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How can I filter contour lines and draw/erase shapes

Hello! Firstly I must admit the title it is not good. I hope that you can help me solving my problem and chaging the title.

After doing image processing I got this output: image description

As you see in detail, there points which has irregular shapes:

image description

My final goal is from this: image description

Achieving something like this:

image description

I don't know how to do it. If I need to filter/smoothe the contour lines and then apply a rectangle shape, for instance, or if there is a way to go straight forward without applying any filter.

During the image process I was able to collect some keypoints, as you can see, When I plotted them they are in between contours on the center of the irregular shape. The figure show them bigger than they really are, because it was created from matplotlib.

image description