Python morphology.binary_dilation方法代码示例

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def _expand_raster(raster, distance = (4,2)):
    try:
        from skimage import draw, morphology
    except:
        raise ImportError("""
            The fill function requires the module "scikit-image"
            to operate.  Please retry after installing scikit-image:

            $ pip install --upgrade scikit-image """)
    if distance[0] <= 0.5 and distance[1] <= 0.5: return raster

    num_pixels = np.array(np.ceil(distance), dtype = int)
    neighborhood = np.zeros((num_pixels[1]*2+1, num_pixels[0]*2+1), dtype=np.bool)
    rr, cc = draw.ellipse(num_pixels[1], num_pixels[0], distance[1]+0.5, distance[0]+0.5)
    neighborhood[rr, cc] = 1

    return morphology.binary_dilation(image = raster, selem=neighborhood) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def get_connected_component_shape(layer, event):
        cords = np.round(layer.coordinates).astype(int)
        val = layer.get_value()
        if val is None:
            return
        if val != 0:
            data = layer.data
            binary = data == val
            if 'Shift' in event.modifiers:
                binary_new = binary_erosion(binary)
                data[binary] = 0
                data[binary_new] = val
            else:
                binary_new = binary_dilation(binary)
                data[binary_new] = val
            size = np.sum(binary_new)
            layer.data = data
            msg = f'clicked at {cords} on blob {val} which is now {size} pixels'
        else:
            msg = f'clicked at {cords} on background which is ignored'
        layer.status = msg
        print(msg) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def compute_binary_mask_sprengel(spectrogram, threshold):
    """ Computes a binary mask for the spectrogram
    # Arguments
        spectrogram : a numpy array representation of a spectrogram (2-dim)
        threshold   : a threshold for times larger than the median
    # Returns
        binary_mask : the binary mask
    """
    # normalize to [0, 1)
    norm_spectrogram = normalize(spectrogram)

    # median clipping
    binary_image = median_clipping(norm_spectrogram, threshold)

    # erosion
    binary_image = morphology.binary_erosion(binary_image, selem=np.ones((4, 4)))

    # dilation
    binary_image = morphology.binary_dilation(binary_image, selem=np.ones((4, 4)))

    # extract mask
    mask = np.array([np.max(col) for col in binary_image.T])
    mask = smooth_mask(mask)

    return mask 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def getEdgeEnhancedWeightMap(label, label_ids =[0,1,2,3], scale=1, edgescale=1, assign_equal_wt=False):
    shape = (0,)+label.shape[1:]
    weight_map = np.empty(shape, dtype='uint8')
    if assign_equal_wt:
        return np.ones_like(label)
    for i in range(label.shape[0]): 
        #Estimate weight maps:
        weights = np.ones(len(label_ids))
        slice_map = np.ones(label[i,:,:].shape)
        for _id in label_ids:
            class_frequency = np.sum(label[i,:,:] == label_ids[_id])
            if class_frequency:
                weights[label_ids.index(_id)] = scale*label[i,:,:].size/class_frequency
                slice_map[np.where(label[i,:,:]==label_ids.index(_id))] = weights[label_ids.index(_id)]
                edge = np.float32(morph.binary_dilation(
                    canny(np.float32(label[i,:,:]==label_ids.index(_id)),sigma=1), selem=selem))
                edge_frequency = np.sum(np.sum(edge==1.0))
                if edge_frequency:    
                    slice_map[np.where(edge==1.0)] += edgescale*label[i,:,:].size/edge_frequency
            # print (weights)
            # utils.imshow(edge, cmap='gray')
        # utils.imshow(weight_map, cmap='gray')
        weight_map = np.append(weight_map, np.expand_dims(slice_map, axis=0), axis=0)
    return np.float32(weight_map) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def test_apply():
    input_mask_collection = binary_mask_collection_2d()
    output_mask_collection = input_mask_collection._apply(binary_dilation)

    assert input_mask_collection._pixel_ticks == output_mask_collection._pixel_ticks
    assert input_mask_collection._physical_ticks == output_mask_collection._physical_ticks
    assert input_mask_collection._log == output_mask_collection._log
    assert len(input_mask_collection) == len(output_mask_collection)

    region_0, region_1 = output_mask_collection.masks()

    assert region_0.name == '0'
    assert region_1.name == '1'

    temp = np.ones((2, 6), dtype=np.bool)
    assert np.array_equal(region_0, temp)
    temp = np.ones((3, 4), dtype=np.bool)
    temp[0, 0] = 0
    assert np.array_equal(region_1, temp)

    assert np.array_equal(region_0[Axes.Y.value], [0, 1])
    assert np.array_equal(region_0[Axes.X.value], [0, 1, 2, 3, 4, 5])

    assert np.array_equal(region_1[Axes.Y.value], [2, 3, 4])
    assert np.array_equal(region_1[Axes.X.value], [2, 3, 4, 5]) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def get_image_area_to_sample(img):
  """
  calculate set g_c, which has two properties
  1) They represent background pixels 
  2) They are within a certain distance to the object
  :param img: Image that represents the object instance
  """

  #TODO: In the paper 'Deep Interactive Object Selection', they calculate g_c first based on the original object instead
  # of the dilated one.

