add --json option and associated logic

closes #6 (closed)

requested review from @mwebster

assigned to @thanayik

Why not template print_value on value type, so you can skip all the string val=blah lines and call directly with value?

        string val = to_string(nzmean);
        print_value(sarg, val, json, jsonOutput);

But in this case the logic to deal with vectors is multiplied, the vector call would be a specialisation. Did the compiler have issues with any other input type? The other approach is to use a stringstream as an intermediary to exploit the << operator.

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• 08e56c46 - add previous avwutils tests and new fslstats test

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I have added all previous avwutils tests from the pyfeeds-tests repo.

There is also a new test for fslstats. I have confirmed that the output for the current fslstats and my proposed changes are identical. See linked files on this comment.

feedsRun_current.log

feedsRun_proposed.log

@mwebster please let me know if you're cool with these tests. If so, I will add a new commit with the final test for the new --json option flag.

changed the description

@thanayik Have you ran the test script on Linux? I suspect that the numpy rng will produce different results on different platforms, so your current approach may not be viable. Perhaps a sufficient test would be to use an image with known (instead of random) data? e.g.:

# taken from fslchpixdim test
def create_image(shape, pixdim):
    pixdim = list(pixdim)
    data   = np.arange(np.prod(shape).reshape(shape).astype(np.float32)
    hdr    = nib.Nifti1Header()
    hdr.set_data_dtype(np.float32)
    hdr.set_data_shape(shape)
    hdr.set_zooms(pixdim[:len(shape)])

    return nib.Nifti1Image(data, np.eye(4), hdr)

mentioned in merge request pyfeeds-tests!53 (merged)

marked this merge request as draft

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• df55aff5 - add json lib; update unit tests; add lfs

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resolved all threads

marked this merge request as ready

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• 475ab8aa - TEST: avscale is part of flirt, not avwutils

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• 6ed1dff6 - add json tests; code cleanup;

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• 2eb99bb1 - update expected values for FSL 6.0.6.5

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merged