Python skimage.morphology方法代码示例

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

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




## Sequence 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def test_different_size_px_arguments(self):
        # different sizes in px
        param1 = iap.FromLowerResolution(iap.Binomial(0.5), size_px=2)
        param2 = iap.FromLowerResolution(iap.Binomial(0.5), size_px=16)

        seen_components = [0, 0]
        seen_pixels = [0, 0]
        for _ in sm.xrange(100):
            samples1 = param1.draw_samples((16, 16, 1))
            samples2 = param2.draw_samples((16, 16, 1))
            _, num1 = skimage.morphology.label(samples1, connectivity=1,
                                               background=0, return_num=True)
            _, num2 = skimage.morphology.label(samples2, connectivity=1,
                                               background=0, return_num=True)
            seen_components[0] += num1
            seen_components[1] += num2
            seen_pixels[0] += np.sum(samples1 == 1)
            seen_pixels[1] += np.sum(samples2 == 1)

        assert seen_components[0] < seen_components[1]
        assert (
            seen_pixels[0] / seen_components[0]
            > seen_pixels[1] / seen_components[1]
        ) 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def test_different_size_px_arguments_with_tuple(self):
        # different sizes in px, one given as tuple (a, b)
        param1 = iap.FromLowerResolution(iap.Binomial(0.5), size_px=2)
        param2 = iap.FromLowerResolution(iap.Binomial(0.5), size_px=(2, 16))

        seen_components = [0, 0]
        seen_pixels = [0, 0]
        for _ in sm.xrange(400):
            samples1 = param1.draw_samples((16, 16, 1))
            samples2 = param2.draw_samples((16, 16, 1))
            _, num1 = skimage.morphology.label(samples1, connectivity=1,
                                               background=0, return_num=True)
            _, num2 = skimage.morphology.label(samples2, connectivity=1,
                                               background=0, return_num=True)
            seen_components[0] += num1
            seen_components[1] += num2
            seen_pixels[0] += np.sum(samples1 == 1)
            seen_pixels[1] += np.sum(samples2 == 1)

        assert seen_components[0] < seen_components[1]
        assert (
            seen_pixels[0] / seen_components[0]
            > seen_pixels[1] / seen_components[1]
        ) 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def test_min_size(self):
        # min_size
        param1 = iap.FromLowerResolution(iap.Binomial(0.5), size_px=2)
        param2 = iap.FromLowerResolution(iap.Binomial(0.5), size_px=1,
                                         min_size=16)

        seen_components = [0, 0]
        seen_pixels = [0, 0]
        for _ in sm.xrange(100):
            samples1 = param1.draw_samples((16, 16, 1))
            samples2 = param2.draw_samples((16, 16, 1))
            _, num1 = skimage.morphology.label(samples1, connectivity=1,
                                               background=0, return_num=True)
            _, num2 = skimage.morphology.label(samples2, connectivity=1,
                                               background=0, return_num=True)
            seen_components[0] += num1
            seen_components[1] += num2
            seen_pixels[0] += np.sum(samples1 == 1)
            seen_pixels[1] += np.sum(samples2 == 1)

        assert seen_components[0] < seen_components[1]
        assert (
            seen_pixels[0] / seen_components[0]
            > seen_pixels[1] / seen_components[1]
        ) 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def test_size_percent(self):
        # different sizes in percent
        param1 = iap.FromLowerResolution(iap.Binomial(0.5), size_percent=0.01)
        param2 = iap.FromLowerResolution(iap.Binomial(0.5), size_percent=0.8)

        seen_components = [0, 0]
        seen_pixels = [0, 0]
        for _ in sm.xrange(100):
            samples1 = param1.draw_samples((16, 16, 1))
            samples2 = param2.draw_samples((16, 16, 1))
            _, num1 = skimage.morphology.label(samples1, connectivity=1,
                                               background=0, return_num=True)
            _, num2 = skimage.morphology.label(samples2, connectivity=1,
                                               background=0, return_num=True)
            seen_components[0] += num1
            seen_components[1] += num2
            seen_pixels[0] += np.sum(samples1 == 1)
            seen_pixels[1] += np.sum(samples2 == 1)