  # Dilate the object by d_margin pixels to extend the object boundary
  img_area = np.copy(img)
  img_area = morphology.binary_dilation(img_area, morphology.diamond(D_MARGIN)).astype(np.uint8)

  g_c = np.logical_not(img_area).astype(int)
  g_c[np.where(distance_transform_edt(g_c) > D)] = 0

  return g_c 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def basin(label_mask, wall):
    h,w = np.shape(label_mask)
    y, x = np.mgrid[0:h, 0:w]
    struct = generate_binary_structure(2,2)
    shifty, shiftx = np.mgrid[0:3, 0:3]
    shifty = (shifty-1).flatten()
    shiftx = (shiftx-1).flatten()

    for i in range(4):
        obdr = label_mask^binary_dilation(label_mask, struct)
        ibdr = label_mask^binary_erosion(label_mask, struct)
        yob, xob = y[obdr], x[obdr]        
        ynb, xnb = yob.reshape(-1,1)+shifty, xob.reshape(-1,1)+shiftx
        
        wallnb = np.min(map_coords(wall, (ynb, xnb))*(map_coords(ibdr, (ynb, xnb))==1)+\
                        5*(map_coords(ibdr, (ynb, xnb))!=1),1)
        keep = (wall[yob,xob]>wallnb)&(wallnb<=4)
        label_mask[yob[keep], xob[keep]]=True
        if np.sum(keep)==0:
            break
    return label_mask 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def binary_dilation(x, radius=3):
    """ Return fast binary morphological dilation of an image.
    see `skimage.morphology.binary_dilation <http://scikit-image.org/docs/dev/api/skimage.morphology.html#skimage.morphology.binary_dilation>`_.

    Parameters
    -----------
    x : 2D array image.
    radius : int for the radius of mask.
    """
    from skimage.morphology import disk, binary_dilation
    mask = disk(radius)
    x = binary_dilation(image, selem=mask)
    return x 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def outline_polygons(self, width=EDGE_WIDTH, color=LABEL_EDGE):
        from skimage.morphology import binary_dilation, disk
        im = np.asarray(self.image).copy()
        outset = binary_dilation(im == LABEL_POSITIVE, disk(width / 2))
        inset = binary_dilation(im != LABEL_POSITIVE, disk(width - width / 2))
        boundary = outset & inset
        im[boundary] = color
        self.image = Image.fromarray(im)
        self.artist = ImageDraw.Draw(self.image) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def compute_binary_mask_lasseck(spectrogram, threshold):
    # normalize to [0, 1)
    norm_spectrogram = normalize(spectrogram)

    # median clipping
    binary_image = median_clipping(norm_spectrogram, threshold)

    # closing binary image (dilation followed by erosion)
    binary_image = morphology.binary_closing(binary_image, selem=np.ones((4, 4)))

    # dialate binary image
    binary_image = morphology.binary_dilation(binary_image, selem=np.ones((4, 4)))

    # apply median filter
    binary_image = filters.median(binary_image, selem=np.ones((2, 2)))

    # remove small objects
    binary_image = morphology.remove_small_objects(binary_image, min_size=32, connectivity=1)

    mask = np.array([np.max(col) for col in binary_image.T])
    mask = smooth_mask(mask)

    return mask


# TODO: This method needs some real testing 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def smooth_mask(mask):
    """ Smooths a binary mask using 4x4 dilation
        # Arguments
            mask : the binary mask
        # Returns
            mask : a smoother binary mask
    """
    n_hood = np.ones(4)
    mask = morphology.binary_dilation(mask, n_hood)
    mask = morphology.binary_dilation(mask, n_hood)

    # type casting is a bitch
    return mask 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def sprengel_binary_mask_from_wave_file(filepath):
    fs, x = utils.read_wave_file(filepath)
    Sxx = sp.wave_to_amplitude_spectrogram(x, fs)
    Sxx_log = sp.wave_to_log_amplitude_spectrogram(x, fs)

    # plot spectrogram
    fig = plt.figure(1)
    subplot_image(Sxx_log, 411, "Spectrogram")

    Sxx = pp.normalize(Sxx)
    binary_image = pp.median_clipping(Sxx, 3.0)

    subplot_image(binary_image + 0, 412, "Median Clipping")

    binary_image = morphology.binary_erosion(binary_image, selem=np.ones((4, 4)))

    subplot_image(binary_image + 0, 413, "Erosion")

    binary_image = morphology.binary_dilation(binary_image, selem=np.ones((4, 4)))

    subplot_image(binary_image + 0, 414, "Dilation")

    mask = np.array([np.max(col) for col in binary_image.T])
    mask = morphology.binary_dilation(mask, np.ones(4))
    mask = morphology.binary_dilation(mask, np.ones(4))

    # plot_vector(mask, "Mask")

    fig.set_size_inches(10, 12)
    plt.tight_layout()
    fig.savefig(utils.get_basename_without_ext(filepath) + "_binary_mask.png", dpi=100) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def create_mask(aseg_data, dnum, enum):
    from skimage.morphology import binary_dilation, binary_erosion
    from skimage.measure import label
    print ("Creating dilated mask ...")

