If your visual assessment and Vicon Shogun Post's diagnostic tools have revealed issues with your recorded data (see Check data quality), you can use its cleanup tools to correct mislabels and fill any gaps.
Before filling gaps, you must find and fix any labeling swaps or errors in your data. Gap-filling in Shogun relies on the data before and after the gaps to predict marker location, so any labeling errors will cause gap-filling to fail.
The following topics provide an introduction to fixing data issues:
. ‌See also the related Vicon videos: and
Note that each time you finish cleaning up a range, you must check its solve (see Solve during cleanup).
Find and fix bad data
To help you identify and fix bad data, you can use the Marker Editing panel.
To find and remove bad data:
- On the Processing menu, click Marker Editing (or click Marker Editing on the Processing tab of the ribbon).
- In the Remove Bad Data section, go to the Find Bad Data button and notice the options:
- Threshold Allowable deviation
- Cut-Off Data filter. Decreasing this value filters the data more heavily.
- Sensitivity Amplifies the effect of the Cut-Off filter.
- Click Find Bad Data.
- Experiment with these values to find out what works best for your data.
- When you have identified the bad data, remove it by clicking the appropriate Cut button, and apply a fill (see Gap-filling options).
Find and fix noise
Noise can be easily identified in a Graph view:
Noisy data also produces flickering as you play through a take in the Perspective view. You can fix it by using the filtering options provided in the Marker Editing panel.
To fix noisy data:
- In a Graph view, ALT+drag to select it.
- At the bottom of the Marker Editing panel, expand the Filter section, and select whether the filtering will apply to Ranges, as in the above example, or to Selected Keys.
- If you're not sure how much filtering to apply to your data, keep the default settings (Cut Off: 0.3 and Threshold: 15) and click Apply. You can reapply this as many times as required, enabling you to stop at the level that is most appropriate.
- In the Graph view and Perspective view, check that the trajectory is now smooth over the selected range.
Remember that to display a tooltip for any of the controls, hover the mouse pointer over the relevant control.
Use the Labeling panel
You can fix labeling issues using the tools in the Labeling panel. The following steps introduce the main components of the labeling panel. To go straight to examples of how to use it to fix labeling issues, see Fix common labeling issues.
To use the Labeling panel:
- On the Processing tab on ribbon, click Labeling.
In the toolbar at the top of the Shogun Post window, ensure that the required subject is selected in the Current Subject list.
By default, the selection in the Current Subject list at the top (middle) of the Shogun Post window determines which subject to label.
If All is selected in the Current Subject list, the labeler uses the last subject it was set to.
If you want to select a subject different from that specified in the Current Subject list, in the Labeling panel, clear the Use Current Subject box and select the required subject from the Subject list at the left of the check box.
On the left of the Labeling panel, a list of labels for the selected subject is displayed. The color variations indicate marker issues:
- Yellow: Mislabels or missing labels (the depth of the color indicates the severity of the issue, eg, more or fewer gaps)
- Red: Labels for this marker are missing from the current frame
- To display a 3D representation of your labels for the current subject, click the 3D button at the top of the Labeling panel. The 3D view helps you to quickly identify where the markers should be. You can drag and drop labels from the 3D Labeling view to the Perspective view pane (and vice versa).
You can use the usual mouse actions (click and drag, right-click and drag, left- and right-click and drag) in the 3D view, in the same way as in a Perspective view.
- At the top of the Labeling panel, in the Manual Labeling Options section, select the Mode option (Select or Label), which affects the way in which you select and label markers.
- Select Click a marker on your subject in a Perspective view and then click a label name in the list in the Labeling panel.
- Label Click name of the label in the marker list and then click the required marker on the subject in the Perspective view.
To quickly switch between labeling and select modes when labeling a subject, you can use the default hot key (L) that duplicates the functionality of the Label and Select buttons at the top of the Labeling panel.
- In the Direction line, choose to label forward
You can also select both options (ie, label both forward and backward), but to help you avoid confusion, at least initially, choose either backward or forward and use only that option. (through time) or backward .
- From the Type options, select the way in which labeling will be applied:
- Whole Labels entire trajectory.
- Fragment Labels the trajectory that intercepts the current frame.
- Cliff Labels the current frame and continues until a specified value is encountered, which stops the labeling (see the text below in the Labeling panel, for example, the default is to skip gaps smaller than 5 frames and stop labeling at cliffs that are larger than 50 mm).