        assert seen_components[0] < seen_components[1]
        assert (
            seen_pixels[0] / seen_components[0]
            > seen_pixels[1] / seen_components[1]
        ) 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [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: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def test_different_size_px_argument_with_stochastic_parameters(self):
        # different sizes in px, given as StochasticParameter
        param1 = iap.FromLowerResolution(iap.Binomial(0.5),
                                         size_px=iap.Deterministic(1))
        param2 = iap.FromLowerResolution(iap.Binomial(0.5),
                                         size_px=iap.Choice([8, 16]))

        seen_components = [0, 0]
        seen_pixels = [0, 0]
        for _ in sm.xrange(100):
            samples1 = param1.draw_samples((16, 16, 1))
            samples2 = param2.draw_samples((16, 16, 1))
            _, num1 = skimage.morphology.label(samples1, connectivity=1,
                                               background=0, return_num=True)
            _, num2 = skimage.morphology.label(samples2, connectivity=1,
                                               background=0, return_num=True)
            seen_components[0] += num1
            seen_components[1] += num2
            seen_pixels[0] += np.sum(samples1 == 1)
            seen_pixels[1] += np.sum(samples2 == 1)

        assert seen_components[0] < seen_components[1]
        assert (
            seen_pixels[0] / seen_components[0]
            > seen_pixels[1] / seen_components[1]
        ) 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def overlay(self, img, imbin, contour=False):
        colim = color.gray2rgb(img)
        colorvalue = (0, 100, 200)
        if contour:
            se = morphology.diamond(2)
            ero = morphology.erosion(imbin, se)
            grad = imbin - ero
            colim[grad > 0] = colorvalue
        else:
            colim[imbin>0] = colorvalue
            
        return colim 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def morpho_rec(self, img, size=10):
        # internal gradient of the cells: 
        se = morphology.diamond(size)
        ero = morphology.erosion(img, se)
        rec = morphology.reconstruction(ero, img, method='dilation').astype(np.dtype('uint8'))
                
        return rec 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def morpho_rec2(self, img, size=10):
        # internal gradient of the cells: 
        se = morphology.diamond(size)
        dil = morphology.dilation(img, se)
        rec = morphology.reconstruction(dil, img, method='erosion').astype(np.dtype('uint8'))
                
        return rec 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def test_morpho2(self, bigsize=20.0, smallsize=3.0, threshold=5.0):
    
        img = self.read_H_image()

        pref = self.morpho_rec(img, 10)
        filename = os.path.join(test_out_folder, 'morpho_00_rec_%s.png' % self.image_name)
        skimage.io.imsave(filename, pref)

        res = self.difference_of_gaussian(pref, bigsize, smallsize)
        filename = os.path.join(test_out_folder, 'morpho_01_diff_%s_%i_%i.png' % (self.image_name, int(bigsize), int(smallsize)))
        skimage.io.imsave(filename, res)
        
        #res = self.morpho_rec2(diff, 15)
        #filename = os.path.join(test_out_folder, 'morpho_02_rec_%s.png' % self.image_name)
        #skimage.io.imsave(filename, res)

        res[res>threshold] = 255
        filename = os.path.join(test_out_folder, 'morpho_03_res_%s_%i.png' % (self.image_name, threshold))
        skimage.io.imsave(filename, res)
        
        se = morphology.diamond(3)
        ero = morphology.erosion(res, se)
        filename = os.path.join(test_out_folder, 'morpho_03_ero_%s_%i.png' % (self.image_name, threshold))
        skimage.io.imsave(filename, ero)
        res[ero>0] = 0
        
        overlay_img = self.overlay(img, res)
        filename = os.path.join(test_out_folder, 'morpho_04_overlay_%s_%i.png' % (self.image_name, int(threshold)))
        skimage.io.imsave(filename, overlay_img)
        
        return 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def get_rough_detection(self, img, bigsize=40.0, smallsize=4.0, thresh = 0):
        diff = self.difference_of_gaussian(-img, bigsize, smallsize)
        diff[diff>thresh] = 1
        
        se = morphology.square(4)
        ero = morphology.erosion(diff, se)
        
        labimage = label(ero)
        #rec = morphology.reconstruction(ero, img, method='dilation').astype(np.dtype('uint8'))
        
