................571

11.1.4 Optimization ...................................573

11.1.5 Controlling the Reﬁnement of the Mesh ....................573

11.1.6 Slider Quality and Grouping ..........................573

11.1.7 Preserve Thin Structures ............................574

11.1.8 Boundary Layer .................................575

11.1.9 Advanced Meshing Mode ............................575

11.1.10 Troubleshooting .................................577

11.1.11 Assigning Boundary Conditions to the Mesh ..................578

11.1.12 Exporting the Mesh ...............................581

11.1.13 Scripting the Room: TCL Command List ....................581

11.1.14 Progress Bar Indications .............................585

11.2 Meshing Workroom Tutorial ...............................585

11.2.1 First Mesh Generation and Inspection .....................586

11.2.2 Global Mesh Reﬁnement ............................588

11.2.3 Mesh Reﬁnement of Groups of Materials ....................591

11.2.4 Advanced Mesh Reﬁnement ..........................591

11.2.5 Boundary Layer Reﬁnement ..........................595

11.2.6 Optimization of Mesh Quality ..........................595

11.2.7 Color Mapping of Material Properties .....................597

CONTENTS xi

11.2.8 Boundary Conditions and Export to CFD/FEA Solvers ............597

11.3 Avizo XWind Extension Measurements .........................600

11.3.1 3D measurements ................................600

11.3.2 Histograms ...................................601

11.3.3 Data probing ...................................603

11.4 Getting Started with reading and visualizing CAE/CFD data ..............605

11.4.1 User interface short overview ..........................606

11.4.2 Reading data ...................................608

11.4.3 Getting started ..................................610

11.4.4 Units and legends ................................611

11.4.5 Saving your project ...............................612

11.4.6 Tip: Template projects ..............................612

11.4.7 Time animation .................................614

11.5 Avizo XWind Extension Models Information and Display ...............616

11.5.1 Properties and parameters ............................616

11.5.2 Colormaps ....................................618

11.5.3 Viewing the grid .................................619

11.5.4 Viewing the boundaries .............................621

11.6 Avizo XWind Extension Scalar Fields Display .....................623

11.6.1 Scalar ﬁeld proﬁle on a cross section ......................624

11.6.2 Scalar ﬁeld isolines ...............................625

11.6.3 Legend and captions ...............................626

11.6.4 Isosurfaces of pressure .............................627

11.7 Avizo XWind Extension Vector Fields Display .....................630

11.7.1 Particles animation ...............................630

11.7.2 Illuminated streamlines (ISL) ..........................632

11.7.3 Line integral convolution (LIC) .........................634

11.7.4 Vectors in a plane ................................634

11.7.5 Stream ribbons ..................................635

11.7.6 Find the 3D critical points ............................637

CONTENTS xii

11.8 Avizo XWind Extension Statistical and Arithmetic Computations ...........638

11.8.1 Surface and volume integrals ..........................638

11.8.2 Arithmetic computation .............................643

11.9 Avizo XWind Extension Vorticity Identiﬁcation ....................645

11.9.1 Vorticity-related variables computation .....................645

11.9.2 Vortex core lines identiﬁcation .........................647

11.9.3 Vortical ﬂow visualization ............................650

11.10 Avizo XWind Extension Measurements .........................651

11.10.1 3D measurements ................................652

11.10.2 Histograms ...................................654

11.10.3 Data probing ...................................655

12 Avizo XLabSuite Extension User’s Guide 659

12.1 Getting started with absolute permeability computation ................661

12.1.1 Theoretical elements ..............................661

12.1.2 Step 1 - Activate Avizo unit management ....................665

12.1.3 Step 2 - Load the data set and select the length unit for voxel size .......666

12.1.4 Step 3 - Set the voxel size ............................668

12.1.5 Step 4 - Create a label image from the data set .................671

12.1.6 Step 5 - Remove non-percolating void space ..................674

12.1.7 Step 6 - Selection of a sub-region ........................677

12.1.8 Step 7 - Absolute permeability experiment simulation .............679

12.1.9 Step 8 - Absolute permeability tensor calculation ...............684

12.1.10 Step 9 - Permeability validation with Kozeny-Carman equation ........688

