def _define_kernel(shape, size, dtype):
"""Build a kernel to apply a filter on images.
Parameters
----------
shape : str
Shape of the kernel used to compute the filter ('diamond', 'disk',
'rectangle' or 'square').
size : int, Tuple(int) or List(int)
The size of the kernel:
- For the rectangle we expect two values (width, height).
- For the square one value (width).
- For the disk and the diamond one value (radius).
dtype : type
Dtype used for the kernel (the same as the image).
Returns
-------
kernel : skimage.morphology.selem object
Kernel to use with a skimage filter.
"""
# build the kernel
if shape == "diamond":
kernel = diamond(size, dtype=dtype)
elif shape == "disk":
kernel = disk(size, dtype=dtype)
elif shape == "rectangle" and isinstance(size, tuple):
kernel = rectangle(size[0], size[1], dtype=dtype)
elif shape == "square":
kernel = square(size, dtype=dtype)
else:
raise ValueError("Kernel definition is wrong.")
return kernel
def segleaf(I):
"""
Leaf segmentation using random walker
:param I: Input image as a float
:return: A binary image that shows the segmentation of the leaf from the background
"""
#Separate the image into it's three colour components
red = 255 * I[:, :, 0]
green = 255 * I[:, :, 1]
blue = 255 * I[:, :, 2]
#Create a new image with the amount of greeness exaggerrated
greenness = 1.97 * green - red - blue
#Find a threshold value
T = filt.threshold_otsu(greenness)
#Create an array of identical size to the image, with seed pixels labelled as fg and bg
seeds = np.zeros_like(I, dtype=np.uint8)
seeds[greenness >= T] = 1 # fg label
try:
seeds[greenness < 5] = 2 # bg label
labels = seg.random_walker(I, seeds, beta=10, multichannel=True)
except:
#For when a IndexError occurs
try:
seeds[greenness < 10] = 2 # bg label
labels = seg.random_walker(I, seeds, beta=10, multichannel=True)
except:
seeds[greenness < 22] = 2 # bg label
labels = seg.random_walker(I, seeds, beta=10, multichannel=True)
#Label the bg labelled pixels as False
labels[labels == 2] = 0
labels = labels[:, :,
0] #All three colour components share the same value now, so only one is needed.
#Perform some region processing to improve the result
labels = morph.opening(labels, selem.diamond(1))
labels = morph.binary_closing(labels, selem.diamond(2.5))
labels = morph.remove_small_objects(labels, 30)
labels = morph.binary_closing(labels, selem.diamond(3))
labels = morph.remove_small_objects(labels, 340)
labels = morph.binary_closing(labels, selem.diamond(6))
return labels
def test_default_selem(function):
strel = selem.diamond(radius=1)
image = np.array(
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8)
im_expected = function(image, strel)
im_test = function(image)
testing.assert_array_equal(im_expected, im_test)
def test_default_selem():
functions = [
binary.binary_erosion, binary.binary_dilation, binary.binary_opening,
binary.binary_closing
]
strel = selem.diamond(radius=1)
image = np.array(
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8)
for function in functions:
im_expected = function(image, strel)
im_test = function(image)
yield testing.assert_array_equal, im_expected, im_test
def test_default_selem(function):
strel = selem.diamond(radius=1)
image = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8)
im_expected = function(image, strel)
im_test = function(image)
testing.assert_array_equal(im_expected, im_test)
def test_default_selem():
functions = [
grey.erosion, grey.dilation, grey.opening, grey.closing,
grey.white_tophat, grey.black_tophat
]
strel = selem.diamond(radius=1)
image = np.array(
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0], [0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8)
for function in functions:
im_expected = function(image, strel)
im_test = function(image)
yield testing.assert_array_equal, im_expected, im_test
def test_default_selem():
functions = [binary.binary_erosion, binary.binary_dilation,
binary.binary_opening, binary.binary_closing]
strel = selem.diamond(radius=1)
image = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8)
for function in functions:
im_expected = function(image, strel)
im_test = function(image)
yield testing.assert_array_equal, im_expected, im_test
def test_default_selem():
functions = [grey.erosion, grey.dilation,
grey.opening, grey.closing,
grey.white_tophat, grey.black_tophat]
strel = selem.diamond(radius=1)
image = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], np.uint8)
for function in functions:
im_expected = function(image, strel)
im_test = function(image)
yield testing.assert_array_equal, im_expected, im_test
def _define_kernel(shape, size, dtype):
"""Build a kernel to apply a filter on images.
