1. Scientific Visualization with ParaView Robert Putnam putnam@bu.edu IS&T Scientific Visualization Tutorial – Spring 2011

2. Outline Introduction ParaView overview ParaView/VTK data geometry/topology Case study Interactive session Scientific Visualization with ParaView – Spring 2011

3. Introduction * Adapted from The ParaView Tutorial, Moreland Visualization: converting raw data to a form that is viewable and understandable to humans. Scientific visualization: specifically concerned with data that has a well-defined representation in 2D or 3D space (e.g., from simulation mesh or scanner).

4. Introduction Scientific Visualization with ParaView – Spring 2011 Paraview – open-source application designed for visualizing two- and three-dimensional data sets. Begun in 2000 as a collaboration between Kitware, Inc. and LANL (funded by DOE) Built on VTK (“Visualization Tool Kit”) Graphics user interface Python scripting Architecture extensible by plugins Available for MS Windows, Linux, OSX Support for large dataset / distributed architecture (client/server model) Online and printed documentation from Kitware

5. Generic visualization pipeline Scientific Visualization with ParaView – Spring 2011 Source(s)Filters(s)Output (Rendering) - - - - - - - - - - - - - - - - - - - - - data/geometry/topologygraphics

6. Slice display Scientific Visualization with ParaView – Spring 2011 heat.vtk (3D dataset) Slice (2D) Display

7. Paraview user interface Scientific Visualization with ParaView – Spring 2011 Menu bar Toolbars Pipeline Browser Object Inspector 3D View

8. Combined filters to file Scientific Visualization with ParaView – Spring 2011 heat.vtk (3D dataset) Slice Filter heat2.jpg Stream Tracer Tube Filter Glyph Filter scalar data Vector data

9. Combined filters to file Scientific Visualization with ParaView – Spring 2011 heat.vtk Slice Stream TubeGlyph

10. ParaView – Pipeline Browser Pipeline Browser located in the upper left corner of the user interface allows you to build a visualization pipeline allows you to interact with the current visualization pipeline top of the pipeline browser is the name of the server to which ParaView is connected below the server name is a tree structure representing each of the reader, source, and filter objects that are in the visualization pipeline. Scientific Visualization with ParaView – Spring 2011

11. ParaView - Object Inspector –Object Inspector located beneath the Pipeline Browser in the user interface contains controls and information for the reader, source, or filter object selected in the Pipeline Browser allows you to interact with the current visualization pipeline content changes based upon the specific object selected Scientific Visualization with ParaView – Spring 2011

12. Object Inspector - Properties –Object Inspector Tabs There are three tabs in the Object Inspector: Properties Display Information The Properties Tab contains controls for specifying various parameters of the object selected in the Pipeline Browser. Here is an example of what is shown in the Properties Tab for a Slice filter. Scientific Visualization with ParaView – Spring 2011

13. Object Inspector - Display –Object Inspector Tabs The Display Tab contains controls for setting the appearance of the object selected in the Pipeline Browser. grouped into several sections: View, Color, Slice, Style, Edge Style, Annotation, Lighting, and Transformation. Here is an example of what is shown in the Display Tab for a Slice filter. Scientific Visualization with ParaView – Spring 2011

14. Object Inspector - Information –Object Inspector Tabs The Information Tab contains statistical information about the output of the object selected in the Pipeline Browser. Here is an example of what is shown in the Information Tab for a Slice filter. Scientific Visualization with ParaView – Spring 2011

15. ParaView - Menus –File menu handles various tasks such as opening data files, saving data files, loading state files, saving state files, saving screenshots, saving animations, and fileserver connections. Scientific Visualization with ParaView – Spring 2011

16. ParaView - Menus –View menu allows you to modify the camera and center of rotation for the 3D view. The view menu also allows you to toggle the visibility of the toolbars, inspectors, and views. Scientific Visualization with ParaView – Spring 2011