        # connectivity=1 corresponds to 4-connectivity.
        morphology.remove_small_objects(labimage, min_size=600, connectivity=1, in_place=True)
        #res = np.zeros(img.shape)
        ero[labimage==0] = 0
        ero = 1 - ero
        labimage = label(ero)
        morphology.remove_small_objects(labimage, min_size=400, connectivity=1, in_place=True)
        ero[labimage==0] = 0
        res = 1 - ero
        res[res>0] = 255
        
        #temp = 255 - temp
        #temp = morphology.remove_small_objects(temp, min_size=400, connectivity=1, in_place=True)
        #res = 255 - temp
        
        return res 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def prefilter_new(self, img, rec_size=20, se_size=3):
    
        img_cc = ccore.numpy_to_image(img, copy=True)        
        im1 = ccore.diameter_open(img_cc, rec_size, 8)        
        im2 = ccore.diameter_close(im1, int(rec_size / 2), 8)        

        #im1 = self.morpho_rec(img, rec_size)
        #im2 = self.morpho_rec2(im1, int(rec_size / 2))

        se = morphology.disk(se_size)        
        im3 = morphology.closing(im2.toArray(), se)
        
        return im3 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def h_minima(self, img, h):
        img_shift = img.copy()
        img_shift[img_shift >= 255 - h] = 255-h
        img_shift = img_shift + h
        rec = morphology.reconstruction(img_shift, img, method='erosion').astype(np.dtype('uint8'))
        diff = rec - img
        return diff 

# 需要导入模块: import skimage [as 别名]
# 或者: from skimage import morphology [as 别名]
def get_segmented_lungs(image):
    #Creation of the markers as shown above:
    marker_internal, marker_external, marker_watershed = generate_markers(image)
    
    #Creation of the Sobel-Gradient
    sobel_filtered_dx = ndimage.sobel(image, 1)
    sobel_filtered_dy = ndimage.sobel(image, 0)
    sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
    sobel_gradient *= 255.0 / np.max(sobel_gradient)
    
    #Watershed algorithm
    watershed = morphology.watershed(sobel_gradient, marker_watershed)
    
    #Reducing the image created by the Watershed algorithm to its outline
    outline = ndimage.morphological_gradient(watershed, size=(3,3))
    outline = outline.astype(bool)
    
    #Performing Black-Tophat Morphology for reinclusion
    #Creation of the disk-kernel and increasing its size a bit
    blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
                       [0, 1, 1, 1, 1, 1, 0],
                       [1, 1, 1, 1, 1, 1, 1],
                       [1, 1, 1, 1, 1, 1, 1],
                       [1, 1, 1, 1, 1, 1, 1],
                       [0, 1, 1, 1, 1, 1, 0],
                       [0, 0, 1, 1, 1, 0, 0]]
    #blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
    blackhat_struct = ndimage.iterate_structure(blackhat_struct, 14) # <- retains more of the area, 12 works well. Changed to 14, 12 still excluded some parts.
    #Perform the Black-Hat
    outline += ndimage.black_tophat(outline, structure=blackhat_struct)
    
    #Use the internal marker and the Outline that was just created to generate the lungfilter
    lungfilter = np.bitwise_or(marker_internal, outline)
    #Close holes in the lungfilter
    #fill_holes is not used here, since in some slices the heart would be reincluded by accident
    lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=np.ones((5,5)), iterations=3)
    
    #Apply the lungfilter (note the filtered areas being assigned threshold_min HU)
    segmented = np.where(lungfilter == 1, image, threshold_min*np.ones(image.shape))
    
    #return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed
    return segmented