Software

5. Software

Libraries

TAQT, ContourLib, VolRen libraries support enhanced volumetric and geometry processing, quantitative and topological analysis, and rendering procedures for both molecular structure and computed properties such as electrostatics potential, hydrophobicity, etc.

TAQT (Topological Analysis and Quantitative Tools)

TAQT computes topological properties of scalar data such as Betti numbers and contour trees.
Contour tree tells us the number of components per isocontour which isocontours merge together or split while modifying the isovalue.

  1. Multi-Resolution Dual Contour Tree
    TAQT introduces an algorithm of matching 3D volumetric functions based on affine-invariant multi-resolution dual contour trees. A dual contour tree structure is constructed from the contour tree of a volume by dividing its functional range into segments such that the connected contour tree edges within a segment become a node in the dual tree. Each node of the dual contour tree corresponds to a connected sub-volume bounded by contours within a certain range segment.
    (User Manual, Paper)
    Download - Please go to our software page, find TAQT Package under Angstrom, and click Download.
    Reference
    X. Zhang, C. Bajaj, N. Baker
    Fast Matching of Volumetric Functions Using Multi-resolution Dual Contour Trees (pdf)
  2. Betti
    Each isosurface has an associated triple of Betti numbers. The kth Betti number of a simplicial complex is the rank of its k-dimensional homology group. In the case of isosurfaces for 3D molecular data sets, only the first three Betti numbers are non-zero.
    (User Manual, Programmer Manual)
    Download – Please go to our software page, find TAQT Package under Angstrom, and click Download.
  3. Contour Spectrum
    A user interface component that improves qualitative user interaction and provides real-time exact quantification in the visualization of isocontours. The contour spectrum is a signature consisting of a variety of scalar data and contour attributes, computed over the range of scalar values.
    Download – Please go to our software page, find TAQT Package under Angstrom, and click Download.
    Reference
    C. Bajaj, V. Pascucci, D. Schikore
    The Contour Spectrum Proceedings of the 1997 IEEE Visualization Conference,167-173, October 1997 Phoeniz, Arizona (pdf) (ps)

ContourLib

This library contains algorithm that is Near-optimal for real-time interaction and modification of isovalues in large datasets. A preprocessing step selects a subset S of the cells which are considered as seed cells. Given a particular isovalue, all cells in S which intersects the given isocontour are extracted using a high-performance range search. Each connected component is swept out using a fast isocontour propagation algorithm.

Download – Please go to our software page, find ContourLib Source under Visual Eyes, and click Download.

Reference
C. Bajaj, V. Pascucci, D. Schikore
Fast Isocontouring for Improved Interactivity
Proceedings: ACM Siggraph/IEEE Symposium on Volume Visualization, ACM
Press, (1996), San Francisco, CA. Pages: 39-46 (text) 99

C. Bajaj, V.Pascucci, and D.Schikore
The Contour Spectrum
Proceedings of the 1997 IEEE Visualization Conference,167-173, October
1997 Phoeniz, Arizona

VolRen Library

It is a library that uses OpenGL to do texture volume rendering. It works on IRIX, Linux, Windows, and MaxOS.

Download – Please go to our software page, find The Volume Rover under Angstrom, and click Download.
The Volume Rover includes Volume Rendering Library.

Reference
Chandrajit Bajaj, Sanghun Park, Sangmin Park
Hardware Accelerated Multipipe Parallel Rendering of Large Data Stream
CS & ICES Technical Report, University of Texas at Austin, 2001 (pdf)

Chandrajit Bajaj, Sangmin Park, Anthony Gene Thane
Parallel Multi-PC Volume Rendering System
CS & ICES Technical Report, University of Texas at Austin, 2002 (pdf)


Applications

VolRover

The VolRover client can act as a 3D roving microscope, allowing users to visualize data that is too large to fit on a single machine.

VolRover encapsulates functionalities, which are computer accelerated methods for contour extraction, dynamic mesh reduction for improved interactive display, real-time rendering working with compressed data stream, and using topological and volumetric quantitative signature for feature extraction, along with the filtering and feature extraction techniques, into volumetric exploratory visualization tool.