12.2 Getting started with molecular diffusitivity computation ................689

12.2.1 Theoretical elements ..............................690

12.2.2 Step 1 - Load the data set ............................694

12.2.3 Step 2 - Set the voxel size ............................695

12.2.4 Step 3 - Create a label image from the data set .................695

12.2.5 Step 4 - Remove non-percolating void space ..................696

12.2.6 Step 5 - Selection of a sub-region ........................696

CONTENTS xiii

12.2.7 Step 6 - Molecular diffusivity experiment simulation ..............697

12.2.8 Step 7 - Molecular diffusivity tensor calculation ................700

12.2.9 Step 8 - Molecular diffusivity computation validation .............702

12.3 Getting started with formation factor and electrical conductivity computation . . . . . 704

12.3.1 Theoretical elements ..............................705

12.3.2 Step 1 - Load the data set ............................708

12.3.3 Step 2 - Set the voxel size ............................709

12.3.4 Step 3 - Create a label image from the data set .................709

12.3.5 Step 4 - Remove non-percolating void space ..................710

12.3.6 Step 5 - Selection of a sub-region ........................711

12.3.7 Step 6 - Formation factor experiment simulation ................712

12.3.8 Step 7 - Effective formation factor calculation .................714

12.3.9 Step 8 - Formation factor computation validation ................716

12.4 Getting started with thermal conductivity computation .................718

12.4.1 Theoretical elements ..............................718

12.4.2 Step 1 - Load the data set ............................722

12.4.3 Step 2 - Set the voxel size ............................723

12.4.4 Step 3 - Create a label image from the data set .................723

12.4.5 Step 4 - Remove isolated conducting materials parts ..............724

12.4.6 Step 5 - Selection of a sub-region ........................724

12.4.7 Step 6 - Thermal conductivity experiment simulation .............725

12.4.8 Step 7 - Effective thermal conductivity calculation ...............729

12.4.9 Step 8 - Thermal conductivity computation validation .............730

13 Avizo XPand Extension 737

13.1 Introduction to Avizo XPand Extension .........................738

13.1.1 Overview of Avizo XPand Extension ......................738

13.1.2 System Requirements ..............................740

13.1.3 Structure of the Avizo File Tree .........................740

13.1.4 Quick Start Tutorial ...............................742

13.1.5 Compiling and Debugging ...........................744

CONTENTS xiv

13.1.6 Maintaining Existing Code ...........................746

13.2 The Development Wizard ................................747

13.2.1 Starting the Development Wizard ........................748

13.2.2 Setting Up the Local Avizo Directory ......................748

13.2.3 Adding a New Package .............................750

13.2.4 Adding a New Component ...........................751

13.2.5 Adding an Ordinary Module ..........................751

13.2.6 Adding a Compute Module ...........................752

13.2.7 Adding a Read Routine .............................752

13.2.8 Adding a Write Routine .............................753

13.2.9 Creating the Build System Files .........................754

13.2.10 The Package File Syntax ............................754

13.3 File I/O ..........................................757

13.3.1 On ﬁle formats ..................................757

13.3.2 Read Routines ..................................758

13.3.3 Write Routines ..................................768

13.3.4 Use the AmiraMesh API to read and write ﬁles in Avizo data format . . . . . 773

13.4 Writing Modules .....................................779

13.4.1 A Compute Module ...............................779

13.4.2 A Display Module ................................787

13.4.3 A Module With Plot Output ...........................795

13.4.4 A Compute Module on GPU ..........................800

13.5 Data Classes .......................................812

13.5.1 Introduction ...................................812

13.5.2 Data on Regular Grids ..............................815

13.5.3 Unstructured Tetrahedral Data .........................821

13.5.4 Unstructured Hexahedral Data .........................823

13.5.5 Unstructured Mixed Models ...........................825

13.5.6 Other Issues Related to Data Classes ......................827

13.6 Documentation of Modules in Avizo XPand Extension .................831

CONTENTS xv

13.6.1 The documentation ﬁle .............................831

13.6.2 Generating the documentation .........................832

13.7 Miscellaneous ......................................833

13.7.1 Time-Dependent Data And Animations .....................833

13.7.2 Important Global Objects ............................835

