The problem with unaligned regions can occur if there are not enough tie points between subsets. If some of such image subsets of the complete dataset are not aligned with each other, they will be grouped into individually aligned parts (so-called "Components"). The components are displayed as a tree structure in the chunk's contents of the Workspace pane. The components feature has been implemented starting from Agisoft Metashape 1.7.0.
The tutorial describes the basic steps to follow in order to align and merge alignment components with the help of markers (available only in the Professional edition).
For the sample dataset, we have used the images of the sports shoe, which consists of the two sub-sets captured in the same conditions: of the top part and bottom part. All images have been processed in a single chunk.
1. Select Align Photos from the Workflow menu.
Working with components
In each of the components, a hint with an epipolar line works, so the markers can be placed rather quickly. Having placed a marker on the first image (using Place Marker > New Marker command from the context menu in the Photo view mode), on the next image there will be a line along which this point has to be searched. When the proper location is found use the corresponding marker label in the context menu Place Marker section of the Photo view.
After defining two projections of the marker, on the remaining images of this component, there will already be a gray flag that suggests the marker projection location, so you just need to pin it on a couple of additional images (click on the gray flag and drag to the proper location - the projection will be then highlighted with the green flag).