Fiber Angle Fit

Description

• These step-by-step instructions will guide you through fitting fibers’ orientation data in 2D space (on a plane)

• Fiber is an important structure of cardiac muscle which plays a critical role in cardiac muscle properties.
  Therefore, the heart model will be realistic if it has fiber data.

• The concept of fiber fitting is to put the initial value of fiber angle (in radian) which should specifically refer from Xi(1) or Xi(2) direction

• An automated script that runs this tutorial is included in the Continuity installation: \examples\data02\cubic_fib_fitting.py. To run it, click File→Read script→Python or session script

Start Continuity

• Launch the Continuity Client

• On the About Continuity startup screen

  • check the fitting box under Use Modules:

• Click OK to bring up the main window

Set up mesh

• Mesh→Edit→Coordinates…

  • Select rectangular cartesian in the Global Coordinates: pop-up menu

  • Click OK to submit Coordinate Form

• Mesh→Edit→Basis…

  • Choose Lagrange Basis Function→2D→Linear-Linear

  • Click Add

  • Choose Hermite Basis Function→2D→Cubic-Cubic

  • Click Add

  • Verify that the list of basis functions now contains:
    • Linear-Linear Lagrange 3*3
    • Cubic-Cubic Hermite 3*3

  • Click OK to submit Basis Form

• Mesh→Edit→Nodes…

  • Click Import/Export/Graph button to open Continuity Table Manager

    • Continuity Table Manager→File→Open…

      • Select tab-delimited nodes file ( nodes.xls )

      • Continuity Table Manager→File→Close and update form

  • You should now have nodes numbered 1-25

  • Click on the Field Vector 1 tab

  • Select Cubic-Cubic under Field Variable 1

  • Click on the Fiber Angle tab

  • Select Cubic-Cubic under Fiber Angle, Transverse Angle, and Sheet Angle

  • Click OK to submit Node Form

• Mesh→Edit→Elements…

  • Click Import/Export button to open Continuity Table Manager

    • Continuity Table Manager→File→Open…

      • Select tab-delimited elements file ( elems.xls )

      • Continuity Table Manager→File→Close and update form

  • You should have 16 elements in the list

  • Click OK to submit Element Form

• Mesh→Render→Elements…

  • Click the lines radio button

  • Click Render

• Mesh→Edit→Material Coordinates…

  • Click on the OK Button

• File→Send

• Mesh→Render→Fibers…

  • Leave default settings and click OK

• The mesh should now look similar to the first screenshot above

Set up fitting

• If the Fitting menu is not loaded, select File→Load Continuity Modules…

  • Select fitting and click OK

  • The menu bar should now show the Fitting command

• Fitting→Edit→Data…

  • Click Import/Export/Graph button to open Continuity Table Manager

    • Continuity Table Manager→File→Open…

      • Select tab-delimited data file ( data.xls )

      • Continuity Table Manager→File→Close and update form

  • You should now have Data numbered 11-169

  • Click OK to submit Data Form

• Fitting→Edit→Fit Weights…

  • Simply click OK after opening the Weights form

• Fitting→Edit→Fit Constraints…

  • Simply click OK after opening the Constraints form

• File→Send

• Mesh→Calculate Mesh…

• Fitting→Fit Data

  • In the Cooridinates tab, select coord_1, coord_2, coord_3 for the three coordinates

  • In the Fibers tab, select field1_Var1 for Fiber Angle

  • In the Fitting Variables tab, *deselect* Coordinate 1, Coordinate 2, Coordinate 3, and Fiber Angle

  • Click the Fit button (Don’t close the Fit Data form yet)

  • Fitting→Render→Raw data…

  • Go back to the Fit Data form. In the Fitting Variables tab, check only the Fiber Angle checkbox

  • Click the Fit button

• Mesh→Render→Fibers… (Note: you should render mesh fibers, not fitting fibers)

  • Leave the default values and click OK

• View→Show Open Mesh…

  • Click on fiber vectors4 in the list on the left

  • Click on the Colors tab

  • Change the R,G,B color field to 1,0,0 to change the color to the brightest red

  • Click on data vectors3 in the list on the left

  • Change the R,G,B color field to 0,1,0 to change the color to the brightest green

  • Click somewhere in the rendered window to refresh the image
• The mesh should now look similar to the second screenshot above

Pre-built model

This cont6 file contains all data and parameters for this problem: fit3.cont6