17. ParaView - Menus –Filters menu provides a list of available filters you can use to process data sets. organized by recent, common, data analysis, temporal, and alphabetical. The most commonly used filters, located under the Common subdirectory, are also located on the Common Filters Toolbar. The filters are context sensitive and will only be available for selection if an appropriate data set has been loaded first and selected in the Pipeline Browser. Scientific Visualization with ParaView – Spring 2011

18. ParaView - Menus –Help menu provides information on the ParaView version, information on client server connections, and provides access to the online manual. You can also visit the online version of the ParaView documentation: http://paraview.org/OnlineHelpCurrent/ Scientific Visualization with ParaView – Spring 2011

19. ParaView - Help Scientific Visualization with ParaView – Spring 2011

20. ParaView – Geometry v. Topology Geometry of a dataset ~= points Scientific Visualization with ParaView – Spring 2011 0,11,12,13,1 0,01,02,03,0 Topology ~= connections among points, which define cells So, what’s the topology here?

21. ParaView – Geometry v. Topology Scientific Visualization with ParaView – Spring 2011 0,11,12,13,1 0,01,02,03,0

22. ParaView – Geometry v. Topology Scientific Visualization with ParaView – Spring 2011 0,11,12,13,1 0,01,02,03,0 or 0,11,12,13,1 0,01,02,03,0

23. ParaView – Geometry v. Topology Scientific Visualization with ParaView – Spring 2011 or 0,11,12,13,1 0,01,02,03,0 0,11,12,13,1 0,01,02,03,0 or 0,11,12,13,1 0,01,02,03,0

24. ParaView – Geometry v. Topology Scientific Visualization with ParaView – Spring 2011 or 0,11,12,13,1 0,01,02,03,0 or 0,11,12,13,1 0,01,02,03,0 0,11,12,13,1 0,01,02,03,0 or 0,11,12,13,1 0,01,02,03,0

25. Geometry/Topology Structure Structure may be regular or irregular –Regular (structured) need to store only beginning position, spacing, number of points smaller memory footprint per cell (topology can be generated on the fly) examples: image data, rectilinear grid, structured grid –Irregular (unstructured) information can be represented more densely where it changes quickly higher memory footprint (topology must be explicitly written) but more freedom examples: polygonal data, unstructured grid Scientific Visualization with ParaView – Spring 2011

26. Characteristics of Data Data is organized into datasets for visualization –Datasets consist of two pieces organizing structure –points (geometry) –cells (topology) data attributes associated with the structure –File format derived from organizing structure Scientific Visualization with ParaView – Spring 2011 Data is discrete –Interpolation functions generate data values in between known points

27. Examples of Dataset Types Structured Points (Image Data) –regular in both topology and geometry –examples: lines, pixels, voxels –applications: imaging CT, MRI Rectilinear Grid –regular topology but geometry only partially regular –examples: pixels, voxels Structured Grid (Curvilinear) –regular topology and irregular geometry –examples: quadrilaterals, hexahedron –applications: fluid flow, heat transfer Scientific Visualization with ParaView – Spring 2011

28. Examples of Dataset Types (cont) Polygonal Data –irregular in both topology and geometry –examples: vertices, polyvertices, lines, polylines, polygons, triangle strips Unstructured Grid –irregular in both topology and geometry –examples: any combination of cells –applications: finite element analysis, structural design, vibration Scientific Visualization with ParaView – Spring 2011

29. Examples of Cell Types Scientific Visualization with ParaView – Spring 2011

30. Data Attributes Data attributes associated with the organizing structure –Scalars single valued examples: temperature, pressure, density, elevation –Vectors magnitude and direction examples: velocity, momentum –Normals direction vectors (magnitude of 1) used for shading –Texture Coordinates used to map a point in Cartesian space into 1, 2, or 3D texture space used for texture mapping –Tensors 3x3 only examples: stress, strain Scientific Visualization with ParaView – Spring 2011

31. File Format – Structured Points Scientific Visualization with ParaView – Spring 2011 Editor structured-points.vtk: # vtk DataFile Version 2.0 first dataset ASCII DATASET STRUCTURED_POINTS DIMENSIONS 3 4 5 ORIGIN 0 0 0 SPACING 1 1 2 POINT_DATA 60 SCALARS temp-point float LOOKUP_TABLE default 0 0 0 1 1 1 1 1 1 0 0 0

