CAVASS (a Computer Assisted Visualization and Analysis Software System) Features and Developments

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CAVASS(a Computer Assisted Visualization and
Analysis Software System)Features and
Developments

• George J. Grevera, Ph.D.

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CAVASS contributors

• Xinjian Chen
• George Grevera
• Tad Iwanaga
• Tingching Kao
• Shipra Mishra

• Dewey Odhner
• Andre Souza
• Jayaram Udupa
• Xiaofen Zheng
• Ying Zhuge

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Talk outline

• Introduction
• User interface
• Key features
• Miscellaneous topics
• Concluding remarks

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Introduction to cavass
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What 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

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3D 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 2008

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What is CAVASS?

• CAVASS is the next generation of 3DVIEWNIX.
• 3DVIEWNIX
• development started in 1987
• released in 1993
• development dates back to the 70s
• free
• 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?

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Significant, 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.

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CAVASS 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
• CAVA operations take object system information
  from one space to another (typically, and
  eventually, to a quantitative space).
• Especially for large, multidimensional (at least
  3D), possibly multimodality, data sets.

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CAVA 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

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Key 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.

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Cavass user interface
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Portable 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.

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Portable graphics user interface

• We also considered Qt, Java, and FLTK.
• Qt proprietary, closed, fees
• Java performance concerns, doesnt leverage
  existing C/C code, parallelism (MPI) lacking
• FLTK free but doesnt maintain native
  look-and-feel

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User interface example Montage
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User interface features

• Standard-style menu bar.
• Window size can be changed.
• Support for multiple windows.
• Copy window contents to clipboard.
• Print window contents.

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Standardized user interface

• Frame CAVASS window

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Standardized user interface

• Canvas upper drawing area

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Standardized 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

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Standardized user interface

• Bar at bottom contains status and mouse button
  information.

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User preferences
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Key cavass features
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Overview of CAVASS functionality
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Data 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.
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An example of the CAVASS DICOM header explorer
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Tools
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Tools

• Tutorials
• Recipes and Tasks
• ShowScreen

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Interface 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.

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Interface to ITK

• CAVASS ITK interface
• Completely table driven.
• Steps
• Display a slice
• Allow user to set parameters.
• Run ITK program.
• Read and display result.

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Interface to ITK
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Image processing
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Image processing example interpolation
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Image processing example threshold
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Image processing example iterative live wire
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Image processing example registration
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Visualize
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Visualize example Montage
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Visualize example overlay
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Visualize example t-shell surface rendering
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Manipulate
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Event handing 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).

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Event handing 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.

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Analyze
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Analyze example density profile
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Miscellaneous topics

• Testing, Parallelism, Getting Started

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Testing

• Test data sets
• Regular 256 x 256 x 46 MR brain image 6 MB
• Large 512 x 512 x 459 CT of thorax 241 MB
• Super 1023 x 1023 x 417 CT of VW head 873 MB

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Parallelism

• Considered
• MPI/OpenMPI
• Message Passing Interface
• OpenMP
• Open specifications for Multi Processing

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Parallelism

• MPI
• 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
• requires purchase of specialized compilers
• multi-threaded, shared memory parallelism model
• requires purchase of expensive multiprocessor
  systems

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Parallelization 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.

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Parallelization 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.

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Getting started with CAVASS

• As a user
• Tutorials
• Tasks and Recipes
• As a programmer
• cvs code repository
• doxygen code documentation
• Data C classes
• Example module

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Data 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.

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doxygen example
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Example module

• C code that consists of ExampleFrame (a
  subclass of MainFrame) and ExampleCanvas (a
  subclass of MainCanvas).

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Concluding remarks
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CAVASS contributors

• Xinjian Chen
• George Grevera
• Tad Iwanaga
• Tingching Kao
• Shipra Mishra

• Dewey Odhner
• Andre Souza
• Jayaram Udupa
• Xiaofen Zheng
• Ying Zhuge

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Thanks for your attention!

• Information about CAVASS is available from
  www.mipg.upenn.edu/cavass.
• The authors gratefully acknowledge NIH grant
  number R01-EB004395-01 for support of this work.