    # treat lateral orbital frontal and parsorbitalis special to avoid capturing too much of eye nerve
    lat_orb_front_mask = np.logical_or(aseg_data == 2012, aseg_data == 1012)
    parsorbitalis_mask = np.logical_or(aseg_data == 2019, aseg_data == 1019)
    frontal_mask = np.logical_or(lat_orb_front_mask, parsorbitalis_mask)
    print("Frontal region special treatment: ", format(np.sum(frontal_mask)))

    # reduce to binary
    datab = (aseg_data > 0)
    datab[frontal_mask] = 0
    # dilate and erode
    for x in range(dnum):
        datab = binary_dilation(datab, np.ones((3, 3, 3)))
    for x in range(enum):
        datab = binary_erosion(datab, np.ones((3, 3, 3)))

    # extract largest component
    labels = label(datab)
    assert (labels.max() != 0)  # assume at least 1 real connected component
    print("  Found {} connected component(s)!".format(labels.max()))

    if labels.max() > 1:
        print("  Selecting largest component!")
        datab = (labels == np.argmax(np.bincount(labels.flat)[1:]) + 1)

    # add frontal regions back to mask
    datab[frontal_mask] = 1

    # set mask
    aseg_data[~datab] = 0
    aseg_data[datab] = 1
    return aseg_data 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def grow_mask(anat, aseg, ants_segs=None, ww=7, zval=2.0, bw=4):
    """
    Grow mask including pixels that have a high likelihood.

    GM tissue parameters are sampled in image patches of ``ww`` size.
    This is inspired on mindboggle's solution to the problem:
    https://github.com/nipy/mindboggle/blob/master/mindboggle/guts/segment.py#L1660

    """
    selem = sim.ball(bw)

    if ants_segs is None:
        ants_segs = np.zeros_like(aseg, dtype=np.uint8)

    aseg[aseg == 42] = 3  # Collapse both hemispheres
    gm = anat.copy()
    gm[aseg != 3] = 0

    refined = refine_aseg(aseg)
    newrefmask = sim.binary_dilation(refined, selem) - refined
    indices = np.argwhere(newrefmask > 0)
    for pixel in indices:
        # When ATROPOS identified the pixel as GM, set and carry on
        if ants_segs[tuple(pixel)] == 2:
            refined[tuple(pixel)] = 1
            continue

        window = gm[
            pixel[0] - ww:pixel[0] + ww,
            pixel[1] - ww:pixel[1] + ww,
            pixel[2] - ww:pixel[2] + ww,
        ]
        if np.any(window > 0):
            mu = window[window > 0].mean()
            sigma = max(window[window > 0].std(), 1.0e-5)
            zstat = abs(anat[tuple(pixel)] - mu) / sigma
            refined[tuple(pixel)] = int(zstat < zval)

    refined = sim.binary_opening(refined, selem)
    return refined 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import binary_dilation [as 别名]
def segment_active_contour(img, centers):
    """ segmentation using acive contours

    :param ndarray img: input image / segmentation
    :param [[int, int]] centers: position of centres / seeds
    :return (ndarray, [[int, int]]): resulting segmentation, updated centres
    """
    logging.debug('segment: active_contour...')
    # http://scikit-image.org/docs/dev/auto_examples/edges/plot_active_contours.html
    segm = np.zeros(img.shape[:2])
    img_smooth = ndimage.filters.gaussian_filter(img, 5)
    center_circles, _, _ = create_circle_center(img.shape[:2], centers)
    for i, snake in enumerate(center_circles):
        snake = segmentation.active_contour(img_smooth, snake.astype(float),
                                            alpha=0.015, beta=10, gamma=0.001,
                                            w_line=0.0, w_edge=1.0,
                                            max_px_move=1.0,
                                            max_iterations=2500,
                                            convergence=0.2)
        seg = np.zeros(segm.shape, dtype=bool)
        x, y = np.array(snake).transpose().tolist()
        # rr, cc = draw.polygon(x, y)
        seg[map(int, x), map(int, y)] = True
        seg = morphology.binary_dilation(seg, selem=morphology.disk(3))
        bb_area = int((max(x) - min(x)) * (max(y) - min(y)))
        logging.debug('bounding box area: %d', bb_area)
        seg = morphology.remove_small_holes(seg, min_size=bb_area)
        segm[seg] = i + 1
    return segm, centers, None