Segmentation_1.py

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    img_rgb = skimage.io.imread(fnamei)

    # 1. RGB to HED
    img_hed = rgb2hed(img_rgb)
    img = img_hed[:, :, 1]

    # 2. Create mask using threshold
    mask = (img > 0.05)

    # 3. Delete small objects and holes
    mask = morphology.remove_small_objects(mask, 40000)
    mask = morphology.remove_small_holes(mask, 40000)

    # 4. Detect labels and properties of the region
    labels = measure.label(mask)
    props = measure.regionprops(labels, img_hed)[0]

    # 6. Find an angle of segmented region
    angle = props.orientation
    angle = periodic(angle, anglep)
    anglep = angle

    # 7. Draw angle and region
    axis_min_length = props.axis_minor_length
    axis_maj_length = props.axis_major_length    
    y0, x0 = props.centroid
    x1 = x0 + math.cos(angle) * 0.5 * axis_min_length
    y1 = y0 - math.sin(angle) * 0.5 * axis_min_length
    x2 = x0 - math.sin(angle) * 0.5 * axis_maj_length
    y2 = y0 - math.cos(angle) * 0.5 * axis_maj_length
    li.append(angle)

    # 7.1 Draw axis of a region
    fig, ax = plt.subplots()
    ax.plot((x0, x1), (y0, y1), '--b', linewidth=2.5)
    ax.plot((x0, x2), (y0, y2), '--b', linewidth=2.5)
    ax.plot(x0, y0, '.g', markersize=15)

    # 7.2 Draw segmented region
    alpha = 0.4
    clr = [46/225., 1., 48/225.]
    for c in range(3):
        img_rgb[:, :, c] = np.where(mask == 1,
                                  img_rgb[:, :, c] *
                                  (1 - alpha) + alpha * clr[c] * 255,
                                  img_rgb[:, :, c])

    ax.imshow(img_rgb)

    # 7.3 Draw a contour of a region
    contours = measure.find_contours(mask, 0.5)
    for contour in contours:
        ax.plot(contour[:, 1], contour[:, 0], linewidth=2, color=[46/225., 1., 48/225.])
    plt.axis('off')    
    plt.savefig('../pics/skimage_red_hed_countour/'+fnamei.split('/')[-1])
    plt.clf()
    plt.close('all')
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