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Contents
Introduction
Unbundling the Software Distribution
Compiling
3DMA
Testing the Compilation
Special Notes for Linux (Intel), Mac, and DEC Alpha Machines
Execution
3DMA
Organization
The Main Menu
Input Data Formats
Data File Name Convention
Supported User Formats
Segmented Data
Erosion Distance (`Burn') Data
Medial Axis Data
Output Graphics Data
Main Menu: Raw/Diffused Data
Segmentation
Global Thresholding
Diffusion
Kriging-Based Segmentation
Mardia-Hainsworth Segmentation Algorithm
Color Values
Main Menu: Segmented Data
Main Menu: Erosion Distance (`Burn') Data
Main Menu: Medial Axis Data
Sample Input Files
General Overview
Main Menu 1: Operations performed on Tomographic Data
case1.1: Generate Images of Input Data
case1.1_ras: Generate Rasterfile Images
case1.1a_ras: Generate Rasterfile Images with Fiducial Polygon
case1.1g_ras: Generate Rasterfile Images without Fiducial Polygon
case1.1_expl: Generate Iris Explorer 3D Image File
case1.2: Generate Attenuation Coefficient Histograms
case1.2/case1.2a.in: Generate Attenuation Coefficient Histograms with Fiducial Polygon
case1.2/case1.2g.in: Generate Attenuation Coefficient Histograms without Fiducial Polygon
case1.2/case1.2l.in: Generate Attenuation Coefficient Histograms without Fiducial Polygon
case1.3: Extract a Rectangular Subvolume of a Data Set
case1.4: Generate Circular Fiducial Polygon
case1.5dfn.slc: Segment Data using Anisotropic Diffusion Method on each Slice Separately
case1.5dfn.vol: Segment Data using Anisotropic Diffusion Method on 3D Data Set
case1.5krig: Segment Data Using Indicator Kriging
case1.5krig/case1.5ent.in: Indicator Kriging on Data Slices with Threshold Window Chosen by Entropy Function
case1.5krig/case1.5ent3d.in: Indicator Kriging on 3D Data Set with Threshold Window Chosen by Entropy Function
case1.5krig/case1.5mix.in: Indicator Kriging on Data Slices with Threshold Window Chosen by Binormal Mixture Fit
case1.5krig/case1.5mix3d.in: Indicator Kriging on 3D Data Set with Threshold Window Chosen by Binormal Mixture Fit
case1.5mh: Segment Data Using Mardia-Hainsworth Algorithm
case1.5mh/case1.5mh.in: Mardia-Hainsworth Segmentation on Data Slices
case1.5mh/case1.5mh.in: Mardia-Hainsworth Segmentation on 3D Data Set
case1.5smpl: Segment Data Using Simple Threshold
case1.6: Investigate Porosity Dependence of Threshold Choice
case1.6/case1.6a: Porosity vs. Threshold: File-by-File Scaling
case1.6/case1.6g: Porosity vs. Threshold: Global Scaling
case1.6/case1.6gu: Porosity vs. Threshold: Global Scaling with User Selected Range
case1.7: Investigate Free Parameter in Anisotropic Diffusion Method
case1.8: Investigate Application of Threshold Value on Diffused Images.
case1.8/case1.8s: Single threshold applied to slice diffused with multiple K values
case1.8/case1.8md: Multiple thresholds applied to single K slice
case1.8/case1.8mr: Multiple thresholds applied to a single slice of the original data set
case1.9: Plot Gradient of Image Intensity
case1.10: Compress Slices
Main Menu 2: Analyses Performed on Segmented Data Sets
case2.1: Generate Burn Data and Print Raster Images with Fiducial Polygon
case2.2: Generate Burn Data and Compute Medial Axis using Lee-Kashyap-Chu Algorithm
case2.2ms: Generate Burn Data and Compute Medial Surface using Lee-Kashyap-Chu Algorithm
case2.3: Compute Disconnected Volume Distributions
case2.3/case2.3.in: Disconnected Volume Distributions Using Erosion Algorithm
case2.3/case2.3.ntrim: Disconnected Volume Distribution Using Tree Search: No Edge Trimming
case2.3/case2.3.trim: Disconnected Volume Distributions Using Tree Search: Edge Trimming
case2.4: Compute Moment of Inertia Analysis on Disconnected Components
case2.5: Generate Images of the Segmented Data
case2.5_ras/case2.5_ras.in: SUN Rasterfile Format
case2.5_ras/case2.5a_ras.in: SUN Rasterfile Format: Convert Isolated Voxels
case2.5_BR: Bio-Rad MRC-600 Format
case2.5_dx: IBM Explorer Format
case2.5_expl: IRIS Explorer Format
case2.5_gl: Open GL Format
case2.5_iv: Inventor Format
case2.6: Convert Segmented Data Files to/from ASCII
case2.6/case2.6.ab.in: Convert ASCII Files to Binary
case2.6/case2.6.ba.in: Convert Binary Files to ASCII
case2.7: Compute Two Point Correlation Function
case2.7/case2.7.ci2.in: Grain - Classical 2D