Images Generated by VolRover

Ribosome Small Subunit (1J5E): Light Yellow and Pale Pink are the 5S and 23S Rrna while the remaining colors are proteins.

High-resolution Iso-surface Rendering of the Thermus Thermophilus small 30S Ribosomal Subunit (1J5E) Low-resolution Iso-surface Rendering of the Thermus Thermophilus small 30S Ribosomal Subunit (1J5E) Medium-resolution Iso-surface Rendering of the Thermus Thermophilus small 30S Ribosomal Subunit (1J5E)

Rice Dwarf Virus (RDV)

Inside view of RDV Outside view of RDV Asymmetric unit of RDV outer shell

Download

Please go to our software page, find The Volume Rover under Angstrom, and click Download.

Reference

C. Bajaj, Z. Yu, M. Auer
Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging.
Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 132-143 (pdf)

LBIE Mesher

The LBIE (Level Set Bounded Interior and Exterior)-mesher produces high quality tetrahedral and hexahedral finite element meshes of molecular surfaces and the surrounding environment, of any structures from the PDB.

LBIE_Mesher (Level Set Boundary Interior and Exterior Mesher) is a meshing software which can extract adaptive and quality triangular, quadrilateral, tetrahedral and hexahedral meshes directly from volumetric data. LBIE_Mesher generates triangular/quadrilateral meshes for a level set surface, and interior and exterior tetrahedral/hexahedral meshes with level sets as boundary surfaces. Given two level sets, LBIE_Mesher can also tetrahedralize/hexahedralize the interval volume between them.

This Developer Studio Project file has been created by the QMsDev plugin and is a basic implementation of a Qt application based on a Main Window interface. The meshing software can be run as follows:

  1. Load the data with size of (2^n+1)^3. If your data size is large than 257^3, please make sure the intermediate file *.err to be deleted before you run the code.
  2. You can select different rendering formats, the default is the flat shading. a. flat shading b. smoothing shading c. smoothing shading + wireframe d. wireframe.
  3. There are four tool bars at the bottom of the interface, the left two are used to choose isovalue, the right two are for adjusting the error tolerance. When you extract two isosurfaces at the same time, the top two controls the inner surface and the bottom two controls the outer surface.The mesh adaptivity can be controlled by choosing different error tolerance. If you want to control by regions, go to function “traverse_qef(…)” in octree.cpp file, you will see some commented options, you can write similar one according to your requirements.
  4. Different mesh types can be chosen.
    1. Triangle mesh for a single level set
    2. Tetrahedral mesh
    3. Hexahedral mesh
    4. Quadrilateral mesh
    5. Triangle mesh for double level sets
    6. Interval volume tetrahedral mesh between two level sets

Images Generated by LBIE Mesher

Ribosome Large Subunit

Big subunit (50S)
residue level with blobbyness -5.0
Big subunit (50S)
atomic level with blobbyness -5.0
Big subunit (50S)
residue level with blobbyness -0.5

Rice Dwarf Virus (RDV)

Small subunit (30S)
residue level with blobbyness -5.0
Small subunit (30S)
atomic level with blobbyness -5.0
Small subunit (30S)
residue level with blobbyness -0.5

Download
Please go to our software page, find LBIE Mesher under Angstrom, and click Download.

Reference
Y. Zhang, C. Bajaj, B-S. Sohn. 3D Finite Element Meshing from Imaging Data.
Accepted in the special issue of Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 2004.

Y. Zhang, C. Bajaj, B-S. Sohn. Adaptive and Quality 3D Meshing from Imaging
Data. Proceedings of 8th ACM Symposium on Solid Modeling and Applications,
pp. 286-291. Seattle, WA. June 16-20, 2003.

Y. Zhang, C. Bajaj. Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data.
Proceedings of 13th International Meshing Roundtable.
Willamsburg, VA. September 19-22, 2004. (To Appear)