Title: (a Computer Assisted Visualization and Analysis Software System) Using CAVASS as the Basis for Imaging Applications George Greveraab, Jayaram Udupab, Dewey Odhnerb aComputer Science Department Saint Joseph
1(a Computer Assisted Visualization and Analysis
Software System)Using CAVASS as the Basis for
Imaging ApplicationsGeorge Greveraab, Jayaram
Udupab, Dewey OdhnerbaComputer Science
DepartmentSaint Josephs UniversitybMedical
Image Processing Group (MIPG), Department of
RadiologyUniversity of Pennsylvania
2CAVASS contributors
- Xinjian Chen
- George Grevera
- Tad Iwanaga
- Tingching Kao
- Shipra Mishra
- Dewey Odhner
- Andre Souza
- Jayaram Udupa
- Xiaofen Zheng
- Ying Zhuge
3Overview
- Introduction
- User interface
- Key features
- Parallelism
- Getting Started with CAVASS
- Concluding remarks
4Introduction to cavass
5What is CAVASS?
- A CAVA Software System
- What is CAVA?
- Computer Assisted Visualization and Analysis
- So CAVASS is a Computer Assisted Visualization
and Analysis Software System
63D CAVA software systems (MIPG)
- DISPLAY mini computer frame buffer 1980
- DISPLAY82 mini computer frame buffer 1982
- 3D83 GE CT/T 8800 1983
- 3D98 GE CT/T 9800 1986
- 3DPC PC-based 1989
- 3DVIEWNIX Unix, X-Windows 1993
- CAVASS platform independent, wxWidgets 2009
7What is CAVASS?
- CAVASS is the next generation of 3DVIEWNIX.
- 3DVIEWNIX
- development started in 1987
- released in 1993
- development dates back to the 70s
- free binaries
- runs on Unix and subsequently Linux
- 60 person years of effort
- distributed to 100s of sites
- basis for over 15 specialized packages/apps
- Why CAVASS?
8Significant, more recent developments
- PC platform matures.
- price spirals downward
- performance increases dramatically
- supplant Unix as the scientific workstation of
choice - Network bandwidth greatly increases.
- Useable parallel processing standards are defined
and become freely available. - Toolkits such as VTK and ITK become freely
available. - GUI concept matures and platform independent
libraries are developed.
9CAVASS features
- Image processing - for enhancing information
about and defining an object system - Visualization - for viewing and comprehending an
object system - Manipulation - for altering an object system
(virtual surgery) - Analysis - for quantifying information about an
object system - Especially for large, multidimensional (at least
3D), possibly multimodality, data sets.
10CAVA user groups
- UG1 CAVA basic researchers/technology
developers - UG2 CAVA application developers
- UG3 Users of CAVA methods in clinical research
- CAVASS is not aimed at
- UG4 Clinical end users in patient care
11Key CAVASS features
- Built upon our experience with 3DVIEWNIX.
- Leverages the existing 3DVIEWNIX software base
and user interface. - Port to Windows and Mac OS with continued support
for Unix and Linux. - Implement parallel algorithms for time consuming
operations. - Support for stereo rendering.
- Interface to ITK.
12Cavass user interface
13Portable graphics user interface
- Based on wxWidgets (wxwidgets.org)
- one C API for all OSs
- maintains native look-and-feel
- free, open source, multiplatform
- portable support for mutex, threads, copy-paste,
drag-and-drop, print, etc.
14User interface features
- Standard-style menu bar.
- Window size can be changed.
- Support for multiple windows.
- Copy window contents to clipboard.
- Print window contents.
15Standardized user interface
- Control area
- appears towards bottom
- can be resized or even removed
- buttons appear towards the right and are
relatively standardized other controls (such as
sliders) appear towards the left as necessary
16Standardized user interface
- Bar at bottom contains status and mouse button
information.
17Key cavass functionality
18Overview of CAVASS functionality
19Data interface
Support for standard image formats such as DICOM,
VTK, Matlab, STL (Stereo Lithography), TIFF, and
JPEG. CAVASS also supports the extended DICOM
format that was proposed and supported by
3DVIEWNIX.