32. File Format – Structured Points Scientific Visualization with ParaView – Spring 2011 Editor structured-points.vtk: # vtk DataFile Version 2.0 first dataset ASCII DATASET STRUCTURED_POINTS DIMENSIONS 3 4 5 ORIGIN 0 0 0 SPACING 1 1 2 POINT_DATA 60 SCALARS temp-point float LOOKUP_TABLE default 0 0 0 1 1 1 1 1 1 0 0 0

33. File Format – Structured Points Scientific Visualization with ParaView – Spring 2011 Editor structured-points.vtk: # vtk DataFile Version 2.0 first dataset ASCII DATASET STRUCTURED_POINTS DIMENSIONS 3 4 5 ORIGIN 0 0 0 SPACING 1 1 2 CELL_DATA 24 SCALARS temp-cell float LOOKUP_TABLE default 0 0 1 1 0 0

34. File Format – Structured Points Scientific Visualization with ParaView – Spring 2011 Editor structured-points.vtk: # vtk DataFile Version 2.0 first dataset ASCII DATASET STRUCTURED_POINTS DIMENSIONS 3 4 5 ORIGIN 0 0 0 SPACING 1 1 2 CELL_DATA 24 SCALARS temp-cell float LOOKUP_TABLE default 0 0 1 1 0 0

35. Work flow – Case Study Student summer project: visualize MRI lung imagery 10 slices of 256x256 MATLAB Read in data Noise removal, isolation of lung Some visualization Scientific Visualization with ParaView – Spring 2011

36. Work flow – Case Study MATLAB -> VTK file Write 256x256x10 float array to ASCII file: Add header, save with ‘.vtk’ extension: Scientific Visualization with ParaView – Spring 2011

37. Work flow – Case Study Read VTK file into Paraview, choose “Volume Visualization” display option, add Cut Filter: Scientific Visualization with ParaView – Spring 2011

38. Work flow – Case Study Change color map, use Paraview animation feature to move cut plane through volume: Scientific Visualization with ParaView – Spring 2011

39. Work flow – Case Study Produce movie Save animation from Paraview, which produces image files (jpegs). Read image files into Adobe Premiere Pro Save as movie (.mov,.wmv,.avi., etc.) Scientific Visualization with ParaView – Spring 2011

40. Starting out - create sphere Scientific Visualization with ParaView – Spring 2011 ParaView: 1. Choose Sources -> Sphere 2. Click Apply in Object Inspector 3. User Interface: - Undo - Color - Lighting - Camera Movement

41. Example – Loading data Scientific Visualization with ParaView – Spring 2011 ParaView: 1. Disconnect from Server File -> Disconnect which clears the pipeline 2. Open data file File -> Open (cylinder.vtk) 3. Click Apply in Object Inspector 4. In Toolbar area (or Object Inspector / Display), color by Pres. Show Legend. 5. Try Multi-view option (above upper right-hand corner of 3D window).

42. Clipping, Cutting, Subsampling Selection Algorithms - Clipping can reveal internal details of surface ParaView - Clip Filter - Cutting/Slicing cutting through a dataset with a surface ParaView - Slice Filter - Subsampling reduces data size by selecting a subset of the original data ParaView - ExtractSubset Filter Scientific Visualization with ParaView – Spring 2011

43. Example – Clipping Scientific Visualization with ParaView – Spring 2011 ParaView: 1. disconnect from Server File -> Disconnect 2. open data file File -> Open (density.vtk) 3. apply Clip filter to density.vtk click on density.vtk in pipeline Filter -> Clip

44. Example – Cutting/Slicing Scientific Visualization with ParaView – Spring 2011 ParaView: 1. disconnect from Server File -> Disconnect 2. open data file File -> Open (density.vtk) 3. apply Slice filter to density.vtk click on density.vtk in pipeline Filter -> Slice