case2.7/case2.7.grain.in: Grain - Classical x and y
case2.7/case2.7.m1d.in: Grain - Moving Window x
case2.7/case2.7.m2d.in: Grain - Moving Window 2D
case2.7/case2.7.m3df.in: Grain - Moving Window 3D Fast Algorithm
case2.7/case2.7.m3ds.in: Grain - Moving Window 3D Slow Algorithm
case2.7/case2.7.void.in: Void Phase - Classical x and y
case2.8: Comparison of 2-Pt Correlation Functions for Tomographic and Segmented Data Sets
case2.9: Compress Slices
case2.9/case2.9max.in: Compress Using Maximum Value
case2.9/case2.9maj.in: Compress Using Majority Value
case2.10: Shell Densities
case2.10/case2.10_cyl.in: Cylindrical Shells
case2.10/case2.10_sph.in: Spherical Shells
Main Menu 3: Analyses on Burn Data Sets
case3.1: Resize Burn Data Files
case3.2: Histogram and Attempt Fits to Burn Data Histogram
case3.2/case3.2.efit: Exponential Fit to Burn Data Histogram
case3.2/case3.2.nfit: Normal Fit to Burn Data Histogram
case3.3: Compute Medial Surface via Burn Algorithm
case3.4: Compute Medial Axis/Surface via LKC Algorithm
case3.4/case3.4.in: Medial Axis, top/bottom image boundaries represent truncated data set, original LKC sweep algorithm
case3.4/case3.4a12.in: Medial Axis, all boundaries capture full image, Stopy Brook sweep algorithm
case3.4/case3.4s.in: Compute Medial Surface via LKC Algorithm
case3.5: Convert Burn Data Files to/from ASCII
case3.5/case3.5.in: Convert Binary Files to ASCII
Main Menu 4: Analyses Available on Medial Axis Data Set
case4.1: Generate Images of the Medial Axis/Surface
case4.1_ras: SUN Rasterfile Format
case4.1_ras/case4.1a_ras.in: SUN Rasterfile Format
case4.1_ras/case4.1b_ras.in: SUN Rasterfile Format: Trim Axis, Add Grains
case4.1_ras/case4.1c_ras.in: SUN Rasterfile Format: Trim Axis
case4.1_BR: Bio-Rad MRC-600 Format
case4.1_dx: IBM Explorer Format
case4.1_dx/case4.1_dx.in: IBM Explorer Format - Image Entire Volume
case4.1_dx/case4.1a_dx.in: IBM Explorer Format - Image SubVolume
case4.1_expl: Iris Explorer Format
case4.1_expl/case4.1_expl.in: Iris Explorer Format - Image Medial Axis
case4.1_expl/case4.1s_expl.in: Iris Explorer Format - Image Medial Surface
case4.1_gl: Open GL Format
case4.1_gl/case4.1_gl.in: Open GL Format - Image Entire Volume
case4.1_gl/case4.1a_gl.in: Open GL Format - Image SubVolume
case4.1_iv: Inventor Format
case4.1_iv/case4.1_iv_a.in: Inventor Format - Image Volume
case4.1_iv/case4.1_iv_b.in: Inventor Format - Image Volume - offset origin
case4.2: Plot Medial Axis on Medial Surface - Iris Explorer Format
case4.3: Convert Medial Surface Files to Segmented File Type
case4.4: Histogram burn data for medial axis voxels only
case4.4/case4.4.ntrim.nper: No Axis Trimming
case4.4/case4.4.ntrim.per: No Axis Trimming, y-axis as percentage
case4.4/case4.4.trim.nper: Axis Trimming
case4.4/case4.4.trim.per: Axis Trimming, y-axis as percentage
case4.5: Embed Search Tree, Generate Histogram
case4.5/case4.5.ntrim: No Axis Trimming
case4.5/case4.5.trim: Axis Trimming
case4.6: Compute shortest path tortuosity distribution
case4.6/case4.6_34.in: Between faces 3 and 4 (x direction)
case4.6/case4.6_36.in: Between faces 3 and 6 (adjoining x-y faces)
case4.6/case4.6_56.in: Between faces 5 and 6 (y direction)
case4.7: Min Cut/Max Flow - Under Development
case4.8: Cluster Analysis - Test file not available
case4.9: Convert Medial Axis Data Files to/from ASCII
case4.9/case4.9.in: Convert Binary Files to ASCII
case4.10: Convert between Medial Axis Data Formats
case4.10cp/case4.10cp.in: voxel-list to cluster-path
case4.10g/case4.10g.in: voxel-list to graph-node
case4.11: Modify Medial Axis
case4.11v/case4.11v.in: output voxel-list format
case4.11cp/case4.11cp.in: output cluster-path format
case4.11g/case4.11g.in: output graph-node format
case4.12: Histogram Medial Axis Statistics
case4.12v/case4.12v.in: Input is voxel-list format
case4.12cp/case4.12cp.in: Input is cluster-path format
case4.13: Compute Throat Size Distribution
case4.13/case4.13_3sph.in: Use 3 sphere test data set
case4.13/case4.13_nl.in: Use 5 sphere test data set
case4.14: Identify Fibers
case4.15: Convert Cluster-Path Format to Graph-Node
case4.16: Construct Neuron - Under development
case4.17: Reconstruct Burn Layers - Under development
case4.18: Isolate Neuron Soma/Dendrite Structures - Under development
Acknowledgements
About this document ...
Brent Lindquist
Thu Sep 30 12:33:54 EDT 1999