Matting

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Matting
Create Matte
Creates a matte, either to one or to multiple layers (Win: Ctrl+Alt+Z, Win [German]: Shift+Z, Mac: macControl+Z).
Quick Track Matte created to a Layer
With one layer selected, this function will create an empty track matte layer to the selected layer. By default, it will be two times the size of the current composition. This is to have extra pixels for when the matte will be parented or animated, so it doesn't get cut off on the edges when moving. If you open up the Settings and go to the Matting tab, you can set another default size for the matte layer.
If the selected layer already has a track matte, Workflower will execute Merge Mattes (see below), so that both mattes will be matted to the selected layer.
By default, mattes are created with Collapse Transformation enabled. In the Matting Settings, you can also disable this option.
Multi-Layer Matte
Matte applied to three Layers at once
With several layers selected, this function will create a Multi-Layer Matte that applies to all selected layers. You have the option of either using a custom matte layer or an already existing layer from the comp.
Group Matte
Creating a Group Matte
A Group Matte applied to every Group Layer
With a group header selected, Workflower will create a Group Matte Layer. By default, the Group Matte Layer is a custom layer, added to the top of the group.
Merge Mattes will be executed on every layer, contained in the group, to apply the Group Matte. (These Matte Merge layers which have been added as the track matte above every group layer and which hold a matting effect, referencing the Group Matte, will be called Group Matte Merge Layers in the following paragraphs. However, Group Matte Merge Layers can also contain other merged mattes.)
You can also choose another layer from the comp as your Referenced Group Matte Layer. Simply choose the desired layer from the dropdown on the Group Matte || Settings effect and hit Refresh Connections. (So note that what is called Referenced Group Matte Layer - the actually visible Group Matte on every layer - can differ from the Group Matte Layer - the custom layer at the top of the group.)
Group Matte Effect
As of version 1.1, when new layers have been added to the group or layers have been released from the group, you have to execute Refresh Layout to add/remove the Group Matte Merge Layers to/from all new/old group layers.
(In prior Workflower versions, or if you have When executing 'Refresh Layout', check whether Group Mattes need to be refreshed disabled (to be found under the Matting Settings), you need to select a group layer or the Group Matte Layer and execute Refresh Connections in order to add/remove the Group Matte Merge Layers to/from the layers.)
If you have sub-groups with Group Mattes themselves, Workflower will apply the Group Matte of the sub-group as well as the Group Matte of the higher group to every layer. 
By default, Group Mattes won't be applied to disabled layers. You can choose to apply them too by going to the Matting Settings and deactivating that setting.
To disable a Group Matte temporarily, just deactivate the effect switch of the Group Matte effect.
Using the Group Header as Referenced Group Matte Layer
(Added in version 1.1)
Using a Mask on the Group Header
You can also use the group header as your Referenced Group Matte Layer. Simply draw masks on the group header and execute Refresh Connections.
(Note: Workflower needs a mask path, not a shape path. However, when you draw a shape path, Refresh Connections will convert it to a mask path.)
If you don't have a Group Matte Layer yet, Workflower will then create it and link the group header as Referenced Group Matte Layer on the Matte Layer control. (If your Group Matte Layer already exists, Workflower will just link the reference.)
Using the group header instead of the Group Matte Layer can be useful if you want to collapse your group and still be able to manipulate the Group Matte.
Please note that only the masks of the group header will be considered. Effects altering the alpha cannot be taken into account as they will already be considered for the Group Linked Adjustment Layer. If you need effects to be taken into account, please use the Group Matte Layer itself or an external layer as your Referenced Group Matte Layer.
By default, the border size of the group header will be expanded to comp size when it holds masks. However, there can be certain situations where the matte could get cut off. To expand the border size, please twirl down the group header and go to Contents > Border > Fill > Size. If you remove the mask/s from your group header, the border size will turn back to the default group header size.
Removing a Group Matte
To remove a Group Matte, either:
1.Select the group header and hit Create Matte again.
2.Use Delete Layer / Clone / Group on the Group Matte Layer.
3.Delete the Group Matte Layer using AE's Delete and then execute Refresh Layout.
4.When using the group header as the Referenced Group Matte Layer, select the group header, remove the mask/s and execute Refresh Connections.
All references to the Group Matte will then be removed from the layers.
If layers have Group Matte Merge Layers which contain only the reference to the deleted Group Matte Layer, the Matte Merge layer and track matte state will be removed.
If multiple matte references on the Matte Merge layer exist, the Matte Merge layer will stay intact, and only the Calculations effect, referencing the Group Matte Layer will be removed. If there's just one matte reference left after removing the reference to the Group Matte Layer, the Matte Merge will be undone and the matte converted back to a single track matte.