- Ranges Lets you select an area on your graph or timeline and label only the selected time range.
In the Manual Labeling Tools section in the middle of the Labeling panel, you can correct swaps, unlabel information, and unlabel markers.
In the Semi-Automated Labelers section, you can access the Velocity Labeler, which is normally used after automated labeling, on a partially labeled take. You can use it to correct labeling where the path of a single marker is made up of multiple trajectories that are consecutive in time with a small gap in between where the marker is unlabeled over a portion of its trajectory. The Velocity Labeler is useful in cases when a marker has been labeled for some range of time, and then becomes unlabeled, yet going forward or backward in time there are multiple trajectories that do not have a large gap between them and are all the same marker. It is best suited for cases when unlabeled trajectories are not many frames away from the labeled marker and the velocity of the marker around the end of the labeled marker and the start of the unlabeled trajectory is fairly constant.
Fix common labeling issues
The following basic procedures are just a few of the ways in which you can use Shogun Post to clean up data.
- To help you identify issues, in the Perspective view, click View Filters, select Custom and ensure that Missing Markers and Labeling Constraints are selected.
- In Perspective view, scrub through the whole take (drag the current time indicator along the timeline, or for finer control, press the A or S key), noting times when markers are likely to be occluded (sitting, crouching, subjects interacting, etc).
In the marker list in the Labeling panel, note any missing (red) markers and watch for ‘popping’ or moving in the Perspective view. Look for any swapped markers (for an example, see the Vicon video , which shows an example of a swap of knee and heel markers). ‌
Missing markers are clearly visible, highlighted in red. However, after you’ve identified the erroneous markers, it may help with labeling to clear Missing Markers and Labeling Constraints.
Correct a swap
- Ensure the Labeling panel is displayed.
- Split the Perspective view (at the top right of the Shogun Post window, click the vertical split button a Perspective view, a Graph view and the Labeling panel.
) and in one of the panes, change to a Graph view, so that you can now see
- In the Labeling panel, ensure Select mode, Forward direction (>), and Cliff are selected.
- In the Perspective view, select a marker that is incorrectly labeled and in the Graph view, zoom in (right-click and drag) and go to the start of the where the swap happens (this should be identifiable on the graph by a sharp change).
- From the position of the marker in the Perspective view, decide which is the correct marker and click it in the 3D view.
In the marker list, its name is displayed in heavier text, and at the top left of the Perspective view, the Selection text displays the name of the selected marker.
- Click the wrongly labeled marker in the Perspective view and then click the correct marker name in the Labeling panel list.
The marker is now correctly labeled. To check, scrub back and forward in the Perspective view and check that the marker is now behaving correctly.
However, you now have a previously incorrectly labeled marker that is unlabeled from this point forward.
Label an unlabeled marker
- In the Perspective view, click on the unlabeled marker to select it. Scrub back and forward to identify where it is correctly labeled. This is the point at which it is correctly colored in the Perspective view and the Labeling panel marker list. You can also observe this on the Graph.
- To label a marker using the tools in the Labeling panel, do one of the following, depending on your chosen Mode:
If you prefer to label using Label mode:
- In the Manual Labeling Options section, in the Mode line, click Label.
- In the marker list in the Labeling panel, click the name of the marker and then in the Perspective view, click the marker that is currently unlabeled.
- In the Manual Labeling Options section, in the Mode line, ensure Select mode is selected.
- In the Labeling panel, click to select the required marker in the 3D view.
- SHIFT+CTRL then click+drag from the selected marker in the Labeling panel to the unlabeled marker in the Perspective view.
- As before, to check the labeling, scrub back and forward in the Perspective view and check that the marker is now behaving correctly.
After you have corrected any swaps, you may want to use Shogun Post's diagnostic tools to help to identify gaps (see Check data quality).
Manually fill gaps
You fill gaps using the Marker Editing panel, normally in conjunction with the Data Health view and/or a Graph view. The Marker Editing panel contains all the tools necessary to fill gaps, alter trajectory keys and filter your data.
For example, you might first notice a gap from the display on the time bar Issues map, then note which marker is affected in the Perspective view:
- To quickly gap-fill the selected marker, on the time bar double-click to move the current time indicator to the relevant frame.
