--- title: "Fix common labeling issues" canonical: "https://help.vicon.com/space/Shogun110/13074530/Fix%20common%20labeling%20issues" format: markdown --- The following basic procedures are just a few of the ways in which you can use Shogun Post to clean up data. > Macro (scroll-only) > > > Macro (toc) See also: > Macro (inline-media-image) [Vicon Shogun 1.3 Post Tutorial - Gap List & Auto Rigid Fill](https://youtu.be/U3jmKTqykOE) on YouTube. > Macro (scroll-pagebreak) > Macro (scroll-ignore) > > > Macro (widget) ## Identify issues 1. 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. 2. 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). 3. 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](https://www.youtube.com/watch?v=BBCqKjJ4ASc), 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 1. Ensure the **Labeling** panel is displayed. 2. Split the **3D Scene** view (at the top right of the Shogun Post window, select the vertical split button > Macro (inline-media-image) ) 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. > Macro (inline-media-image) 3. In the **Labeling** panel, ensure **Select** mode, Forward direction (**>**), and **Cliff** are selected. 4. 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). 5. 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. 6. 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. ![image](media://c0c26882-89dc-4739-b263-e10323e2a40d) > Macro (scroll-pagebreak) ## Label an unlabeled marker 1. 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**. 2. 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. 3. 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](https://vicon-help.atlassian.net/wiki/spaces/Shogun110/pages/13074970)). ## 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.) ![image](media://c5047bd3-5e88-45a8-b4e5-8db1152747ae) 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. ![image](media://e0e343f0-970c-45d9-a1bc-579608dbf87c) When you select a gap in the list, it is automatically displayed in the Graph view, enabling you to edit it. ![image](media://432e0e1e-bff0-488b-a471-f6b4055c0530) > Macro (scroll-pagebreak) 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](#AutoFillRigid)). - 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](#ManualGapFill)). :check_mark: **Tip**: To undo unwanted gap-filling, click Undo on the quick access toolbar > Macro (inline-media-image) . > Macro (anchor) ## 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. ![image](media://b68fa316-b130-4004-a4a7-e60e4114b1c9) This process is also available via scripting, using the [selectMarkersForRigidFill](https://vicon-help.atlassian.net/wiki/spaces/Shogun110/pages/13075883) command to select the markers and the [autoFillGaps](https://vicon-help.atlassian.net/wiki/spaces/Shogun110/pages/13075160) command to fill them. For information on these commands, see *HSL scripting with Vicon Shogun*. > Macro (scroll-pagebreak) **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: 1. 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. 2. Select a marker with a gap. 3. Ensure the current time is in the gap. 4. 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: 1. 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. 2. 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. 3. Select **Auto-select markers for fill** and ensure the options are as required (see above). 4. 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. > ℹ️ **Note** > ℹ️ 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. > Macro (scroll-pagebreak) > Macro (anchor) ## 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: ![image](media://99fa1aeb-f611-454e-ac9d-71ae17de3274) 1. 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). 2. 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 > Macro (inline-media-image) at the top of the Shogun Post window and change the views in the new panes. 3. If the **Marker Editing** panel is not already open, on the **Processing** tab on the ribbon, selecting **Marker Editing**. 4. In the **Data Health** view, find the relevant marker's line, which shows a gray rectangle that represents the gap. 5. In the **Data Health** view, double-click to select the range of the gap. 6. 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. 7. In the **3D Scene** view and **Graph** view, check that your fill has given the required result. 8. If the fill does not give an appropriate result, you can click Undo on the quick access toolbar > Macro (inline-media-image) , and try other gap-filling options in the **Marker Editing** panel (see [Options for gap filling](#GapFillOptions)). > Macro (scroll-pagebreak) > Macro (anchor) ### Options for manual gap-filling The appropriate option to use depends on the type of gap that you want to fill. > Macro (scroll-only) > > > Macro (toc) ##### Short gaps 1. Manually select a short gap by double-clicking in a **Graph** view or**Data 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. 2. Check that the result looks reasonable in a **3D Scene** view and **Graph** view. ##### Sequence of short gaps 1. 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. 2. In the **Fill Using Interpolation** area, select **Selected Ranges**, and then click **Fill Using Interpolation**. > Macro (scroll-pagebreak) #### 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. 1. 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. 2. In the **Marker Editing** panel, expand the **Fill Gaps** section. 3. In the **Fill Rigid** area, select **Selected Ranges** and select **Fill Rigid**. The pattern of the present markers is copied onto the missing marker. 4. 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. > Macro (scroll-pagebreak) #### 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.