Blood Flow Aneurysm Tutorial Dataset Exploration

Simulation Data

This tutorial uses the aneurysm dataset -- available at: http://www.visitusers.org/index.php?title=Tutorial_Data

To begin:

  • Launch VisIt
  • In VisIt's GUI, under the [Sources] section, click Open
  • Navigate your file system to select the aneurysm.visit file.

Plotting Mesh Topology

First we will examine the finite element mesh used in blood flow simulation.

Create a Mesh Plot
  • [Plot List] Add->Mesh->Mesh

Bflow tutorial mesh plot add.png

  • [Plot list] Click Draw

After this, the mesh plot is rendered in VisIt's Viewer window. Modify the view by rotating and zooming in the viewer window.

Modify the Mesh Plot Settings
  • Expand the Mesh plot in the [Plot List] and double click to open the Mesh Plot Attributes Window.

Bflow tutorial mesh plot atts.png

  • Experiment with settings for:
    • Mesh color
    • Opaque color
    • Opaque mode - When the Mesh plot’s opaque mode is set to automatic, the Mesh plot will be drawn in opaque mode unless it is forced to share the visualization window with other plots, at which point the Mesh plot is drawn in wireframe mode. When the Mesh plot is drawn in wireframe mode, only the edges of each externally visible cell face are drawn, which prevents the Mesh plot from interfering with the appearance of other plots. In addition to having an automatic opaque mode, the Mesh plot can be forced to be drawn in opaque mode or wireframe mode by clicking the On or Off. Best demonstrated with the pressure pseudocolor plot present.
    • Show internal zones

You will need to click Apply to commit the settings to your plot.

Bflow tutorial mesh plot .png

Query Mesh Properties

VisIt's Query interface provides several quantitative data summarization operations. We will use the query interface to learn some basic information about the simulation mesh.

  • [Controls Menu]->Query
    • Select NumZones and click Query
      • This returns the number of elements in the mesh.
    • Select NumNodes and click Query
      • This returns the number of vertices in the mesh

Note: The terms zones, elements, and cells are overloaded in scientific visualization, as are the terms nodes, points, and vertices.


Exercises

  • What type of finite element was used to construct the mesh?
  • How many elements are used to construct the mesh?
  • How many vertices are used to construct the mesh?
  • On average, how many vertices are shared per element?

Examining Scalar Fields

In addition to the mesh topology, this dataset provides two mesh fields:

  • A scalar field pressure, associated with the mesh vertices.
  • A vector field velocity, associated with the mesh vertices.

VisIt automatically defines an expression that allows us to use the magnitude of the velocity vector field as a scalar field on the mesh. The result of the expression is a new field named velocity_magnitude .

We will use Pseudocolor Plots to examine the pressure and velocity_magnitude fields.

  • [Plot List] Add->Pseudocolor->Pressure
  • Expand the Pseudocolor plot and double click to bring up the Pseudocolor Plot Attributes Window.
  • Change the color table to Spectral and check the Invert button
  • Click Apply
  • [Plot List] Click Draw
  • [Time Slider] Click Play

You will see the pressure field animate on the exterior of the mesh as the simulation evolves.

Bflow tutorial pressure plot .png

  • Experiment with:
    • Setting the Pseudocolor plot limits
    • Hiding and showing the Mesh plot

When you are done experimenting, stop animating over time steps using the [Time Slider] Stop button.

Query the Maximum Pressure Over Time

We can use the pressure field to extract the heart beat signal. We want to find the maximum pressure value across the mesh elements at each time step of our dataset. VisIt provides a Query over time mechanism that allows us to extract this data.

First, we need to set our query options to use time as the independent variable for our query.

  • [Controls Menu]->Query over time options
    • Select Time
    • Click Apply and dismiss the window

Bflow tutorial q over time options .png

Now we can execute the Max query on all of our time steps and collect the results into a curve.

  • [Plot list] Click to make sure your Pseudocolor plot is active
  • [Controls Menu]->Queries
    • Select Max
    • Check Do Time Query
    • Click Query

This will process the simulation output files and create a new window with a curve that contains the maximum pressure value at each time.

Bflow tutorial q over time result .png


Exercises

  • How many heart beats does this dataset cover?
  • Estimate the number of beats per minute of the simulated heart.

Contours and Sub-volumes of High Velocity

Examining the Velocity Magnitude

Next we create a Pseudocolor plot to look at the magnitude of the velocity vector field.

  • [Plot List] Select and Delete your current plots
  • Add a Pseudocolor Plot of velocity_magnitude
    • [Plot List] Add->Pseudocolor->velocity_magnitude
    • Open Pseudocolor Plot Attributes Window and set the color table options as before.
  • [Plot List] Click Draw

Bflow tutorial vel mag ext.png

Notice that the velocity at the surface of the mesh is zero. To get a better understanding of the flow inside the mesh, we will use operators to extract regions of high blood flow.

Creating a Semi-Transparent Exterior Mesh Plot

When looking at features inside the mesh, it helps to have a partially transparent view of the whole mesh boundary for reference. We will add a Subset plot to create this view of the mesh boundary.

  • [Plot List] Uncheck Apply operators to all plots

Dbreak3d water uc all all.png

  • [Plot List] Add->Subset->Mesh
  • Open the Subset Plot Attributes Window
    • Change the color to Light Blue
    • Set the Opacity slider to 25%
    • Click Apply
  • [Plot List] Click Draw

Bflow tutorial trans boundary.png

Contours of High Velocity

Now we will extract contour surfaces at high velocity values using the Isosurface Operator.

  • [Plot list] Click to select your Pseudocolor Plot
  • Add an Isosurface Operator
    • [Plot List] Operators->Slicing->Isosurface
  • Open the Isosurface Operator Attributes Window
    • Set Select by to Value, and use 10 15 20
    • Click Apply and dismiss the window.
  • Click Draw and use the Play button to animate

You will see the contour surfaces extracted from the velocity_magnitude field animate as the simulation evolves.

Bflow tutorial vel mag iso .png

Sub-volumes of High Velocity

As an alternative to contours, we can also extract the sub-volume between two scalar values using the Isovolume Operator.

  • [Time Slider] Click Stop
  • Remove the Isosurface Operator
  • Add an Isovolume Operator
    • [Plot List] Operators->Selection->'Isovolume
  • Open the Isovolume Operator Attributes Window
    • Set the Lower bound to 10 and the Upper Bound to 20
    • Click Apply and dismiss the window.
  • Click Draw and use the Play button to animate

Bflow tutorial vel mag isovol .png


Next: Visualizing the Velocity Vector Field

Aneurysm Tutorial Index