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Thermo ScientificTM AvizoTM Software 9
User’s Guide
Copyright Information
Copyright (c) 1995-2018 Konrad-Zuse-Zentrum f¨
ur Informationstechnik Berlin (ZIB), Germany
Copyright (c) 1999-2018 FEI SAS, a part of Thermo Fisher Scientific
All rights reserved.
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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