Insight VisREU Site. Agenda. Introduction to Scientific Visualization Using 6/16/2015. The purpose of visualization is insight, not pictures.

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1 2015 VisREU Site Introduction to Scientific Visualization Using Vetria L. Byrd, Director Advanced Visualization VisREU Site Coordinator REU Site Sponsored by NSF ACI Award Introduction to SciVis(High level) Visualization Applications Introducing ParaView Hands-on Test Drive Agenda High Level Overview INTRODUCTION The purpose of visualization is insight, not pictures. ~Ben Shneiderman What s Missing? Explanation Insight Tells a Story... What were the 6 things from last week s lecture that insight leads to? WHAT DOES INSIGHT LEAD TO? June 15,

2 Visualization Applications Data Visualization Process Input Data Biological Data Non- Numerical Data Research Fields BioVis InfoVis An iterative process obtain the data remove all but the data of interest choose a basic visual model, such as a bar graph, list or tree Add methods for manipulating the data or controlling what features are visible VISUALIZATION Geospatial Data Simulated, 3D Phenomena GeoVis SciVis provide structure Where are you in your projects? apply methods from statistics or data mining to discern patterns or place the data in mathematical context Visualizing Data: Exploring and Explaining Data with the Processing Environment by Ben Fry, O Reilly (p 15) improve the basic representation to make it clearer and more visually engaging Scientific Visualization Pipeline Scientific Visualization Pipeline What s Missing? Step 1: Produce Data Simulated Data Images Numerical Some measured value Observed Phenomena WHAT DOES YOUR DATA LOOK LIKE? June 15,

3 Step 2: Analyze, Filter, Reformat Cleaning up the data Removing noise Replacing missing values Clamping values to be within a specific range of interest Performing operations to yield more useful data Step 3: Apply SciVis Techniques Converts raw information into something more understandable Visually extracting meaning from a scientific data set using various techniques Contour Clip Threshold Glyphs Streamlines Step 4: Map to Geometry Scalars, vectors, tensors 1D, 2D, 3D Mesh Step 5: Render, Post Process Step 6: View Results 2015 VisREU Site Introduction to Scientific Visualization Using 3

4 On The Agenda Basics of Visualization Scientific Visualization Pipeline Features of ParaView Introduction to ParaView Additional Resources The process of visualization is taking raw data and converting it to a form that is viewable and understandable to humans. Basics of Visualization There are a number of steps between raw data and a finished visualization Single tool or multiple tools might be used Scientific Visualization Primarily concerned with the visualization ofthree-dimensionalphenomena (architectural, meteorological, medical,biological, etc.), Where the emphasis is on realistic renderings of volumes, surfaces, illumination sources, and so forth, perhaps with a dynamic (time) component. Wikipedia.com Multi-platform parallel data analysis and visualization application Mature, feature-rich interface Good for general purpose, rapid visualization Mac Windows Linux Open Source... It s Free! Built upon the Visualization Toolkit (VTK) library Primary contributors: Kitware, Inc. Sandia National Laboratory Los Alamos National Laboratory Army Research Laboratory 4

5 Supported Data Types Supported Data Types Curvilinear regularly gridded mesh shaping function applied Grid regular structure, all voxels (cells) are the same size and shape Unstructured grid irregular mesh typically composed of tetrahedra, prisms, pyramids, or hexahedra Supported Data Types Point data Polygonal data Images Multi-block Supported Data Types Adaptive Mesh Refinement(AMR) Time series support Isosurfaces Supported Visualization Cutting planes Algorithms Streamlines Glyphs Volume rendering Clipping Height maps & more Special Features Supports derived variables Scriptable via Python Saves animations Can run in parallel / distributed mode for large data visualization 5

6 Supported File Formats Visualization Pipeline All processing operations (filters) produce data sets Can further process the result of every operation to build complex visualizations Extract a cutting plane, Apply glyphs (i.e. vector arrows) to the result Gives a plane of glyphs through your 3D volume Many more... Demonstration WRF weather forecast data set Rectilinear grid Multiple scalar and vector variables Time series Can show: Clouds Wind Temperature Visualizing your Data Using ParaView Three Basic Steps: First your data must be readinto ParaView Next, you may apply any number of filters that process the data to generate, extract, or derive features from the data Finally, a viewable image is rendered from the data Sample Data GETTING STARTED WITH PARAVIEW Download from Find ParaView Section Right click on headsq.vti Save Link As: headsq Save as type: VTI file (.vti) Remember where you save the data file! June 15,

