Orient3D Overview: Difference between revisions
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[[File:O3D_FileMenu.png|right]] | [[File:O3D_FileMenu.png|right]] | ||
;Load Subject (Ctrl + O) | |||
: loads a subject file. Note: Only available with a DSX Suite license. | |||
;Save Subject (Ctrl + S) | |||
: saves the currently loaded subject to its existing subject file. Note: Only available with a DSX Suite license. | |||
;Save Subject As | |||
: saves the currently loaded subject to a new subject file. Note: Only available with a DSX Suite license. | |||
;Load Surface... | |||
: loads a single surface model file. If you load a surface with this command, there is no way to save the local coordinate system or any landmarks you may define, because these items are saved in the subject file. Orient3D is able to load the following formats: | |||
::[https://en.wikipedia.org/wiki/Wavefront_.obj_file Wavefront<sup>1</sup> (*.obj)] | ::[https://en.wikipedia.org/wiki/Wavefront_.obj_file Wavefront<sup>1</sup> (*.obj)] | ||
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After the file is loaded the surface model is automatically triangulated to facilitate additional processing, such as decimation and smoothing. Note: Orient3D currently ignores color and texture definitions from MTL and COL files that sometimes accompany Wavefront OBJ files. | After the file is loaded the surface model is automatically triangulated to facilitate additional processing, such as decimation and smoothing. Note: Orient3D currently ignores color and texture definitions from MTL and COL files that sometimes accompany Wavefront OBJ files. | ||
;Save Surface (global frame) | |||
: saves the current surface model in the global reference frame as an OBJ file. If a subject file is loaded, it will be updated with the name of the saved surface file. The file dialog contains an option for specifying the units of the vertex coordinates. | |||
;Save Surface (local frame) | |||
: saves the current surface model in its local reference frame as an OBJ file. If a subject file is loaded, it will be updated with the name of the saved surface file. The file dialog contains an option for specifying the units of the vertex coordinates. Meters should be chosen if you plan to import the surface model into Visual3D. | |||
;Exit | |||
: exits the program. The program can also be closed using the X in the top right corner of the program window. | |||
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[[File:O3D_LCSMenu.png|right]] | [[File:O3D_LCSMenu.png|right]] | ||
;Reset to Identity | |||
: resets the LCS to the identity matrix (i.e., aligned with the global frame). | |||
;Load from File... | |||
: loads a 4x4 transform matrix from a file and assigns it to the LCS. The transform must be specified as 16 comma-separated values defining the row-major transform from the global frame to the local frame. | |||
;Save to Subject Object | |||
: saves the current LCS to the subject object in the subject file. It is useful for saving the LCS when you have manually moved it on the surface model in the 3D window. If you use an algorithm to calculate the LCS, or load it from a file, the subject file is automatically updated, so you do not need to use this command. | |||
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[[File:O3D_SurfaceMenu.png|right]] | [[File:O3D_SurfaceMenu.png|right]] | ||
;Erase ROI Polygons (Alt + E) | |||
: Toggles in and out of <i>Erase ROI Polygons</i> mode. In this mode, the cursor changes to a crosshair with the label <i>ROI eraser</i>. If you press and hold the left mouse button and drag the cursor over the surface model, all polygons under the cursor will be removed from any ROIs. This is useful for "cleaning up" an ROI if it projected onto an undesired part of the surface model. Press <i>Esc</i> to exit this mode.</br> | |||
Note: There is no undo for this command. | Note: There is no undo for this command. | ||
;Align with Cylinder | |||
: aligns and scales the oriented bounding box of the surface model with the "Visual3D cylinder". There is no undo for this command.</br>Note: This command is not intended to be used in a DSX context. | |||
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[[File:O3D_ViewMenu.png|right]] | [[File:O3D_ViewMenu.png|right]] | ||
;Display Global Axes (Alt + G) | |||
: toggles the display of the global coordinate system in the 3D view. | |||
;Display Local Axes (Alt + L) | |||
: toggles the display of the local coordinate system in the 3D view. | |||
;Display Cylinder (Alt + C) | |||
: toggles the display of a cylinder to which the surface model can be aligned when preparing the surface for use in Visual3D. The Z-coordinates of the cylinder range between -1.0 and 0.0 and its radius is currently hard-coded to 0.2.</br> | |||
Note: This command is not intended to be used in a DSX context. | Note: This command is not intended to be used in a DSX context. | ||
;Display ROI Annotations (Alt + R) | |||
: toggles the display of annotations on the subregions of each ROI. | |||
;Object Configuration (Ctrl + Shift + O) | |||
: toggles the appearance of the dockable <i>Object Configuration</i> widget.</br> | |||
Note: Only available with a DSX Suite license. | Note: Only available with a DSX Suite license. | ||
;Image/Surface Match (Ctrl + Shift + I) | |||
: toggles the appearance of the dockable <i>Image/Surface Match</i> widget.</br> | |||
Note: Only available with a DSX Suite license. | Note: Only available with a DSX Suite license. | ||
;Image Data Generator (Ctrl + Shift + G) | |||
: toggles the appearance of the dockable <i>Image Data Generator</i> widget.</br> | |||
Note: Only available with a DSX Suite license. | Note: Only available with a DSX Suite license. | ||
;Landmarks (Ctrl + Shift + L) | |||
: toggles the appearance of the dockable <i>Landmarks</i> widget. | |||
