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utils

is_overlapping(patch1, patch2)

Check if two patches are overlapping.

Parameters:

Name Type Description Default
patch1 list of tuples

A list of tuples representing the ranges of each axis in patch1.

 required
patch2 list of tuples

A list of tuples representing the ranges of each axis in patch2.

 required

Returns:

Name Type Description
bool

True if the two patches overlap, False otherwise.
Note

This function assumes that each patch is represented by a list of tuples, where each tuple represents the range of an axis in the patch. The range of an axis is represented by a tuple (start, end), where start is the start value of the range and end is the end value of the range. The patches are considered overlapping if there is any overlap in the ranges of their axes.

Source code in fmcib/datasets/utils.py 
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def is_overlapping(patch1, patch2):
    """
    Check if two patches are overlapping.

    Args:
        patch1 (list of tuples): A list of tuples representing the ranges of each axis in patch1.
        patch2 (list of tuples): A list of tuples representing the ranges of each axis in patch2.

    Returns:
        bool: True if the two patches overlap, False otherwise.

    Note:
        This function assumes that each patch is represented by a list of tuples, where each tuple represents the range of an axis in the patch.
        The range of an axis is represented by a tuple (start, end), where start is the start value of the range and end is the end value of the range.
        The patches are considered overlapping if there is any overlap in the ranges of their axes.
    """
    overlap_by_axis = [max(axis1[0], axis2[0]) < min(axis1[1], axis2[1]) for axis1, axis2 in zip(patch1, patch2)]

    return np.all(overlap_by_axis)

resample_image_to_spacing(image, new_spacing, default_value, interpolator='linear')

Resample an image to a new spacing.

Source code in fmcib/datasets/utils.py 
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def resample_image_to_spacing(image, new_spacing, default_value, interpolator="linear"):
    """
    Resample an image to a new spacing.
    """
    assert interpolator in SITK_INTERPOLATOR_DICT, (
        f"Interpolator '{interpolator}' not part of SimpleITK. "
        f"Please choose one of the following {list(SITK_INTERPOLATOR_DICT.keys())}."
    )

    assert image.GetDimension() == len(new_spacing), (
        f"Input is {image.GetDimension()}-dimensional while " f"the new spacing is {len(new_spacing)}-dimensional."
    )

    interpolator = SITK_INTERPOLATOR_DICT[interpolator]
    spacing = image.GetSpacing()
    size = image.GetSize()
    new_size = [int(round(siz * spac / n_spac)) for siz, spac, n_spac in zip(size, spacing, new_spacing)]
    return sitk.Resample(
        image,
        new_size,  # size
        sitk.Transform(),  # transform
        interpolator,  # interpolator
        image.GetOrigin(),  # outputOrigin
        new_spacing,  # outputSpacing
        image.GetDirection(),  # outputDirection
        default_value,  # defaultPixelValue
        image.GetPixelID(),
    )  # outputPixelType

slice_image(image, patch_idx)

Slice an image.

Source code in fmcib/datasets/utils.py 
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def slice_image(image, patch_idx):
    """
    Slice an image.
    """

    start, stop = zip(*patch_idx)
    slice_filter = sitk.SliceImageFilter()
    slice_filter.SetStart(start)
    slice_filter.SetStop(stop)
    return slice_filter.Execute(image)