20Tools
21Interface to ITK
- ITK
- Extensive C image processing library.
- Provides no user interface.
- CAVASS ITK interface
- Optionally provide ITK with a user interface.
- Added code to ITK to enable it to read and write
CAVASS files.
22Interface to ITK
- CAVASS ITK interface
- Completely table driven.
- Steps
- Display a slice
- Allow user to set parameters.
- Run ITK program.
- Read and display result.
23Interface to ITKmedian filter
24Interface with ITKCanny edge detection
25Image processinglive wire interpolation
26Visualizeslice/cine surface rendering
27Manipulate
28Event handling for visualization and manipulation
- wxWidgets supports and implements the
Windows-style event callback mechanism. - Very efficient and fine for most user
interaction. - X-Windows supports and implements the event queue
mechanism. - Most flexible for intensive user interaction w/
possible delays due to computation time (e.g.,
rendering).
29Event handling for visualization and manipulation
- We implemented an X-Windows style event queue
w/in CAVASS using only the wxWidgets callback
mechanism - Create a separate thread of execution that
responds to events in an event queue (of our own
creation) performs compute intensive tasks runs
at a lower priority. - The main thread continues to respond to events
via the callback mechanism intelligently
queues the events for execution by the other
thread runs at a higher priority.
30Analyze
31PARALLELISM
32Parallelism
- MPI (Message Passing Interface)
- free (for both Windows, Linux, and Unix)
- part of base Linux install
- COW (cluster of workstations model)
- leverages existing hardware/computers
- optional, inexpensive network upgrade
- easily expandable
- OpenMP (Open specification for Multi Processing)
- requires purchase of specialized compilers
- multi-threaded, shared memory parallelism model
- requires purchase of expensive multiprocessor
systems
33Parallelization of operations in CAVASS
- Divide the input image into chunks and assign
each chunk to a processor. - A chunk represents data contained in a contiguous
set of slices, either image or object structure
data.
34Parallelization of operations in CAVASS
- CAVA operations can be divided into the following
three groups. - Type 1 Operation chunk-by-chunk, each chunk
accessed only once. - Ex slice interpolation.
- Type 2 As in Type 1, but significant further
operation needed to combine results. - Ex 3D rendering.
- Type 3 Operation chunk-by-chunk, but each chunk
may have to be accessed more than once. - Ex graph traversal.
- CAVASS parallelizes all three groups of
operations when necessary.
35GETTING STARTED WITH CAVASS
36Getting started with CAVASS
- As a user
- Tutorials
- Tasks and Recipes
- As a programmer
- cvs code repository
- doxygen code documentation
- Data C classes
- Example module
37Data C classes
- CavassData
- Given the name of a data file, CavassData will
read in the entire data set. - ChunkData
- Given the name of a data file, ChunkData will
read in a set of contiguous slices (a chunk). - When slices are accessed w/in the cached chunk,
no additional reads are necessary. - When a slice is accessed outside of the current
chunk, a chunk containing the new slice is read. - Subclass of CavassData.
- SliceData
- Given the name of a data file, SliceData will
read in a single slice of data. - A different slice can be read at any time.
- Subclass of CavassData.
38Doxygen documentation example
39Example module
- C code that consists of ExampleFrame (a
subclass of MainFrame) and ExampleCanvas (a
subclass of MainCanvas).
40Concluding remarks
41Concluding remarks
- User interface
- Key features (image processing, visualization,
manipulation, and analysis) - Parallelism
- Getting Started with CAVASS
42CAVASS contributors
- Xinjian Chen
- George Grevera
- Tad Iwanaga
- Tingching Kao
- Shipra Mishra
- Dewey Odhner
- Andre Souza
- Jayaram Udupa
- Xiaofen Zheng
- Ying Zhuge
43Thanks for your attention!
- Information about CAVASS is available from
www.mipg.upenn.edu/cavass. - The authors gratefully acknowledge NIH grant
number R01-EB004395 for support of this work.