45. Example – Subsampling Scientific Visualization with ParaView – Spring 2011 ParaView: 1. disconnect from Server File -> Disconnect 2. open data file File -> Open (density.vtk) 3. Apply Extract Subset filter to density.vtk click on density.vtk in pipeline Filter -> Extract Subset 4. Apply Threshold filter to ExtractSubset click on ExtractSubset filter Filter -> Threshold

46. Color Mapping Scalar Algorithms –Color Mapping maps scalar data to colors implemented by using scalar values as an index into a color lookup table –ParaView Color panel in Display tab of object inspector of data –Color by –Edit Color Map Scientific Visualization with ParaView – Spring 2011

47. Example – Color Mapping Scientific Visualization with ParaView – Spring 2011 1. Disconnect from Server File -> Disconnect 2. Open data file File -> Open (subset.vtk) 3. go to the the color section in the Display Tab in the Object Inspector The "Color by" menu lists the names of the attribute arrays. Selecting an array name causes the dataset’s coloring to be based on the underlying scalar values in that array.

48. Example – Color Mapping (cont) Scientific Visualization with ParaView – Spring 2011 ParaView: 1. The color map may be edited in the Color Scale Editor window which appears when you click the Edit Color Map button in the Color section of the Display Tab. 2. Another way to change the mapping of data values to colors is by setting the Data Range. -- The default Data Range is set from the minimum data value in the data set to the maximum data value. -- click on the Rescale Range button to explicitly set these values. The values between the minimum and maximum are then linearly interpolated into the color table.

49. Contouring Scalar Algorithms (cont) –Contouring construct a boundary between distinct regions, two steps: –explore space to find points near contour –connect points into contour (2D) or surface (3D) 2D contour map (isoline): –applications: elevation contours from topography, pressure contours (weather maps) from meteorology 3D isosurface: 3D isosurface: –applications: tissue surfaces from tomography, constant pressure or temperature in fluid flow, implicit surfaces from math and CAD –ParaView Contour Filter Scientific Visualization with ParaView – Spring 2011

50. Example – Isoline / 2D Contours Scientific Visualization with ParaView – Spring 2011 ParaView: 1. Disconnect from Server File -> Disconnect 2. Open data file File -> Open (subset.vtk) 3. Apply Contour filter to subset.vtk click on subset.vtk in pipeline Filter -> Contour 4. to color the contour line based upon its scalar value and the current color map, make sure the Compute Scalars checkbox in the Contour section of the Properties tab is selected

51. Example – Isosurface / 3D Contours Scientific Visualization with ParaView – Spring 2011 ParaView: 1. Disconnect from Server File -> Disconnect 2. Open data file File -> Open (density.vtk) 3. Apply Contour filter to density.vtk click on density.vtk in pipeline Filter -> Contour

52. Scalar Generation Scalar Algorithms (cont) –Scalar Generation extract scalars from part of data example: extracting z coordinate (elevation) from terrain data to create scalar values –ParaView Elevation Filter Scientific Visualization with ParaView – Spring 2011

53. Example – Scalar Generation Scientific Visualization with ParaView – Spring 2011 ParaView: 1. disconnect from Server File -> Disconnect 2. open data file File -> Open (honolulu.vtk) 3. apply Elevation filter to density.vtk click on honolulu.vtk in pipeline Filter -> Elevation

54. Oriented Glyphs Vector Algorithms –Oriented Glyphs orientation indicates direction length indicates magnitude color indicates magnitude, pressure, temperature, or any variable –ParaView Glyph Filter –Set type to arrow Scientific Visualization with ParaView – Spring 2011

55. Example – Oriented Glyphs Scientific Visualization with ParaView – Spring 2011 ParaView: 1. disconnect from Server File -> Disconnect 2. open data file File -> Open (density.vtk) 3. apply Glyph filter to density.vtk click on density.vtk in pipeline Filter -> Glyph 4. in the Object Inspector (Properties Tab) set the “Scalars” menu to Density set the “Vectors” menu to Momentum set the “Glyph Type” to Arrow