(Fixed in version 1.1 ->) Do not simply delete the Group Matte layer. If you would then execute Refresh Layout, the Group Matte will be removed - however, Matte Merge layers will remain above the group layers, even if they have no matting effect left on them. (Tip: If you quickly want to delete empty Matte Merge layers, select them and execute Delete Layer / Clone / Group. This will remove the matte layers as well as the track matte state of the layer below.)
Shying of Group Matte Merge Layers
(Added in version 1.1)
Left: Group Matte Merge Layers visible; Right: Group Matte Merge Layers shy'd (Shy Mattes)
When using a Group Matte, Matte Merge layers will be added above every group layer as a track matte (Group Matte Merge Layers). This, however, makes it more difficult to see the structure of layers. That's why you have the option to shy Group Matte Merge Layers that solely contain Group Matte effects (called Shy Mattes). (This is disabled by default. Go to Settings > Matting to enable it.)
If you want to move a group layer, select it and execute Select Group. This will additionally select the Shy Matte above.
If enabled under Settings > Matting > Temporarily unshy Shy Mattes when executing 'Select Group', all Shy Mattes within your comp will be temporarily unshy'd so that you can move your layers without accidentally moving your layers in between another layer and its Shy Matte. When you execute Refresh Layout afterwards, all Shy Mattes will be shy'd again. 
If Temporarily unshy Shy Mattes is not enabled, the selection icon [   ] will indicate that the Shy Matte above has been selected as well so that you know you can now move your layers. Having the setting disabled guarantees a faster workflow since the layers don't have to be unshy'd. However, you also have to pay more attention so that you don't move your layers in between another layer and its Shy Matte. If you move them in between, Workflower will give you an error message, telling you either to undo your action or to hit Refresh Layout so that track mattes will be arranged correctly.
Illegal Shy Matte Movement Error Message
If you want to temporarily unshy all Shy Mattes but you don't want to select anything via Select Group (or you don't have Temporarily unshy Shy Mattes enabled), you can also execute Unshy Layers. This will unshy all Shy Mattes until the next time you execute Refresh Layout. Useful when you, for example, want to move a layer without an existing Shy Matte into a group with group matte and you want to be able to easily place it at the correct position.
You don't always have to execute Select Group first to select the Shy Matte. The following Workflower functions will consider Shy Mattes even if they are not within the selection:
​Duplicate Group will duplicate the selected layers as well as their Shy Mattes above.
​Create Group will move all selected layers along with their Shy Mattes into the new group.
​Delete Layer / Clone / Group will delete all corresponding Shy Mattes of the selected layers.
Order of Group Mattes, Group Clones, and Group Linked Adjustment Layers
Group Mattes, Group Clones, and Group Linked Adjustment Layers have a specific layer order when used in conjunction. Read up here for more information.
Merge Mattes
Merges multiple mattes into one track matte layer to a layer (Win: Ctrl+Alt+Shift+Z, Mac: no default shortcut).
Creating the Matte Merge Layer
Left: Base and Matte Layers selected before Matte Merge; Right: The created Matte Merge Layer and Matte Collection Group
First, select the layer you want the mattes to be matted to. If the layer already has a track matte, you can also select the track matte. After that, select your desired matte layers and hit Merge Mattes. A Matte Merge Layer will be created and used as a track matte for the layer that the mattes should be matted to. On the Matte Merge Layer, matting effects, using AE's Calculations effect, for each matte layer will have been created. If the matte layers are directly above the base layer and are disabled, they will be put into a Matte Collection Group. (For more information on this, see below.)
If the matte layers have Collapse Transformation enabled, or have comp dimensions and are unmoved, the matte effects on the Matte Merge Layer will reference those layers directly. For all other matte layers, a Precomp Clone of the layer will be created in order to fit it to comp dimensions.
(Fixed in version 1.0.4 ->) As of now, when changing the comp size, Matte Merge layers will not be adjusted to the new size automatically. To make the Matte Merge layer work again, you need to go to its Solid Settings and hit Make Comp Size. It is recommended to disable Affect all layers that use this solid. (Only when you are sure that no Workflower layer other than the Matte Merge layers of the comp with a new size use this solid, you may enable Affect all layers that use this solid.)
Modifying Mattes
Multiple Matting Effects
On the Matte Merge Layer, you can use the Calculations effects to modify your mattes by changing the blending modes (either to Normal, Stencil Alpha, Stencil Luma, Silhouette Alpha, or Silhouette Luma), the opacity, the inverted state, and the matte order by moving the Calculations effects around.
