AMASS Shell

This program is the control center that provides easy access to all AMASS functions, parameters, and data.

The controls are divided into three groups; the Input files group, the Project group, and the Function group. Below is a detailed description of all items and their functionality.

Input files group

This area allows the selection of any number of data files for processing.

The name of the folder containing the files is displayed in the Folder edit box, and it may be edited, or changed by use of the Browse… button. ' The radio buttons under the Folder edit box indicate the file extension we wish to work with. For example, if the cen button is selected then the large list box will show all files that have the .cen extension that are contained in the folder named in the Folder edit box. AMASS projects allow each different file type to reside in a different folder if desired. Hence you can specify in which folder .seg files are to be stored by clicking on the seg radio button and then entering or browsing for the desired folder name.

Note that setting a folder name by browsing will set that folder name for all extension types to the right of the currently selected radio button.

The leftmost radio button is only active if raw camera data files are being supplied from another motion capture system. See Convert.

Input files

The large list box displays all files present in the folder indicated by the Folder edit box that have the extension selected by the radio button.

By dragging the mouse over the file names or the use of the standard Windows list selection mechanisms (via Shift and Control keys), the user can select the files that will be processed by the next Function command.

Specific buttons are provided for Selecting all files, Clearing all files, Refreshing the file list, and Deleting selected files.

Folders

The folder names can be independently specified for each extension type and are stored in the current project file. ' The folder name for any extension can be modified by pressing the Browse...' button which brings up a window that allows a folder to be chosen, or by typing a folder name into the edit window. Anytime the folder name is modified, the file list is updated to reflect all files with the currently selected extension.

Project group

The Project group has a non-editable window, and Edit, Open…, and New… buttons. The name of the current project is shown in the edit window.

NOTE: The Project file name is stored in the registry, so that subsequent AMASS sessions will remember the project. This can be convenient for laboratories that consistently use one protocol. For laboratories that are running multiple protocols, and multiple project files, it is important to take note of which project is currently active.

Editing a project

Clicking the Edit button launches the parameter edit dialog which allows the user to change certain parameters that are used for the processing of data. The edit dialog provides a tab for each of the processing functions ( Convert, Calibrate, Track, Identify) as well as a Comment tab in which the user can enter comment information about this particular Project file. See Parameters.

Opening a project

The Open… button allows the user to select any existing Project file. Upon file selection, all parameters and folder information for that project are loaded and presented to the user for immediate use. The data for the current Project file are automatically saved before the selected file is loaded.

Creating a new project

On pressing the New… button the current project file is saved and the user is presented with a dialog where he or she can enter a new project name, and select a folder where the new project file will be stored. The initial contents of the new project file will be identical to the current project file and should be customized by use of the Edit command.

Function group

After the user has selected one or more Input files, he or she can click on any of the active buttons in the Function group to perform the required processing. Note that only those functions that can operate on the selected input files are enabled at any one time. The following provides an overview of the actions of the various functions.

Capture2D

This program starts the C-Motion camera Capture2D program that can be used to collect .cen files from supported camera systems. The Capture… button will only be active if the cen file extension is selected for Input files, and Capture is selected in the Input page of the Parameters dialog.

Note that the parameters for the Capture program are not stored in the Project file. The Capture program is designed to operate in conjunction with the AMASS shell program and normally both will be open simultaneously. If the output folder in the Capture program is the same as the .cen input file folder in AMASS, the AMASS Input window will reflect files created (or deleted) in the Capture program.

Convert

This button becomes enabled if one or more camera raw data files are selected in the Input files list. The extension of the raw data file(s) will depend upon the camera system that created the file(s), and the system type must be set in the Input section of the parameters. For systems that produce individual camera files for each data capture only the lowest numbered file is displayed in the input file list. The conversion process creates a single .cen file for each capture even if multiple camera files were produced by the originating system.

ViewCen

ViewCen is a utility program for quickly checking the quality of data in .cen files. If one or more .cen files are selected, you can click on ViewCen to display a window which allows the viewing of the image data from each camera, over all frames. A Parameter button in the window also provides information on some internal camera parameters stored in the .cen file. If you check the ViewCen box in Convert parameters, the ViewCen program will be automatically called after each file conversion.

Calibrate

The AMASS Calibrate program performs the camera system calibration from the selected input .cen file using the Calibration parameters in the current project file, and if successful, writes the resulting calibration data to a .cal file in the cal folder designated via the Input files group. This calibration file can then be used by the Tracking program to generate 3D marker trajectories. During a system calibration data capture an AMASS wand must be moved throughout the volume where it is desired to perform 3D measurements. The requirements for wand motions during the calibration trial capture are rather specific, and must be carefully done in order to provide a successful and accurate calibration. An accurate calibration in turn leads to good, clean marker trajectories, which makes the task of segment identification much easier.

The calibration software performs a series of complex computations in order to determine, among other things, each camera’s lens distortions, lens focal length, internal camera geometry, and location and orientation in a global coordinate system. Simultaneously the program also deduces the distribution of the markers on the wand, and the wand’s location in the global coordinate system for every frame. Examination of the Calibration parameters will show that the parameter input to the program is very limited, greatly reducing the possibility of erroneous user input. The user should read and pay close attention to section ---- which discusses detailed instructions on setting up cameras and collecting calibration data.

ViewLin

Every .cal file can be examined with the ViewLin utility program. In addition to a view of the area of the image that was calibrated and can participate in 3D reconstruction for each camera, the display provides some overall information on the quality of the calibration. See details in section ----. ViewLin also provides a button to designate the currently displayed .cal file as the calibration file to be used in subsequent Track operations.

Track

This program acts on the selected .cen files to generate .seg files using the calibration file and Track parameters specified in the project file. The tracking process is automatic and involves a complex computation that associates the centroids of each marker from different cameras, reconstructs the markers' locations in 3D space, and assigns the markers to 3D trajectories. These 3D trajectories extend over five or more consecutive frames, and are called segments. The segments are arbitrarily numbered according to the order of their commencement, and typically vary in length because of interruptions due to marker image loss from camera views. The resulting .seg file is a binary file containing every segments of every marker that could be reconstructed from the .cen file.

ViewSeg

This function operates on the selected .seg files and for each file provides a graphical overview of the number of segments generated by the tracking, and the length of the segments with respect to the total number of frames processed. If Connect gap in the Track parameters is greater than zero, the Track program connects discontinuous segments which have a high probability of belonging to the same marker to form a single segment. Hence the ViewCen display may show gaps in some segments indicating that a marker could not be specifically tracked for one or more frames.

Identify

The Identify program allows the user to associate each segment with a marker name and then write the identified marker data to a .c3d file. Input consists of a .seg file and the Identify parameters. The marker names are supplied through a marker (.mrk) file supplied in the Identify parameters.