;Local Coordinate System (Ctrl + Shift + C) | |||
: toggles the appearance of the dockable <i>Local Coordinate System</i> widget. | |||
;Regions of Interest (Ctrl + Shift + R) | |||
: toggles the appearance of the dockable <i>Regions of Interest</i> widget. | |||
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[[File:O3D_OptionsMenu.png|right]] | [[File:O3D_OptionsMenu.png|right]] | ||
;Settings | |||
: Opens the Settings dialog. | |||
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[[File:O3D_HelpMenu.png|right]] | [[File:O3D_HelpMenu.png|right]] | ||
;Help (F1) | |||
: opens the Orient3D wiki page in the default browser. | |||
;About... | |||
: displays a dialog with information about Orient3D, including the installed version number. It also contains the <i>Deactivate</i> button, for deactivating your license. | |||
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Revision as of 17:21, 13 January 2021
Language: | English • français • italiano • português • español |
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Orient3D prepares surface models created by Surface3D (or third-party software such as Mimics and ScanIP) for use in kinematic analyses after they have been tracked in X4D or Locate3D. With it you can define a local coordinate system (LCS) for each object, landmarks, such as ligament attachment sites, and regions of interest (ROIs), which are used in the calculation of distance maps. The local coordinate system of an object is usually, but not necessarily, its “anatomical” reference frame. 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. To analyze tracking results from X4D in Visual3D, the surface model, landmarks, and regions of interest must be saved in the local coordinate system. Even if you are not exporting your data for kinematic analysis in Visual3D, it is still recommended to define the anatomical coordinate system in Orient3D. X4D's tracking results are output using this coordinate system, and it is easier to manipulate the bone in X4D when an anatomical coordinate system is defined.
Tutorials
How To: Define the LCS of an Object
How To: Define Regions of Interest on an Object
Menus
File Menu |
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After the file is loaded the surface model is automatically triangulated to facilitate additional processing, such as decimation and smoothing. Note: Orient3D currently ignores color and texture definitions from MTL and COL files that sometimes accompany Wavefront OBJ files.
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Options Menu |
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Widgets
Landmarks |
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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.
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Local Coordinate System (LCS) | ||||
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![]() This widget lets you create a local coordinate system (LCS) for each object in your data set. Before tracking an object in X4D or Locate3D, you should define an LCS for it because the tracking output for each X-ray frame is the transform from the X-ray lab frame to the object's LCS. The LCS is stored in the subject file, and is expressed as the transform from the object's segmented image frame to its local coordinate system (as if you were traveling from the segmented frame to the LCS). There are three methods of defining an LCS, as described in How To: Define the LCS of an Object.
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Image/Surface Match |
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This widget lets you check if an object's surface model is in the same reference frame as its image data. This is important in X4D so that the surface models are aligned with the DRRs. It works by creating an image surface from the image data, and displaying it in the 3D view with the object's surface model. If they are not aligned, you can use the widget controls to scale, rotate, and translate the image surface so that it aligns with the surface model. Then you can apply the inverse of this transformation to the surface model, so that it aligns with the initial pose of the image surface. ![]()
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Image Data Generator | ||||||||
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This widget creates 3D image data from surface models of objects. X4D tracks objects in X-ray images by generating DRRs from 3D image data (usually CT) of the objects. In some cases CT data is not appropriate for a particular subject and only surface models are available. These surface models could be CAD files of metal implants, or surfaces made from MRI or some other imaging modality that does not represent bone density. This widget creates simulated CT data from the surface models so that the objects can be tracked in X4D. For implants you would typically start with a CAD model of the device, and create a solid object within the image data. For bones, it is recommended that you obtain an outer surface (the outer boundary of the cortical bone), and an inner surface (the inner boundary of the cortical bone), to create more realistic image data. If an inner surface is not available, you can specify the cortical thickness in order to create a shell of constant depth. ![]()
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3D View |
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The 3D View shows the surface model of the currently loaded object. It can also display the global and local coordinate systems. You can change the view camera using these commands:
R: Resets the view camera such that the surface model is centered in the window.
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Settings |
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