7 User Interface File Open - Menu Bar Tool Bars headsq.vti Click Apply Pipeline Browser Object Inspector 3D View Create an Isosurface Click Filters Common Contour Should see an outline of the data set A new object appeared in the pipeline browser (Contour 1) Lets explore the Isosurfaces section: Value Range: [0, 4095] Default value: Click Apply Contour Extracts the points, curves, or surfaces where a scalar field is equal to a userdefined value. The surface is often also called an isosurface. 7

8 Isosurfaces Click Delete All Click New Range Isosurfaces Click Delete All Click New Range Add Range window appears You can change the range of data values For this tutorial, keep the default Click OK Notice the range of values 8

9 Clip Isosurface Select Contour1 Select Filters Select Common Select Clip This may take few seconds to render CLIP -Intersects the geometry with a half space. The effect is to remove all the geometry on one side of a userdefined plane. 9

10 Drag arrow point around to front of surface (arrow turns red when selected) It may take a few seconds to render Depending on where you placed the clipping plane the results may be easily seen: parts of the ears are clipped, area around the neck Rotating the view reveals the clipped isosurface CLIP Intersects the geometry with a half space. The effect is to remove all the geometry on one side of a user-defined plane. 10

11 6/16/2015 Slice Isosurface Click eye next to Clip1 to hide the clip plot Select Coutour1 Select Filters Select Common Select Slice SLICE Intersects the geometry with a plane. The effect is similar to clipping except that all that remains is the geometry where the plane is located. Rotated view Drag arrow point around to front of surface (arrow turns red when selected) 11

12 Clip1 has been made visible along with Slice1 SLICE Intersects the geometry with a plane. The effect is similar to clipping except that all that remains is the geometry where the plane is located. Pipeline Browser headsq.vti Clip1 Contour1 Slice1 GETTING YOUR DATA INTO PARAVIEW (A SAMPLE FILE) 12

13 Supported Data Formats VTK ( EnSight Plot3D Various polygonal formats Users can write data readers to extend support to other formats Conversion to the VTK format is straightforward ASCII or binary Supports all VTK grid types Easiest for data conversion VTK Simple Legacy Formats VTK simple legacy format ( Simulated Temperature The data Simulated temperature values Sample size: 100 x 100 Rectilinear Grid vtk Format # vtk DataFile Version 2.0 Rectilinear grid of temperature values ASCII DATASET RECTILINEAR_GRID * * vtk Format # vtk DataFile Version 2.0 Rectilinear grid of temperature values ASCII DATASET RECTILINEAR_GRID DIMENSIONS X_COORDINATES 100 float Y_COORDINATES 100 float Z_COORDINATES 1 float 0 * Although this is a 2D grid, the z-coordinate must be included and represented in the DIMENSIONS vtk Format # vtk DataFile Version 2.0 Rectilinear grid of temperature values ASCII DATASET RECTILINEAR_GRID DIMENSIONS X_COORDINATES 100 float Y_COORDINATES 100 float Z_COORDINATES 1 float 0 POINT_DATA x-dimension * y-dimension * z-dimension SCALARS temperature float LOOKUP_TABLE default * * 13

14 vtk Format # vtk DataFile Version 2.0 Rectilinear grid of temperature values ASCII DATASET RECTILINEAR_GRID DIMENSIONS X_COORDINATES 100 float Y_COORDINATES 100 float Z_COORDINATES 1 float 0 POINT_DATA SCALARS temperature float LOOKUP_TABLE default : : Open data file Click Apply Add a Contour Plot Filters Common Contour 14

15 Split Window Click in the second window to select it Save Your Work ParaView User s Guide Included in the installation More tutorials available: Additional Resources Congratulations! This concludes the Introduction to Scientific Visualization using ParaView Vetria L. Byrd, PhD Director of Advanced Visualization Clemson University vlbyrd@clemson.edu 15