The affected marker is automatically highlighted in the Perspective view (you can right-click and drag to zoom in further to check the marker).
- To open a Data Health view and a Graph view, as well as a Perspective view, split the screen by clicking the Three Views Split Left button at the top of the Shogun Post window and change the views in the new panes.
- If the Marker Editing panel is not already open, on the Processing tab on the ribbon, click Marker Editing.
- In the Data Health view, find the relevant marker's line, which shows a gray rectangle that represents the gap.
- In the Data Health view, double-click to select the range of the gap.
- In the Marker Editing panel, expand the Fill Gaps section, select Selected Ranges (to fill only the current selection), and then click Fill Using Interpolation.
This looks at the keys on either side of the gap and fills it by interpolating between them. It works well for small gaps.
- In the Perspective view and Graph view, check that your fill has given the required result.
- If the fill does not give an appropriate result, you can click Undo on the quick access toolbar Options for gap filling). , and try other gap-filling options in the Marker Editing panel (see
Options for gap filling
The appropriate option to use depends on the type of gap that you want to fill.
- Manually select a short gap by double-clicking in a Graph view or Data Health view, and in the Marker Editing panel, in the Fill Gaps section, select Fill Using Interpolation.
This looks at data before and after the gap and uses a spline fill to interpolate between them.
- Check that the result looks reasonable in a Perspective view and Graph view.
Sequence of short gaps
- For a sequence of small gaps with smooth line running through the gap in the Graph view, ALT+drag to select the affected data.
- Under Fill Using Interpolation, select Selected Ranges, and then click Fill Gap Using Interpolation.
For non-linear motion, for example, where rotational movement is involved, as interpolation does not account for this kind of motion, a different approach is needed. If a missing marker is part of set of markers that are rigid (ie, remain in the same relation to each other, for example, a pelvis), you can use three or more markers in the rigid object (three in addition to the marker that has the gap is recommended) to help fill in the data for the missing marker.
- As before, to select the range of the gap, double-click in a Graph view or Data Health view, then select (CTRL+click) the three other markers in the rigid object.
In the Marker Editing panel, the Fill Rigid option is enabled.
- Select Selected Ranges and click Fill Rigid.
The pattern of the present markers is copied onto the missing marker.
- As usual, check in the Graph view and in a Perspective view that the fill looks sensible.
Other rigid objects you can use in default marker set include hands, forearm, upper arm, shoulders, thorax, and head.
Non-linear motion where rigid fill impossible
In cases where the motion is non-linear, but a rigid fill is not possible due to all the related markers being absent, you can use the Fill Using Constraints option. This uses the labeling or solving skeleton to produce the fill. It requires a skeleton be present, the skeleton to be constrained by markers, and enough markers to have data that the solve is fairly good. The marker being filled must be constrained to the skeleton because it is the constraint offset that is used to determine where the marker should be during the fill.
Before using this type of fill, check that the bones and missing markers (by default displayed in red in the Perspective view), are in sensible locations.
Processing during cleanup
Note that the previous steps for fixing data issues assume that your existing .mcp data is largely of acceptable quality. However, in some circumstances (for example when you are trying to produce better quality data), rather than persisting in trying to fix a problematic .mcp file, you may need to clear the scene and start from the .x2d file, or unlabel all the data first. In this case, do not just open the Processing panel and click Reconstruct or Label or run other Combined Processing operations as this will not fix problems with the underlying data.
Clear existing data
To remove all unlabeled data and clear existing labels and solves, at the top of the Processing panel, select the Reset Scene check box. You can then run Reconstruct, etc.
To remove existing labels from the current file, on the Labeling settings tab of the Processing panel, select Clear Existing Labels and then run Labeling as required.
To remove occlusion fixing from your data, in the Marker Editing panel, expand the Restore section and select the required option.
Solve during cleanup
During the cleanup operation, each time you finish cleaning up a range, check its solve. To do this:
- Ensure the range you cleaned up is selected.
- On the Processing tab on the ribbon, click the arrow on the Solve Solving button.
- Click Solve Solving Ranges.
The selected range is solved, enabling you to quickly check that your cleanup has been successful, without having to solve the whole take.
- Proceed to clean up the next range that contains mislabels, gaps or noisy markers, etc.
After you have completed all the cleanup required, finish by solving the entire take. For more information see Solve the data.