segtools.py 文件源码

def roi_from_bbox(
        input_file,
        bbox,
        output_file):
    """ Create a ROI image from a bounding box.

    Parameters
    ----------
    input_file: str
        the reference image where the bbox is defined.
    bbox: 6-uplet
        the corner of the bbox in voxel coordinates: xmin, xmax, ymin, ymax,
        zmin, zmax.
    output_file: str
        the desired ROI image file.
    """
    # Load the reference image and generate a grid
    im = nibabel.load(input_file)
    xv, yv, zv = numpy.meshgrid(
        numpy.linspace(0, im.shape[0] - 1, im.shape[0]),
        numpy.linspace(0, im.shape[1] - 1, im.shape[1]),
        numpy.linspace(0, im.shape[2] - 1, im.shape[2]))
    xv = xv.astype(int)
    yv = yv.astype(int)
    zv = zv.astype(int)

    # Intersect the grid with the bbox
    xa = numpy.bitwise_and(xv >= bbox[0], xv <= bbox[1])
    ya = numpy.bitwise_and(yv >= bbox[2], yv <= bbox[3])
    za = numpy.bitwise_and(zv >= bbox[4], zv <= bbox[5])

    # Generate bbox indices
    indices = numpy.bitwise_and(numpy.bitwise_and(xa, ya), za)

    # Generate/save ROI
    roi = numpy.zeros(im.shape, dtype=int)
    roi[xv[indices].tolist(), yv[indices].tolist(), zv[indices].tolist()] = 1
    roi_im = nibabel.Nifti1Image(roi, affine=im.get_affine())
    nibabel.save(roi_im, output_file)