Your pet door has two major parts: the frame and the flap. The inner and outer parts of the frame fit together in the cutout to hold the flap in place. The flap is the part that covers the cut-out hole in the door, the part your pet goes through to use the door.
Please note that all measurements are approximate and prone to user error, so don't worry if you measure your door and your measurements aren't exactly the same as the dimensions given online or in your manual. Your door's dimensions will also change over time; doors expand and contract, and flaps may shrink or warp.
Outer Frame: The outer measurements of the door's frame.
Flap Opening: The measurement of the part of the door your pet goes through. This is not the measurement of the flap itself, but the space your pet has to go into. This is measured using the interior door frame.
Flap Size: The overall measurements of the door flap.
Cut-Out Size: The hole you cut in your door to install the door. After installation, you can get this measurement again by taking the pet door out.