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Create a Setup Scene

In this step, 3D models of the bones and their markers will be imported into Maya. Then the XYZ coordinates of the markers, relative to the polygonal models of the bones, will be measured and saved as CTmarkerCoordinates. This step is done in Maya using the XROMM Maya Tools

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**UNDER CONSTRUCTION**

There are two methods for calculating marker model coordinates

  1. vAvg – calculates centroid for each individual marker based on the average position of selected vertices.
  2. vAvg2 – breaks all unconnected elements into separate objects and automatically calculates the centroid of each element.

For both methods, import .obj files for the bones and the markers, and set up for easy marker selection (make the bones transparent and unable to be selected).

  1. Click the imp button on the XROMM Maya tools shelf.
  2. Click impObjs,  Shift+select(pc) or command+select (mac) bone and marker models and open.
  3. Click Hshd on the shelf. In the "Create" window (bottom left) click Lambert to create a new shader (probably named Lambert2). On the right side of the screen, set the color, and drag the transparency slider towards the right. Minimize the hypershade window.

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  4. Select all bone models (but not the markers)

    . Hit ctrl+h on the keyboard to hide all of the bones. Only the markers are showing.
  5. Select the marker object
  6. right click and select vertex from the marking menu
  7. drag select the vertices for a single marker
  8. click vAvg on the shelf bar or type vertAvg on the command line. If you are using XROMM_Maya_tools_2.0.5 or earlier, the window will look like this:
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    If you have a window like the one above, follow the instructions below. If you are using XROMM_Maya_tools_2.0.6 or later, scroll past these instructions to the picture of the newer vertAvg window.
  9. Type in the number of markers you have and press enter. In the above example, we had 10 markers.
  10. Select the marker number from the list that corresponds to the vertices you selected and hit the "calculate centroid" button.
  11. A locator is created with the xyz coordinates of the marker centroid. It will be name "marker##" where ## is the number you typed.
  12. repeat for all markers
  13. (hint: if you need to see the bones to determine marker numbers Shift+h will unhide the bones)
    If you are using XROMM_Maya_tools_2.0.6 or later, the window will look like this:
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  14. Export the CT marker locator data
  15. This step can be done in the vAvg window. Once you have created centroid locators for all of the makers, the "export centroids" button will become black. Press this button and save the file it produces.
  16. If you closed the vAvg window, you can also export the marker locations by doing the following:
  17. select all of the locators that you just created.
  18. click the CTex

    , reopen the hypershade window, right click on the lambert2 icon and select Assign Material to Selection. Close the hypershade window. You should now be able to see your model markers through the transparent bones, however, it will still be difficult to select the marker models because the bone models are in the way.

  19. With the bone models still selected, create and place them on a new layer using the button shown below. If you do not the layer editor, click the Channel Box/ Layer Editor tab on the right side of the screen.
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  20. Click the blank 3rd box twice which changes to the letter R and the bone models become unselectable but still show smooth shading.
  21. Now you should be able to see and select the marker mesh through the transparent bone model.

For a single marker object:  vAvg

  1. Select the marker object.

  2. Click vAvg on the XROMM tool shelf.

  3. Right click-hold and select vertex from the marking menu 
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  1. Drag your mouse over a single marker (selected vertices should become yellow).

  2. In the Marker Name box, enter a name for the marker.

  3. Press the Calculate Centroid button and a locator will be created.
  4. Repeat steps 3 - 8 for each marker.

 

For all markers in a single object: vAvg2

  1. Select the marker object.

  2. Click Calculate Centroid

  3. Click the Hgph button on the shelf. Note there are two groups created by vAvg two. The first group are the isolated meshes from the marker model. The second group are the calculated centroids with the suffix vAvg2.

  4. Renaming markers from vAvg2 is best done in the next step; CTexport.
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Export the CT marker locator data

  1. Click the CTex from the XROMMtools Shelf, or type CTMexport in the MEL box
  2. Save the .csv file
  3. Save the scene. You will reference this for all animations involving this individual animal

Converting .wrl (VRML) models into Maya-friendly format (Windows only). Note: it is more convenient to export 3D models in .obj format from Amira (or Microscan Tools) because .obj files can be imported directly into Maya. These instructions are provided in case only VRML models are available.

If using older SmoothData MATLAB script, then Reset Bone element pivots(**this step omitted if using rigidBody MATLAB script)

  1. Select all marker locators for single bone (using shift select for multiple selection)
  2. Shift select the bone associated with the selected locators
  3. click the mvPv button on the XROMMtools shelf
  4. repeat for each bone
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  2. If using vAvg2, you may want to rename your markers. To do this, select the marker from the view window, hypergraph or All Locators list, type the new name in the Rename Centroid text field and click rename. The list will update with the new name for the object. 

  3.  Select markers that you want to export in the left window and click Move Right. You should export marker sets for each rigid body as a single file for easier use with XMALab.

  4. Click Export to .csv File.