Orient3D Overview

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Orient3D is a utility program for preparing surface models created by Surface3D (or third-party software such as Mimics) for use in kinematic analysis in Visual3D.

With it you can define a local coordinate system for each object, as well as regions of interest (ROIs), which are used in the calculation of distance maps. The local coordinate system of an object is usually its “anatomical” reference frame, but it does not have to be. When a local coordinate system is defined for an object, it is stored in the subject file as a transform from the frame of the object’s segmented image data to the local coordinate system. The program is developed as part of the DSX suite, but it will also be a stand-alone application in the future.

O3D FullScreen.png


     Menus
     File Menu
     O3D LoadSurfaceButton.png
The Load Surface option allows the user to open a file dialog that enables them to browse to and select a surface model to be loaded into the program.
Currently the program is able to load the following formats:
STL (*.stl, *.stla, *.stlb)
Wavefront1 (*.obj)
Open Inventor (*.iv)
COLLADA (*.dae)
After the file is loaded the surface model is automatically triangulated to facilitate additional processing if desired, for example decimating.
Note: Orient3D currently ignores color and texture definitions from *.mtl and *.col files that sometimes accompany Wavefront *.obj files.
     O3D LoadSubjectButton.png
The Load Subject option allows a user to load a subject file that has previously been saved as a *.xml file.
This control can also be accessed by using the Alt + L shortcut.
     O3D SaveSurfaceGlobalButton.png
The Save Surface Global option allows the user to save the current surface model in the global reference frame as a *.obj file.
     O3D SaveSurfaceLocalButton.png
The Save Surface Local option allows the user to save the current surface model in its local reference frame as a *.obj file.
     O3D SaveSubjectButton.png
The Save Subject option allows the user to save the currently loaded subject to the existing *.xml file.
This control can also be accessed by using the Alt + S shortcut.
     O3D SaveSubjectAsButton.png
The Save Subject As option allows the user to saves the currently loaded subject to a new *.xml file.
     O3D ExitButton.png
The Exit option allows the user to exist the program and all unsaved data will be lost.
The program can also be closed by using the X in the top right corner of the screen.
     Transform Menu
     O3D ResetLCS.png
Returns the LCS to identity.
     O3D AlignWithCylinderButton2.png
This control allows the user to transform the loaded surface model such that its main axes is parallel to the z-axis.
The mean value of the x and y coordinates will be 0 and the z coordinates range between -1 and 0 (see: Transforming an obj file).
     O3D DecimateButton2.png
This control tries to reduce the amount of triangles in the model to 75% of the original amount.
The decimation can be initiated multiple times in order to reduce the size of the model more.
It is recommended to save the model before each decimation, because the resulting amount of triangles could suddenly be insufficient to allow for an accurate representation of the model and there is no undo capability.
     O3D EraseROIPolygonsButton.png
Toggles in and out of ROI erase mode.
     View Menu
     O3D DisplayGlobalAxes2.png
The Display Global Axes control allows the user to display the global coordinate system in the 3D view.
This can also be activated by using the Alt + G shortcut.
     O3D DisplayLocalAxesButton2.png
The Display Local Axes control allows the user to display the local coordinate system in the 3D view.
This can also be activated by using the Alt + L shortcut.
     O3D DisplayCylinderButton2.png
The Display Cylinder control allows the user to displays a transparent cylinder to which the loaded surface model with be transformed after selecting the Align option of the Transform menu.
The z-coordinates of the cylinder range between -1 and 0 and its radius is currently hard-coded to 0.2.
This can also be activated by using the Alt + C shortcut.
     O3D DisplayROIAnnotations.png
The Display ROI Annotations control displays subregion annotations on the ROIs.
This can also be activated by using the Alt + R shortcut.
     O3D ShowBoundingBox2.png
The Show Bounding Box control allows the user to display a wire frame around the object displayed in the 3D view to indicate the boundaries of the object that fall parallel with the X, Y, and Z axis of the main axis.
     O3D ShowObjectOrientedBoundingBox2.png
The Show Object-Oriented Bounding Box control allows the user to display a wire frame around the object displayed in the 3D view to indicate the boundaries of the object that fall parallel with the X, Y, and Z axis of the object's local main axis.
     O3D ObjectConfigurationButton2.png
The Object Configuration control allows the user to control the appearance of the dockable Object Configuration widget.
When there is a blue box with a checkmark on the left side the widget is active.
The check will disappear when the widget isn't active.
The Object Configuration widget can also be controlled using the Ctrl + Shift + O shortcut.
     O3D LandmarksButton2.png
The Landmarks control allows the user to control the appearance of the dockable Landmarks widget.
When there is a blue box with a checkmark on the left side the widget is active.
The check will disappear when the widget isn't active.
The Landmarks widget can also be controlled using the Ctrl + Shift + L shortcut.
     O3D LocalCoordinateSystemButton2.png
The Local Coordinate System controls the appearance of the dockable Local Coordinate System widget.
When there is a blue box with a checkmark on the left side the widget is active.
The check will disappear when the widget isn't active.
The Object Configuration widget can also be controlled using the Ctrl + Shift + C shortcut.
     O3D RegionOfInterestsButton2.png
The Region of Interests controls the appearance of the dockable Regions of Interest widget. When there is a blue box with a checkmark on the left side the widget is active. The check will disappear when the widget isn't active. The Object Configuration widget can also be controlled using the Ctrl + Shift + R shortcut.
     O3D ParametersButton2.png
The Parameters controls the appearance of the dockable Parameters widget.
Note: this menu item is only visible once a subject file is loaded.
When there is a blue box with a checkmark on the left side the widget is active.
The check will disappear when the widget isn't active.
The Object Configuration widget can also be controlled using the Ctrl + Shift + P shortcut.
     Help Menu
     S3DHelpButton.png
The Help option opens the application's wiki documentation in the default browser.
     S3DAboutButton.png
The About option displays the About dialog.
     Widgets
The widgets in Orient3D are controlled by the View dropdown menu. The widgets can also be manipulated in the following ways:
they can be removed by clicking on the X in the top right corner of the widget,
they can be moved around the screen by selecting the grey bar at the top of the widget and then dragging it into the new position,
and they can be undocked from the main window by using the double square symbol at the top right of the widget.
     Object Configuration