Modifying Matte Source Layers
Matte Layer Settings Effect
To all matte source layers, a Matte Layer Settings effect will be applied. Using the effect, you can choose whether in/out points should be respected and modify the blending mode, inverted state, and opacity. Modifying these states on the layer itself - as compared to modifying it on the Matte Merge Layer effect - is useful when having a matte that is applied to multiple layers so that changes don't have to be made on each Matte Merge Layer individually.
Invisible Mattes
On the Matte Layer Settings effect, you also have the option to enable Invisible Matte. That means that the layer will be set to 0% opacity while it is still enabled. That way, the layer will behave like a regular track matte: It is not visible but you can move it with your cursor around in the composition viewer (which would not be possible with a disabled layer).
You can also very quickly show the layer itself again by clicking on Show Matte. This will temporarily set the opacity back to its actual value.
On Invisible Mattes, you can't set the Opacity on the Matte Layer Settings effect to From this Layer (since it will be at 0% opacity). You can only set it to either Custom Opacity or From Matte Merge Layer Effect.
Layers that are put into a Matte Collection Group will be set to Invisible Matte. Other matte source layers won't be set to Invisible Matte by default, however.
Adding new Mattes
To add new mattes to an already existing Matte Merge Layer, simply select the Matte Merge Layer first (or its matted layer), then the new matte layers, and hit Merge Mattes again. You can also add new mattes using Add / Remove Layer References. (Be aware, though, that, using this function, the order of selection is reversed.)
As of version 1.1, the blending mode of new mattes added to the Matte Merge Layer will be set to Stencil Alpha by default. (In prior versions it would have been set to Normal.)
If you select either the matted layer or the Matte Merge Layer and execute Create Matte, an empty matte will be created to the Matte Merge.
Updating Effect Names & Clones
If you have no layer selected and you execute Merge Mattes, all matting effects on the Matte Merge Layer will be renamed to the current name of the referenced layer. Perform this action after having changed layer names and then working on the Matte Merge Layer since it is difficult to read the layer name from the layer control on the matting effect.
When executing Merge Mattes with no layer selected, all unused matte clones will be deleted, too. 
Matte Collection Groups
A Matte Collection Group above the Matte Merge Layer
Creating a Matte Collection Group
If the selected matte layers are directly above the layer that they should be matted to AND they are disabled, a Matte Collection Group will be created above the Matte Merge Layer, into which the matte layers will be put. The Matte Collection Group always needs to stay directly above the Matte Merge Layer if new mattes should be put into it as well. If new mattes are added to the Matte Merge Layer and the Matte Collection Group is not directly above, they won't be automatically added. (However, you can of course still put them into the group yourself.)
All layers that are put into the Matte Collection Group will be turned into an Invisible Matte. Read up more about Invisible Mattes here. (On the other hand, layers that are not put into a Matte Collection Group, won't be turned into Invisible Mattes.)
You can disable the creation of Matte Collection Groups too by going to the Matting Settings.
Properties of Matte Collection Groups
A Matte Collection Group differs from a normal group insofar that it inherits the label color from its containing group, as well as its parent if the containing group is a parented group.
If Precomp Clones are created for a Matte Merge, they will be put into a custom Matte Clone Collection Group.
Matte Collection Groups are symbolized by the Icon ∆, Matte Clone Collection Groups by ∆∆.
Converting Matte Collection Groups
You can convert a regular group to a Matte Collection Group by selecting it and hitting Merge Mattes. If you select a Matte Collection Group and hit Merge Mattes, it will convert it to a Matte Clone Collection Group - but only if it doesn't already exist - otherwise, it will just convert it back to a regular group. If you select a Matte Clone Collection Group and hit Merge Mattes, it will convert it to a regular group.
Select Shy Matte
(Added in version 1.1)
To select Shy Mattes, select the desired group layers which have Shy Mattes above and execute Select Group.
Unshy Layers
(Added in version 1.1)
Temporarily unshys Matte Merge layers that only have Group Matte effects applied to them, a.k.a. Shy Mattes (Win: Alt+F5, Mac: no default shortcut).
Useful when you, for example, want to move a layer without an existing Shy Matte into a group with group matte and you want to be able to easily place it at the correct position.
If you execute Refresh Layout afterwards, all Shy Mattes will be shy'd again.
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Miscellaneous Group Functions
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Outline
Creating the Matte Merge Layer
Modifying Mattes
Modifying Matte Source Layers
Adding new Mattes
Updating Effect Names & Clones
Matte Collection Groups
Select Shy Matte
Unshy Layers