== Fiber Angle Fit ==
[[Gallery]]

[[TableOfContents(3)]]

=== 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. [[BR]] 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 [:Continuity/Documentation/Help/ReadPythonScript:File→Read script→Python or session script]
=== Start Continuity ===
 * Launch the Continuity Client
 * On the [:Continuity/Documentation/Help/HelpAboutContinuity:About Continuity startup screen]
  * check the '''fitting''' box under {{{Use Modules:}}}
 * Click '''OK''' to bring up the main window
=== Set up mesh ===
 * [:Continuity/Documentation/Help/MeshEditCoordinates:Mesh→Edit→Coordinates...]
  * Select '''rectangular cartesian''' in the {{{Global Coordinates:}}} pop-up menu
  * Click '''OK''' to submit {{{Coordinate Form}}}
 * [:Continuity/Documentation/Help/MeshEditBasis: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}}}
 * [:Continuity/Documentation/Help/MeshEditNodes:Mesh→Edit→Nodes...]
  * Click '''Import/Export/Graph''' button to open [:Continuity/Documentation/Help/TableManager:Continuity Table Manager]
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Open...]
    * Select tab-delimited nodes file ( attachment:nodes.xls )
    * [:Continuity/Documentation/Help/TableManager#FileMenu: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}}}
 * [:Continuity/Documentation/Help/MeshEditElements:Mesh→Edit→Elements...]
  * Click '''Import/Export''' button to open [:Continuity/Documentation/Help/TableManager:Continuity Table Manager]
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Open...]
    * Select tab-delimited elements file ( attachment:elems.xls )
    * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form]
  * You should have 16 elements in the list
  * Click '''OK''' to submit {{{Element Form}}}
 * [:Continuity/Documentation/Help/MeshRenderElements:Mesh→Render→Elements...]
  * Click the '''lines''' radio button
  * Click '''Render'''
 * [:Continuity/Documentation/Help/MeshEditMaterialCoordinates:Mesh→Edit→Material Coordinates...]
  * Click on the '''OK''' Button
 * [:Continuity/Documentation/Help/FileSend:File→Send]

 * [:Continuity/Documentation/Help/MeshRenderFibers: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 [:Continuity/Documentation/Help/FileLoadModule:File→Load Continuity Modules...]
  * Select '''fitting''' and click '''OK'''
  * The menu bar should now show the Fitting command
 * [:Continuity/Documentation/Help/FittingEditData:Fitting→Edit→Data...]
  * Click '''Import/Export/Graph''' button to open [:Continuity/Documentation/Help/TableManager:Continuity Table Manager]
   * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Open...]
    * Select tab-delimited data file ( attachment:data.xls )
    * [:Continuity/Documentation/Help/TableManager#FileMenu:Continuity Table Manager→File→Close and update form]
  * You should now have Data numbered 11-169
  * Click '''OK''' to submit {{{Data Form}}}
 * [:Continuity/Documentation/Help/FittingEditData:Fitting→Edit→Fit Weights...]
  * Simply click '''OK''' after  opening the {{{Weights}}} form
 * [:Continuity/Documentation/Help/FittingEditData:Fitting→Edit→Fit Constraints...]
  * Simply click '''OK''' after  opening the {{{Constraints}}} form
 * [:Continuity/Documentation/Help/FileSend:File→Send]
 * [:Continuity/Documentation/Help/MeshCalculateMesh:Mesh→Calculate Mesh...]
 * [:Continuity/Documentation/Help/FittingFitData: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)
  * [:Continuity/Documentation/Help/FittingCalculateDataXi: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
 * [:Continuity/Documentation/Help/MeshRenderFibers:Mesh→Render→Fibers...] (Note: you should render '''mesh''' fibers, not fitting fibers)
  * Leave the default values and click '''OK'''
 * [:Continuity/Documentation/Help/ViewShowOpenMesh: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: attachment:fit3.cont6