O3D ObjectConfigurationWidget.png

     Subject
The Subject field is automatically populated with the name of the subject in the subject's xml file.
     Session
The Session drop down menu is automatically populated with all of the sessions available for the current subject.
     Object
The Object table is automatically populated with all objects available for the currently selected session.
The object that is selected in the list is the object that is presented in the 3D View.
     Landmarks

O3D LandmarksWidget.png

Landmarks are 3D locations on a surface model, such as ligament attachment points, that you digitize for later use in other applications.
Their coordinates are expressed in the reference frame of the object’s segmented image data (not the “local coordinate system”), and are stored in the subject file.
     Add Landmark
The Add Landmark button allows the user to create new landmarks.
Click on the button and move the cursor over the 3D window.
The cursor will change into a crosshair with the landmark name next to it.
Hold down the Shift key and click the left-mouse button on the surface model to create the landmark.
     Table
The Table lists all of the landmarks that are associated with the object in the 3D View, including their names and their X, Y, and Z coordinates.
To change the name of a landmark, double-click with the left mouse button on its name in the name column and type in a new name.
To move an existing landmark, select the landmark in the list and then click on the new location on the surface model.
     Remove Landmark
The Remove Landmark button allows the user to delete an existing landmark.
Select the landmark from the table and click the Remove Landmark button.
     Local Coordinate System

O3D LocalCoordinateSystemWidget2.png

The local coordinate system of an object coincides with the global coordinate system unless a local coordinate system is defined for the object in the Local Coordinate System widget.
The axes for each of these coordinate systems can be displayed in the 3D window.
The global coordinate system is controlled by the Display Global Axes button in the View menu.
The local coordinate system is controlled by the Display Local Axes button in the View menu.
To define a local frame for the current object:
Select one of the algorithms in the Algorithms panel.
Create any digitized landmarks that are needed by the algorithm, then press Apply.
Note: To reset the local coordinate system of an object back to the global frame, click on the Reset LCS button item in the Transform menu.
To analyze the tracking results in Visual3D:
The surface model will need to be saved in its local (anatomical) coordinate system after specifying the desired ROIs.
To analyze the results in a 3rd party program:
The surface model might have to be saved in another coordinate system.
     LCS Algorithms
The LCS algorithms are implemented in a dll plugin framework, allowing the user to integrate his/her own LCS code.
The currently implemented algorithms are:
  1. Vertebra [Anderst] Anderst, W., personal communication.
  2. Distal Femur [Miranda] Miranda, D., et al. J Biomech 43(8), pp. 1623–26, 2010.
  3. Proximal Tibia [Miranda] Miranda, D., et al. J Biomech 43(8), pp. 1623–26, 2010.
     Landmarks
Landmarks are Visual3D`s way of defining a local coordinate system.
     Regions of Interest

Like the LCS algorithms, the ROIs are implemented in a dll plugin framework, allowing the user to integrate his/her own ROI code. There are currently three types of ROIs:

O3D RegionOfInterestsWidget.png

     Rectangle [NxM]
Rectangle [NxM] is a flat rectangular ROI whose “top” surface is specified by the orientation parameter. It is divided into NxM subregions, and is projected onto the object along the negative of its orientation axis. Its initial placement on the object is specified by four landmarks: edge1, edge2, edge3, and edge4. These landmarks do not need to be placed in any specific order, or in any specific locations relative to each other. They are used to define the minimum and maximum extents of the ROI in the two non-principal dimensions in the object’s local coordinate system. For example, if the ROI’s orientation is +Z or -Z, then the minimum and maximum X and Y coordinates of the four landmarks define the ROI rectangle in the XY plane.
     Swept Rectangle [NxM]
Swept Rectangle [NxM] is a curved rectangular surface divided into NxM subregions. It is useful for defining ROIs on curved bone surfaces such as the femoral condyles. Its placement is defined by four landmarks: curve1, curve2, curve3A, and curve3B. The first three landmarks define the arc along which the ROI is swept. They also define the direction with N subregions. Curve3B should be placed such that the vector from curve3A to curve3B is perpendicular to the arc, and along the orientation axis of the ROI. Curve3A and curve3B define the direction with M subregions and the distance between them defines the width of the ROI. When the ROI is projected, each subregion is projected along [the negative of] its normal. Because the normals of adjacent subregions along the length of the arc are not parallel, their projections on the object surface will overlap. In these cases the overlapping surface is bisected and divided equally between the two subregions.
     Disk
Disk is a circular flat circular ROI whose “top” surface is specified by the orientation parameter. It is divided into NxM subregions, and is projected onto the object along the negative of its orientation axis. Its placement is defined by two mandatory and two optional landmarks. The mandatory landmarks are Center and Outer Radius which defined the center and of the ROI, respectively. These mandatory landmarks also define the direction with N subregions. The optional Inner Radius defines the radius of the hole inside the ROI, and the other optional landmark Pie Angle allows to define a pie-shaped ROI whose angle is defined by the angle Pie Angle-Center-Outer Radius.
     Add
The Add button creates a new ROI and adds it to the list.
     Remove
The Remove button deletes the selected ROI but does not modify the object surface.
     Place
The Place button places the ROI in the search box on the object.
     Adjust
The Adjust button allows the user to enter the manual ROI adjustment mode. In this mode the placed ROI can be moved using the three mouse buttons. Pressing the button a second time allows the user to exit adjust mode.
     Project
The Project button projects the placed ROI onto the object.
     Clear Surface
The Clear Surface button allows the user to clear all of the ROI labels from the object.
     Parameters

The Parameters widget is populated when a subject xml file is loaded.

O3D ParametersWidget.png
     Principal ROI Expand
The Principal ROI Expand control allows the user to enter a scale factor for the search box in the principal direction of the ROI, which is specified by the ROI orientation.
The default value is 5.0.
     ROI Offset Factor
The ROI Offset Factor control allows the user to enter the amount to offset the ROI surface along the principal axis, specified as a percentage (0.0 to 1.0) of the maximum dimension of the object. The default value is 0.03.
     Secondary ROI Expand
The Secondary ROI Expand control allows the user to enter a scale factor for the search box in the two non-principal directions of the ROI. The default value is 2.0.
     3D View

The 3D View is the large black area in the center of the Orient3D screen. The 3D View displays the 3D graphics that are loaded into the program.

O3D 3DView.png

     Adding Images
A surface file can be added to the 3D view by using the Load Surface option in the File Drop Down menu.
Other components can be added to the 3D view by using the options in the View Drop Down menu.
These components include:
Display Global Axes
Display Local Axes
Display Cylinder
Display ROI Annotations
Show Bounding Box
Show Object-Oriented Bounding Box
     Interactive Manipulation
The user can change the point of view of the 3D view by using the mouse.
The interaction represents a trackball interaction: the magnitude of the mouse motion is proportional to the change in the point of view associated with a particular mouse binding.
For a 3-button mouse:
the left button is for rotation,
the right button for zooming,
the middle button for panning, and
ctrl + left button for spinning.
Rotating the mouse wheel also enables zooming.
If the mouse or computer has fewer buttons then the ctrl + shift + left button is for zooming, and shift + left button is for panning.
     Transformation Widget

The transformation widget consists of three perpendicular lines parallel to the global x, y, and z axes and three transparent green ellipsoids. At the ends of the lines are spherical handles.

A handle gets selected by pointing at it with the mouse cursor and pressing the left mouse button. The sphere, representing the handle, becomes red when it is selected and the line attached to it becomes green. Everything becomes deselected by releasing the left mouse button.

O3DTransfWidget.png

Translation

When a handle is selected while holding the Z key, the surface model can be translated along the line with the selected handle by moving the mouse while holding the left button depressed.

Rotation

When a handle is selected while holding the X key, the two ellipsoids that pass through this handle become more opaque. The surface model can be rotated in the planes of these ellipsoids by moving the mouse while keeping the left mouse button depressed.

     Key Shortcuts

R: Focuses the point of view to the center of the scene.

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