56. Field Lines Vector Algorithms (cont) –Field Lines Fluid flow is described by a vector field in three dimensions for steady (fixed time) flows or four dimensions for unsteady (time varying) flows Three techniques for determining flow –Pathline (Trace) tracks particle through unsteady (time-varying) flow shows particle trajectories over time rake releases particles from multiple positions at the same time instant reveals compression, vorticity –Streamline tracks particle through steady (fixed-time) flow holds flow steady at a fixed time snapshot of flow at a given time instant –Streakline particles released from the same position over a time interval (time-varying) snapshot of the variation of flow over time example: dye steadily injected into fluid at a fixed point Scientific Visualization with ParaView – Spring 2011

57. Field Lines Streamlines Lines show particle flow ParaView - StreamTracer Filter Streamlets half way between streamlines and glyphs ParaView - StreamTracer and Glyph Filters Streamribbon rake of two particles to create a ribbon ParaView - StreamTracer and Ribbon Filters Streamtube circular rake of particles to create a tube ParaView - StreamTracer and Tube Filters Scientific Visualization with ParaView – Spring 2011

58. Stream Tracer Filter generates streamlines in vector field from collection of seed points first need to set up the integrator to do the numerical integration next need to specify the seeds points Scientific Visualization with ParaView – Spring 2011

59. Example – Streamlines Scientific Visualization with ParaView – Spring 2011 ParaView: 1. open data file File -> Open (density.vtk) 2. apply StreamTracer filter to density.vtk click on density.vtk in pipeline Filter -> Stream Tracer 3. in the Object Inspector (Properties Tab) set “Vectors” menu to Momentum set “Max Propagation” to Time 100 set “Initial Step Length” to Cell Length 0.1 set “Integration Direction” to Both set “Max Steps” to 1000 set “Integrator Type” to Runge-Kutta 4 set “Seed Type” to Point Source, Center on Bounds set “Number of Points” to 100

60. Annotation Annotation –used for annotating visualizations –ParaView Text Source Source -> Text Color Legend “Edit Color Map” button in Display tab “Show Color Legend” box in color legend tab of the Color Scale Editor Axes Edit -> View Settings Scientific Visualization with ParaView – Spring 2011

61. Example – Annotation Example – Annotation Scientific Visualization with ParaView – Spring 2011 ParaView: 1. open data file File -> Open (density.vtk) 2. apply Clip filter to density.vtk click on density.vtk in pipeline Filter -> Clip 3. Create a Text source Sources -> Text 4. Turn on Color Legend Edit Color Map for Clip in Display Tab Color Legend tab in Color Scale Editor select “Show Color Legend” check box 5. Turn on orientation axis Edit -> View Settings select “Orientation Axes” check box

62. Saving Images Scientific Visualization with ParaView – Spring 2011 Saving Images –common formats: jpg (lossy) png (lossless) pdf tiff (lossless) –ParaView File -> Save Screenshot

63. Example – Saving Images Scientific Visualization with ParaView – Spring 2011 ParaView: 1. open data file File -> Open (density.vtk) 2. apply Clip filter to density.vtk click on density.vtk in pipeline Filter -> Clip 3. save Screenshot File -> Save Screenshot 4. set Resolution 5. set File Type to JPG

64. ParaView - Resources Scientific Visualization with ParaView – Spring 2011 Tutorials –Using ParaView to Visualize Scientific Data scv.bu.edu/documentation/tutorials/ParaView/ –ParaView Examples scv.bu.edu/documentation/software-help/scivis/paraview_examples/index.html -- “The Tutorial” www.paraview.org/Wiki/The_ParaView_Tutorial Texts –The ParaView Guide, v3 Edition, Kitware, Inc, 2006. –The Visualization Toolkit, 4th Edition, Will Schroeder, Ken Martin, Bill Lorensen, Kitware, 2006. Websites –www.paraview.orgwww.paraview.org –www.paraview.org/OnlineHelpCurrent/ –www.paraview.org/Wiki/ParaViewwww.paraview.org/Wiki/ParaView –www.kitware.com

65. Questions? Tutorial survey: - http://scv.bu.edu/survey/spring11tut_survey.htmlhttp://scv.bu.edu/survey/spring11tut_survey.html Scientific Visualization with ParaView – Spring 2011