In this course we will be using tools based on a very large software library called the Visualization Toolkit (VTK). ParaView is a fairly simple application that allows users to graphically load data sets and visualize them with a commonly used subset of VTK components. VolView is commercial software that provides a simple interface to VTK's 3D scalar field (volume) visualization components. VisTrails is a more in-depth tool that exposes all of VTK and enables quick graphical programming. Each student may find one tool more useful than another for a given task.
The ParaView web page at www.paraview.org is a portal to all sorts of information about ParaView, which is a 3D viewing program that is built on top of VTK. Don't let the Para in the name (which stands for parallel) throw you: it works just fine on single-processor machines. Click on the Resources -> Download link on the toolbar at the top of the page and then on the file entry in the Latest Stable Release table in the Windows (installer) row.
Save the file in your favorite folder. Open that folder and run the executable to install ParaView. The installer will create a new ParaView entry in your Start/All Programs menu.
Download the data zip file ParaViewData3.4.zip that contains example data sets and save it where you saved the ParaView installer.
Download the ParaView Users's Guide. Save this somewhere you can find it easily. This guide is for a previous version, but will still help in learning how to interact with the basic controls.
Go to the www.vistrails.org web site and click on the Download link in the menu bar on the left side of the page. Click on Source and Binaries and select vistrails-setup-1.2-rev1336.zip. Unzip the file and run the installer vistrails-setup-1.2-rev1336.exe.
Download the VisTrails User's Guide. Save this in the same place you saved the ParaView User's Guide. This guide is in draft form, but it contains an introduction to the VisTrails and discusses how to do basic tasks in the program.
Go to the product website at www.kitware.com/products/volview.html. Click on the link in the left toolbar for downloading Volview 2.0 for a 30-day trial. (The program will run in professional mode for 30 days, and will then revert to free mode. Free mode has advanced features turned off, but it will do what we need it to for this course.) Fill out the form and then click the download button. Click on the VV20p5.exe link to download the version for windows (you can try the Linux version if you prefer, but I won't be providing instructions for installing it). Also download the user manual (by right-clicking on the link and selecting 'Save link target as'.
Save the files in the same place you saved the ParaView installer. Open that folder and run the executable to install VolView. You do not need to check for an upgrade during the installation process.
This will create a new VolView20 entry in your Start/All Programs menu. The first time you run the program it will ask you to register in one of several modes. I selected the choice to run the program in free mode.
Run the ParaView application from the Start/All Programs/ParaView 3.4.0 entry. Click the left mouse button in the large gray interaction box and drag the mouse, which will tumble the set of red, green, and yellow axes. The right mouse button will zoom in and out, and the middle one will translate the axes. A second set of axes (red, green, and blue) tumble in the corner; they are labeled with X, Y, and Z to indicate the orientation of the object you are viewing.
Select File/Open from the pull-down menu at the upper-left corner of the application. Browse into the directory where you extracted the ParaView data set and go into the Data directory, selecting the file bluntfin.vts. Click on the Apply button under the Object Inspecto. This will bring up a white wire-frame outline of the data set. Select the Display tab in the control panel to the left of the 3D View window. Click on the menu labeled Representation in the Style panel and select Points from the list that appears. Click on the menu labeled Color by in the Color panel and select Density from the list. Adjust the Point size within the Style panel by clicking on the arrow to the right of 1 and adjusting the spinner control that appears. Type Enter to update the display.
If you want to get a jump-start on the ParaView, VolView, and VisTrails homework, go to the ParaView tutorial and follow along. It will be easiest to follow if you quit and restart ParaView.
Start VolView from the 'All Program -> VolView20' submenu of your Start Menu. Open the
'IronProtein.vtk' data set, which should be in '
This type of image is called a 'Direct Volume Rendering'. We will be discussing this in more detail later on in the semester. You can play with the parameters yourself in the 'View -> Appearance' tab on the left side of the screen.
Go to Start/All Programs/VisTrails and launch the VisTrails application. Make sure the VisTrails Builder window is on top. Go to File/Open and load the file brain_vistrail.vt. You will see the History display. Find the opacity node and click on it. In the tool bar, click on the Execute menu. If the VisTrails - Spreadsheet does not come up, bring the window it to the top. You will see a grid of cells, 3 to a row and 2 to a column. A visualization of one hemisphere of a human brain will appear in the top left cell. Go back to the VisTrails Builder window and click on color 3 node. Click the Execute button. Go back to VisTrails - Spreadsheet. Another view of the brain should appear in the top middle cell of the spreadsheet. VisTrails lets you compare several visualizations of the same data within the spreadsheet. You can link the viewing parameters of the two views by clicking on the skinny cell labeled '1' to the left of the top left cell. This will highlight the row of visualizations. Click on one of the visualizations and manipulate it with the mouse. The other visualization will move according to your interaction.
Go back to the VisTrails Builder window. Click on the Pipeline item in the tool bar. This shows the workflow used to build the visualization color 3. Note that at the top of the window there are two boxes labeled vtkDataSetReader. These so-called modules are responsible for loading data. They are connected to various modules that convert the data into a visualization. At the bottom of the work flow, there is a VTKCell module. This represents a cell in the spreadsheet where the results of the visualization workflow will appear.
Click on the vtkContourFilter module. On the right side of the window there will be a panel called Set Methods. In the panel, there is a subpanel labeled SetValue. Change the Float parameter to 0.1. You should be able to see the outer surface of the brain more clearly now.
The VisTrails tutorial is located here. You can run through it if you want to get a head start on Homework 1.