myshow.py

import SimpleITK as sitk
import matplotlib.pyplot as plt


def myshow(img, title=None, margin=0.05, dpi=80):
    nda = sitk.GetArrayFromImage(img)
    spacing = img.GetSpacing()

    if nda.ndim == 3:
        # fastest dim, either component or x
        c = nda.shape[-1]

        # the the number of components is 3 or 4 consider it an RGB image
        if not c in (3, 4):
            nda = nda[nda.shape[0] // 2, :, :]

    elif nda.ndim == 4:
        c = nda.shape[-1]

        if not c in (3, 4):
            raise Runtime("Unable to show 3D-vector Image")

        # take a z-slice
        nda = nda[nda.shape[0] // 2, :, :, :]

    ysize = nda.shape[0]
    xsize = nda.shape[1]

    # Make a figure big enough to accomodate an axis of xpixels by ypixels
    # as well as the ticklabels, etc...
    figsize = (1 + margin) * ysize / dpi, (1 + margin) * xsize / dpi

    fig = plt.figure(figsize=figsize, dpi=dpi)
    # Make the axis the right size...
    ax = fig.add_axes([margin, margin, 1 - 2 * margin, 1 - 2 * margin])

    extent = (0, xsize * spacing[1], ysize * spacing[0], 0)

    t = ax.imshow(nda, extent=extent, interpolation=None)

    if nda.ndim == 2:
        t.set_cmap("gray")

    if (title):
        plt.title(title)


def myshow3d(img, xslices=[], yslices=[], zslices=[], title=None, margin=0.05, dpi=80):
    size = img.GetSize()
    img_xslices = [img[s, :, :] for s in xslices]
    img_yslices = [img[:, s, :] for s in yslices]
    img_zslices = [img[:, :, s] for s in zslices]

    maxlen = max(len(img_xslices), len(img_yslices), len(img_zslices))

    img_null = sitk.Image([0, 0], img.GetPixelIDValue(), img.GetNumberOfComponentsPerPixel())

    img_slices = []
    d = 0

    if len(img_xslices):
        img_slices += img_xslices + [img_null] * (maxlen - len(img_xslices))
        d += 1

    if len(img_yslices):
        img_slices += img_yslices + [img_null] * (maxlen - len(img_yslices))
        d += 1

    if len(img_zslices):
        img_slices += img_zslices + [img_null] * (maxlen - len(img_zslices))
        d += 1

    if maxlen != 0:
        if img.GetNumberOfComponentsPerPixel() == 1:
            img = sitk.Tile(img_slices, [maxlen, d])
        # TODO check in code to get Tile Filter working with VectorImages
        else:
            img_comps = []
            for i in range(0, img.GetNumberOfComponentsPerPixel()):
                img_slices_c = [sitk.VectorIndexSelectionCast(s, i) for s in img_slices]
                img_comps.append(sitk.Tile(img_slices_c, [maxlen, d]))
            img = sitk.Compose(img_comps)

    myshow(img, title, margin, dpi)