Amplitude arrays incorrectly filled in diagrams.Amplitude

[ulupo]

Description

The transform method in diagrams.Amplitude calls the _parallel_pairwise utility function for joblib-parallel computation of amplitudes of persistence diagrams. This function first calculates all amplitudes for different homology dimensions and across different slices of the input array of diagrams:

https://github.com/giotto-learn/giotto-learn/blob/a5f2024375fd24c84614b9b77ffc39e79cb71cac/giotto/diagrams/_metrics.py#L204

Then, we have to carefully arrange all amplitudes into an array of the correct shape:

https://github.com/giotto-learn/giotto-learn/blob/a5f2024375fd24c84614b9b77ffc39e79cb71cac/giotto/diagrams/_metrics.py#L210

Unfortunately, the final result at present is incorrect, primarily because the top for in the call to Parallel is on the slices, while it should be on the list of homology dimensions. Changing the order of the for loops as well as replacing the final line before return with

amplitude_arrays = np.concatenate(amplitude_arrays).reshape(len(homology_dimensions), X.shape[0]).T

woud yield correct results.

Steps/Code to Reproduce

Create

diagrams = np.array([
    [[0, 1, 0.],
     [0, 0, 0.],
     [0, 4, 1.]],  # Expected bottleneck ampl: [sqrt(2)/2, 2*sqrt(2)] 
    
    [[0, 2, 0.],
     [0, 1, 0.],
     [0, 0, 1.]],  # Expected bottleneck ampl: [sqrt(2), 0] 
    
    [[3, 3.5, 0.],
     [0, 0, 0.],
     [5, 9, 1.]]  # Expected bottleneck ampl: [0.5*sqrt(2)/2, 2*sqrt(2)] 
])

Expected Results

The expected amplitude array when using bottleneck amplitude is

array([[0.70710678, 2.82842712],
       [1.41421356, 0.        ],
       [0.35355339, 2.82842712]])

Actual Results

The current result is

array([[0.70710678, 1.41421356],
       [2.82842712, 0.        ],
       [0.35355339, 2.82842712]])

Versions

giotto-learn: 0.1.2