How ROIs work in SamuROI

Note

In the following we will use mask as synonym for ROI.

SamuROI comes with a set of predefined types of ROIs. Those are:

• pixel based ROI (samuroi.masks.pixel.PixelMask):

  This roi holds a list of pixels for which the trace is calculated as average over all those pixels.

• circle shaped ROI (samuroi.masks.circle.CircleMask):

  This roi is defined by a center and radius. The resulting trace takes all pixels into account that intersect with the circle.

• branch ROI (samuroi.masks.branch.BranchMask):

  This roi is intended for one dimensional structures within the video data. It provides functionality to be split into child sub segments. Child masks can be accessed with samuroi.masks.branch.BranchMask.children.

• polygon ROI (samuroi.masks.polygon.PolygonMask):

  As the name states, this class represents arbitrary polygon shapes.

• segmentations (samuroi.masks.segmentation.Segmentation):

  This class is rather special, since it is not a real ROI, but a set of rois defined by a 2D array with the same shape as the video resolution.

All of these classes inherit from a common base class samuroi.masks.mask.Mask which requires the derived classes to implement an “apply” function samuroi.masks.mask.Mask.__call__(). Whenever a trace of a roi is calculated this function will be called on the respective roi object.

The samuroi.masks.branch.BranchMask and the samuroi.masks.segmentation.Segmentation also have a set of child masks.

For examples how to work with these classes see Working with ROIs.