Cannot create edgelist #2
Description
Trying to reproduce the results you provided as in SkeletonMatching.ipynb
Running on: Google Colab
The errors while creating edgelist using
_, edgeList1, _, _, _, _, _, _ = skeleton2Graph(s1,s1)are as follows
/content/SkeletonMatching/skeleton2Graph.py:260: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
skeletonTemp[edgePoints.T.tolist()] = - edgeNumber
/content/SkeletonMatching/skeleton2Graph.py:288: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
skeletonTemp[edgePoints.T.tolist()] = - edgeNumber
/content/SkeletonMatching/skeleton2Graph.py:313: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
endGaussianValue = gaussianKernelMatrix[vector2EndGaussian.T.tolist()]
/content/SkeletonMatching/skeleton2Graph.py:314: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
endFluxValue = fluxMap[np.array(edgePoints).T.tolist()] * endGaussianValue
/content/SkeletonMatching/skeleton2Graph.py:318: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
startGaussianValue = gaussianKernelMatrix[vector2StartGaussian.T.tolist()]
/content/SkeletonMatching/skeleton2Graph.py:319: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
startFluxValue = fluxMap[np.array(edgePoints).T.tolist()] * startGaussianValue
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
[<ipython-input-6-ae6ce59447cc>](https://localhost:8080/#) in <module>()
1 s1 = mat2gray(io.imread(os.path.join(os.getcwd(), 'SkeletonMatching/img/s1.png'),as_gray=True)).astype('float64')
2 s2 = mat2gray(io.imread(os.path.join(os.getcwd(), 'SkeletonMatching/img/s2.png'),as_gray=True)).astype('float64')
----> 3 _, edgeList1, _, _, _, _, _, _ = skeleton2Graph(s1,s1)
4 _, edgeList2, _, _, _, _, _, _ = skeleton2Graph(s2,s2)
5 s1Tangent, s1PointsList = sc.skeletonTangentEstimate(edgeList1)
[/content/SkeletonMatching/skeleton2Graph.py](https://localhost:8080/#) in skeleton2Graph(skeleton, fluxMap, sigma)
327 if (~ edgeLinkedNumber.any()):
328 continue
--> 329 edgeLinkedLength = np.array(edgeLength)[map(int, list(np.abs(edgeLinkedNumber) - 1))].tolist()
330 searchDepth = min(edgeLinkedLength)
331 for el in edgeLinkedNumber:
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices