The following basic procedures are just a few of the ways in which you can use Shogun Post to clean up data.

See also: Vicon Shogun 1.3 Post Tutorial - Gap List & Auto Rigid Fill on YouTube.

Identify issues

To help you identify issues, in the 3D Scene view, select View Filters, and ensure that in the Scene section, Missing Markers is selected. Also ensure that in the Subjects section, Label is selected and that in the L(abeling) column of the views matrix, Constraints is selected.
In 3D Scene 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 3D Scene view. Look for any swapped markers (for an example, see the Vicon video 5 - Shogun Post – Labeling Data, which shows an example of a swap of knee and heel markers).

Missing markers are clearly visible, and 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 3D Scene view (at the top right of the Shogun Post window, select the vertical split button ) and in one of the panes, change to a Graph view, so that you can now see a 3D Scene view, a Graph view and the Labeling panel.
In the Labeling panel, ensure Select mode, Forward direction (>), and Cliff are selected.
In the 3D Scene 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 where the swap happens (this should be identifiable on the graph by a sharp change).
From the position of the marker in the 3D Scene 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 3D Scene view, the Selection text displays the name of the selected marker.
Select the wrongly labeled marker in the 3D Scene view and then select the correct marker name in the Labeling panel list.

The marker is now correctly labeled. To check, scrub back and forward in the 3D Scene 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 3D Scene view, select the unlabeled marker. Scrub back and forward to identify where it is correctly labeled. This is the point at which it is correctly colored in the 3D Scene 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:
1. In the Manual Labeling Options section, in the Mode line, select Label.
2. In the marker list in the Labeling panel, select the name of the marker and then in the 3D Scene view, select the marker that is currently unlabeled.
Or, if you prefer to label by dragging, using Select mode:
1. In the Manual Labeling Options section, in the Mode line, ensure Select mode is selected.
2. In the Labeling panel, select the required marker in the 3D view.
3. SHIFT+CTRL then click+drag from the selected marker in the Labeling panel to the unlabeled marker in the 3D Scene view.
As before, to check the labeling, scrub back and forward in the 3D Scene 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).

View and select gaps

You can view all the gaps in your scene in the Marker Editing panel, in the Fill Gaps section, by looking at the Gap List. (If you can't see the list, at the top of the Marker Editing panel, click the Gap List button.)

To make it easy to find the longest gaps, click the Length column heading to rearrange the list, with the longest gap at the top.

When you select a gap in the list, it is automatically displayed in the Graph view, enabling you to edit it.

You can then decide the best approach for filling the gaps:

As a first step, try automatically filling as many gaps as possible (see Auto-fill with intelligent rigid fill).
If your scene still contains gaps after using the automatic fill, or if auto-fill is unsuitable, try manually filling the gaps (see Manually fill gaps).

Tip: To undo unwanted gap-filling, click Undo on the quick access toolbar .

Auto-fill with intelligent rigid fill

Shogun Post enables you to automatically fill gaps using a rigid fill operation. This looks at all the markers in your scene and then compares them against the marker you are trying to fill. It then uses a combination of similarly moving markers to fill the gap. Finally, it checks the fill to make sure it looks correct and if not, it chooses another set of markers.

This process is also available via scripting, using the selectMarkersForRigidFill command to select the markers and the autoFillGaps command to fill them. For information on these commands, see HSL scripting with Vicon Shogun.

To auto-fill a selected marker:

The following procedure for rigid gap-filling is semi-automated, in that you choose a marker for the fill:

In the Marker Editing panel, expand the Fill Gaps section and in the Fill Rigid area, select the Auto-select markers for fill check box.
To change the default options for auto-selection, click the Show Options button next to the check box. The options are:
- Max Deviation: Specifies in mm how rigid the set of markers used to fill must be, as the maximum deviation in distance between all pairs in the set. For example, a value of 60 enables the markers to flex in rigidity by 6 cm.
- Max Distance: Specifies in mm how far away the candidate can be from the selected marker. The default of900 is just under 3 feet (1 m), because a greater distance is likely to be another subject or body part, which is unlikely to move rigidly during the gap.
- Percent Time Rigid: Specifies the percentage of time over the adjacent fragment ranges that the selected marker must be rigid with the chosen set. The default of 0.75 means 75% of the time.
Select a marker with a gap.
Ensure the current time is in the gap.
Select Fill Rigid.
Gaps are filled using the intelligent rigid fill.

To auto-fill selected markers or all markers:

In addition to the semi-automated procedure described above, you can also automatically fill all gaps on either all markers, or only those currently selected. To do this:

Depending on which markers you want to fill:
- Only selected markers. Ensure you have selected the required markers.
- All markers. Ensure no markers are selected.
In the Marker Editing panel, expand the Fill Gaps section and in the Fill Rigid area, select the Current Frame, Selected Ranges or All Time option.
Select Auto-select markers for fill and ensure the options are as required (see above).
Click Fill Rigid.

All gaps on the selected markers, or on all markers if no markers are selected, are filled over the play range, or selected ranges.

Note that in the case of all markers, only labeled markers are filled, though unlabeled markers can be auto-selected for filling the labeled marker.

Note
After running automated gap-filling, if Shogun did not find a set of rigid markers based on the settings, you may find that not all gaps are filled. You can either fill the remaining gaps manually, or you can try changing the settings, specifically by increasing Max Deviation from the default.

You can run automated gap-filling multiple times to achieve the required results, in particular, when:

After first run, it either made an unwanted fill or wasn't able to fill a gap due to a mislabel. Fix the mislabel and then run it again to fill the remaining gaps.
After first run, it either made an unwanted fill or wasn't able to fill a gap due to the gap being too complex. Fill the gap manually, then run automated gap-filling again to fill any remaining gaps. These can now can be filled due to more data being available.
After first run, some gaps remain. Loosen the rigidity settings (see Note above) and run it again.

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 3D Scene 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 3D Scene 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 3D Scene view, split the screen by selecting 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, selecting 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. In the Fill Using Interpolation area, select Selected Ranges (to fill only the current selection), and then select 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 3D Scene 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 , and try other gap-filling options in the Marker Editing panel (see Options for gap filling).

Options for manual gap-filling

The appropriate option to use depends on the type of gap that you want to fill.

Short gaps

Manually select a short gap by double-clicking in a Graph view orData Health view, and in the Marker Editing panel, expand the Fill Gaps section and 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 3D Scene view and Graph view.

Sequence of short gaps

For a sequence of small gaps with a smooth line running through the gap in the Graph view, ALT+drag to select the affected data.
In the Fill Using Interpolation area, select Selected Ranges, and then click Fill Using Interpolation.

Non-linear motion

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.

To select the range of the gap, double-click in a Graph view orData Health view, then select (CTRL+click) the three other markers in the rigid object.
In the Marker Editing panel, expand the Fill Gaps section.
In the Fill Rigid area, select Selected Ranges and select Fill Rigid.
The pattern of the present markers is copied onto the missing marker.
As usual, check in the Graph view and in a 3D Scene view that the fill looks sensible.

Other rigid objects you can use in a default marker set include hands, forearm, upper arm, shoulders, thorax, and head.

Non-linear motion where rigid fill is 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 3D Scene view), are in sensible locations.

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