Parameters
----------
shape : str
Shape of the kernel used to compute the filter (`diamond`, `disk`,
`rectangle` or `square`).
size : int, Tuple(int) or List(int)
The size of the kernel:
- For the rectangle we expect two values (`height`, `width`).
- For the square one value (`width`).
- For the disk and the diamond one value (`radius`).
dtype : type
Dtype used for the kernel (the same as the image).
Returns
-------
kernel : skimage.morphology.selem object
Kernel to use with a skimage filter.
"""
# build the kernel
if shape == "diamond":
kernel = diamond(size, dtype=dtype)
elif shape == "disk":
kernel = disk(size, dtype=dtype)
elif shape == "rectangle" and isinstance(size, (tuple, list)):
kernel = rectangle(size[0], size[1], dtype=dtype)
elif shape == "square":
kernel = square(size, dtype=dtype)
else:
raise ValueError("Kernel definition is wrong. Shape of the kernel "
"should be 'diamond', 'disk', 'rectangle' or "
"'square'. Not {0}.".format(shape))
return kernel
def _segmentation(img_row, img_Red_row, result_denoise, tp=5):
# segmentation of img_row:
#----------------------------------------------------------------------
img_denoise = result_denoise[tp]
#img_denoise = result_denoise
#Random walker
segmentation_rw = _rand_walk(img_denoise)
# Watershed
segmentation_ws = _water(img_denoise)
labeled_image = _join_seg(segmentation_rw, segmentation_ws)
# Constructing the h-dome for analysis under the pic:
# calculate hdome to have stronger difference in S/N
#----------------------------------------------------------------------
#seed = np.copy(img_denoise)
#seed[1:-1, 1:-1] = img_denoise.min()
#mask = img_denoise
#dilated = reconstruction(seed, mask, method='dilation')
#hdome = img_denoise - dilated
props = regionprops(labeled_image, intensity_image=img_denoise)
#props_hdome = regionprops(labeled_image, intensity_image = hdome)
# Denoising / processing / segmentation of img_row red:
#----------------------------------------------------------------------
Red_binary = threshold_adaptive(img_Red_row[tp, :, :], block_size=37)
d = selem.diamond(radius=4)
Red_binary_open = opening(Red_binary, d)
Red_binary_open = binary_erosion(Red_binary_open, selem=disk(2))
Red_binary_open = binary_dilation(Red_binary_open, selem=disk(2))
Red_binary_open_labeled = label(Red_binary_open)
Red_binary_open_labeled_overlay = label2rgb(Red_binary_open_labeled,
image=img_Red_row[tp, :, :])
props_Red = regionprops(Red_binary_open_labeled,
intensity_image=img_denoise)
# Getting property out
#----------------------------------------------------------------------
#Cells property
#------------------
cell_coord = []
mean_intensity = []
numb_para = []
prop_green = []
#Red property
#------------------
prop_red = []
for cell, prop in enumerate(props):
prop_green.append(props[cell])
for cell, prop in enumerate(props):
# Cell part:
#------------------
ycent, xcent = props[cell]['centroid']
mean_intensity.append(props[cell]['mean_intensity'])
cell_coord.append((ycent, xcent))
# Parasite part:
#------------------
Para_masked = np.copy(Red_binary_open_labeled)
Mask = (labeled_image == cell + 1)
Para_masked[~Mask] = 0
para_ID = list(np.unique(Para_masked[Para_masked != 0]))
numb_para.append(len(para_ID))
### Get the all parasite not just the piece that overlap i
lst_prop_para_ID = []
for para, prop in enumerate(props_Red):
ID = props_Red[para]['label']
if ID in para_ID:
lst_prop_para_ID.append(prop)
prop_red.append((lst_prop_para_ID))
result1 = np.array(cell_coord)
result2 = np.array(mean_intensity)
result3 = np.array(prop_red)
result4 = np.array(prop_green)
result = np.concatenate((result1, result2[:, np.newaxis],
result3[:, np.newaxis], result4[:, np.newaxis]),
axis=1)
return result, labeled_image, prop_red, Red_binary_open