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python - How to convert NumPy arrays obtained from cv2.findContours to Shapely polygons?

I am using CV2 to find contours from an image and then converting them into polygons using Shapely. I am currently stuck because when I try putting one of the contour arrays into Polygon() from Shapely it throws an unspecified error.

I have double-checked that I imported everything I needed, and that creating a Shapely polygon works when I manually enter the array coordinate points.

Here is the problematic section of the code:

contours, hierarchy = cv2.findContours(thresh, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_SIMPLE)
testcontour = contours[1]

ply = Polygon(testcontour)

Where the list of contours looks like this:

contours = [np.array([[[700, 700]],
                      [[700, 899]],
                      [[899, 899]],
                      [[899, 700]]]), 
            np.array([[[774, 775]], 
                      [[775, 774]],
                      [[824, 774]],
                      [[825, 775]],
                      [[825, 824]],
                      [[824, 825]],
                      [[775, 825]],
                      [[774, 824]]]), 
            np.array([[[200, 200]],
                      [[200, 399]],
                      [[399, 399]],
                      [[399, 200]]]), 
            np.array([[[274, 275]],
                      [[275, 274]],
                      [[324, 274]],
                      [[325, 275]],
                      [[325, 324]],
                      [[324, 325]],
                      [[275, 325]],
                      [[274, 324]]])]

The error I get is:

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-65-4124f49b42e1> in <module>
----> 1 ply = Polygon(testcontour)

~AppDataLocalContinuumanaconda3envsgeocomplibsite-packagesshapelygeometrypolygon.py in __init__(self, shell, holes)
    238 
    239         if shell is not None:
--> 240             ret = geos_polygon_from_py(shell, holes)
    241             if ret is not None:
    242                 self._geom, self._ndim = ret

~AppDataLocalContinuumanaconda3envsgeocomplibsite-packagesshapelygeometrypolygon.py in geos_polygon_from_py(shell, holes)
    492 
    493     if shell is not None:
--> 494         ret = geos_linearring_from_py(shell)
    495         if ret is None:
    496             return None

~AppDataLocalContinuumanaconda3envsgeocomplibsite-packagesshapelyspeedups\_speedups.pyx in shapely.speedups._speedups.geos_linearring_from_py()

AssertionError: 
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by (71.8m points)

The problem is that for some reason cv2.findContours returns each contour as a 3D NumPy array with one redundant dimension:

>>> contours[1]
array([[[774, 775]],
       [[775, 774]],
       [[824, 774]],
       [[825, 775]],
       [[825, 824]],
       [[824, 825]],
       [[775, 825]],
       [[774, 824]]])

but Shapely expects a 2D array in this form (see the docs):

array([[774, 775],
       [775, 774],
       [824, 774],
       [825, 775],
       [825, 824],
       [824, 825],
       [775, 825],
       [774, 824]])

So, what we can do is to use np.squeeze to remove that redundant dimension, and use the result to obtain our polygon:

import numpy as np
from shapely.geometry import Polygon

contour = np.squeeze(contours[1])
polygon = Polygon(contour)
print(polygon.wkt)
# POLYGON ((774 775, 775 774, 824 774, 825 775, 825 824, 824 825, 775 825, 774 824, 774 775))

In case if you want to convert all of the contours at once, I would do it like this:

contours = map(np.squeeze, contours)  # removing redundant dimensions
polygons = map(Polygon, contours)  # converting to Polygons
multipolygon = MultiPolygon(polygons)  # putting it all together in a MultiPolygon

The resulting multipolygon will look like this:

enter image description here

And to get the second polygon from here you would just write:

my_polygon = multipolygon[1]
print(my_polygon.wkt)
# POLYGON ((774 775, 775 774, 824 774, 825 775, 825 824, 824 825, 775 825, 774 824, 774 775))

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