13.7.3 Save-Project Issues ...............................837

13.7.4 Troubleshooting .................................838

14 Avizo XMetrology Extension 840

14.1 Data Selection ......................................840

14.1.1 General .....................................840

14.1.2 Metrology Surface Determination ........................841

14.2 Data Visualization ....................................843

14.2.1 Metrology 3D Display ..............................843

14.2.2 Volume Rendering Options ...........................843

14.2.3 Surface Options .................................844

14.2.4 Ortho Views Options ..............................844

14.3 Geometries Fitting ....................................844

14.3.1 General .....................................844

14.3.2 Geometry Fitting Toolbar ............................846

14.3.3 Fitting Tools ...................................846

14.3.4 Fitting Methods .................................847

14.4 Inherited Geometries ...................................854

14.4.1 General .....................................854

14.4.2 Inherited Geometry Editor ...........................854

14.4.3 Intersection ...................................855

14.4.4 Composition ...................................855

14.4.5 Projection ....................................856

14.4.6 Inherited Geometry Updates ..........................856

14.5 Local Coordinate Systems (LCS) Creation .......................856

14.5.1 General .....................................856

CONTENTS xvi

14.5.2 LCS Toolbar ...................................856

14.6 Measurements Creation .................................857

14.7 Test Plans Usage .....................................858

15 Avizo XRecipe Extension 859

15.1 Creating and Editing Recipes ..............................862

15.2 Using Breakpoints ....................................865

15.3 Recipes in a TCL Command ...............................868

15.4 Recipe Limitations ....................................868

16 Avizo XReporting Extension 870

17 Avizo XPoreNetworkModeling Extension User’s Guide 877

17.1 Pore Space Analysis ...................................879

17.1.1 Preparing the Data ................................879

17.1.2 Generating and Analyzing the Network .....................883

18 Avizo XBioFormats Extension 890

19 Avizo XDigitalVolumeCorrelation Extension User’s Guide 894

19.1 Digital Volume Correlation Analysis ..........................895

19.1.1 Preparing the Subset-Based Approach .....................895

19.1.2 Compute a Good Initial Guess using the Subset-Based Approach .......897

19.1.3 Run a Robust FE-Based DVC Technique ....................900

19.1.4 Visualize and Animate the Results of the Global Approach ..........904

19.1.5 Dialog between experience and simulation ...................908

19.1.6 Additionnal post processing ...........................908

19.1.7 References ....................................909

CONTENTS xvii

Chapter 1

Introduction

Avizo is a 3D data visualization, analysis and modeling system. It allows you to explore and analyze

data sets from various areas, including:

•Scientiﬁc visualization, physics, chemistry, astrophysics, archaeology, and others

•Material sciences, non-destructive testing, tomographic imaging and microscopy

•Computer-aided Engineering, computational ﬂuid dynamics, numerical simulation

•Oil and gas, mining, Earth science

•Climate, oceanography, environment

Examples from these disciplines are illustrated by several demo scripts contained in the online version

of the user’s guide.

3D data can be quickly explored, analyzed, compared, and quantiﬁed. 3D objects can be represented

as image volumes or geometrical surfaces and grids suitable for numerical simulations, notably as tri-

angular surface and volumetric tetrahedral grids. Avizo provides methods to generate such grids from

voxel data representing an image volume, and it includes a general-purpose interactive 3D viewer.

Section 1.1 (Overview) provides a short overview of the fundamentals of Avizo, i.e., its object-oriented

design and the concept of data objects and modules.

Section 1.2 (Features) summarizes key features of Avizo, for example direct volume rendering, image

processing, and surface simpliﬁcation.

Section 1.3 (Editions and Extensions) brieﬂy describes optional extensions and editions available for

Avizo and for what they can be used for.

Section 1.4 (System Requirements) provides system speciﬁc information.

Section 1.5 (Avizo License Manager) details for entering and managing Avizo license passwords.

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Thermo Fisher Scientific Avizo Software Industrial Inspection 9.5 User guide

Thermo Fisher Scientific Avizo Software Industrial Inspection 9.5 User guide

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