Exemplo n.º 1
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def filter(input, output, **kwargs):

    # Load the input streamlines using the requested parameters.
    streamlines = load(input)
    streamlines.filter(**kwargs)

    # Save the streamlines to the output file.
    save(streamlines, output)
Exemplo n.º 2
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def merge(inputs, output):

    # Load all the input streamlines and merge them.
    streamlines_list = [load(i) for i in inputs]
    streamlines = reduce(operator.iadd, streamlines_list)

    # Save the streamlines to the output file.
    save(streamlines, output)
Exemplo n.º 3
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    def setUpClass(cls):
        """Generates streamlines files used to test the CLI"""

        cls.test_dir = tempfile.TemporaryDirectory()

        # A file with all short streamlines.
        streamlines = Streamlines([
            np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]]),
            np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0]]),
            np.array([[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]]),
        ])
        filename = os.path.join(cls.test_dir.name, 'short.trk')
        save(streamlines, filename)

        # A file with a single random streamline.
        streamlines = Streamlines([
            np.random.randn(100,3)
        ])
        filename = os.path.join(cls.test_dir.name, 'random.trk')
        save(streamlines, filename)

        # A file with no streamlines.
        streamlines = Streamlines()
        filename = os.path.join(cls.test_dir.name, 'empty.trk')
        save(streamlines, filename)

        # A file with a bundle.
        points = np.array([
            np.linspace(0, 100, 1000),
            np.zeros((1000,)),
            np.zeros((1000,))]).T
        points_list = [points + np.random.randn(*points.shape)
                       for _ in range(100)]

        streamlines = Streamlines(points_list)
        filename = os.path.join(cls.test_dir.name, 'bundle.trk')
        save(streamlines, filename)

        # Also save the bundle with flipped orientations.
        flip = [np.random.rand() < 0.5 for _ in points_list]
        flip[0] = False
        points_list = [p[::-1] if f else p for f, p in zip(flip, points_list)]
        streamlines = Streamlines(points_list)
        filename = os.path.join(cls.test_dir.name, 'bundle-flipped.trk')
        save(streamlines, filename)
Exemplo n.º 4
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def filter(input_filename, output_filename, **kwargs):
    """Removes streamlines from a file based on features

    Removes streamlines from a file based on their features. For example,
    remove all streamlines with a length below 50mm using --min-length 50.

    Args:
        input_filename: The file that contains the streamlines to filter.
        output_filename: The file where the remaining streamlines will be
            saved.

    """

    # Load the input_streamlines using the requested parameters.
    streamlines = load(input_filename)
    streamlines.filter(**kwargs)

    # Save the streamlines to the output file.
    save(streamlines, output_filename)
Exemplo n.º 5
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def smooth(input_filename, output_filename, **kwargs):
    """Smooths streamlines in a file

    Smooths streamlines using a least square b-spline. The distance between
    knots controls the smoothness of the output streamline with larger
    distances being smoother

    Args:
        input_filename: The file that contains the streamlines to smooth.
        output_filename: The file where the smoothed streamlines will be saved.

    """

    # Load the input streamlines using the requested parameters.
    streamlines = load(input_filename)
    streamlines.smooth(**kwargs)

    # Save the streamlines to the output file.
    save(streamlines, output_filename)
Exemplo n.º 6
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def transform(input, output):
    """Transforms streamlines from one fileformat to another"""
    streamlines = load(input)
    save(streamlines, output)