def test_empty_selem():
# check that min, max and mean returns zeros if structuring element is
# empty
image = np.zeros((5, 5), dtype=np.uint16)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
res = np.zeros_like(image)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[0, 0, 0], [0, 0, 0]], dtype=np.uint8)
rank.mean(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_equal(res, out)
rank.geometric_mean(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_equal(res, out)
rank.minimum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_equal(res, out)
rank.maximum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_equal(res, out)
def filter_img(img):
selem = square(11)
img[:, :, 0] = rank.mean(img[:, :, 0], selem=selem)
img[:, :, 1] = rank.mean(img[:, :, 1], selem=selem)
img[:, :, 2] = rank.mean(img[:, :, 2], selem=selem)
#return np.array(img, dtype=float)
return img_as_float(img)
def test_inplace_output(self):
# rank filters are not supposed to filter inplace
selem = disk(20)
image = (np.random.rand(500, 500) * 256).astype(np.uint8)
out = image
with pytest.raises(NotImplementedError):
rank.mean(image, selem, out=out)
def test_random_sizes():
# make sure the size is not a problem
niter = 10
elem = np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8)
for m, n in np.random.random_integers(1, 100, size=(10, 2)):
mask = np.ones((m, n), dtype=np.uint8)
image8 = np.ones((m, n), dtype=np.uint8)
out8 = np.empty_like(image8)
rank.mean(image=image8, selem=elem, mask=mask, out=out8,
shift_x=0, shift_y=0)
assert_equal(image8.shape, out8.shape)
rank.mean(image=image8, selem=elem, mask=mask, out=out8,
shift_x=+1, shift_y=+1)
assert_equal(image8.shape, out8.shape)
image16 = np.ones((m, n), dtype=np.uint16)
out16 = np.empty_like(image8, dtype=np.uint16)
rank.mean(image=image16, selem=elem, mask=mask, out=out16,
shift_x=0, shift_y=0)
assert_equal(image16.shape, out16.shape)
rank.mean(image=image16, selem=elem, mask=mask, out=out16,
shift_x=+1, shift_y=+1)
assert_equal(image16.shape, out16.shape)
rank.mean_percentile(image=image16, mask=mask, out=out16,
selem=elem, shift_x=0, shift_y=0, p0=.1, p1=.9)
assert_equal(image16.shape, out16.shape)
rank.mean_percentile(image=image16, mask=mask, out=out16,
selem=elem, shift_x=+1, shift_y=+1, p0=.1, p1=.9)
assert_equal(image16.shape, out16.shape)
def test_selem_dtypes():
image = np.zeros((5, 5), dtype=np.uint8)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
for dtype in (np.uint8, np.uint16, np.int32, np.int64, np.float32, np.float64):
elem = np.array([[0, 0, 0], [0, 1, 0], [0, 0, 0]], dtype=dtype)
rank.mean(image=image, selem=elem, out=out, mask=mask, shift_x=0, shift_y=0)
assert_equal(image, out)
rank.mean_percentile(image=image, selem=elem, out=out, mask=mask, shift_x=0, shift_y=0)
assert_equal(image, out)
def zoom(imName, img, imageclass, conf): imName = imName+1 im = Image.open(img) if not isdir(conf.output_folder+imageclass): try: mkdir(conf.output_folder+imageclass) except: pass fileMatch = 0 for file in listdir(conf.output_folder+"/"+imageclass): if fnmatch.fnmatch(file, str(imName)+"_zoom_"+'*.jpg'): fileMatch = fileMatch+1 if fileMatch>=3: if conf.VERBOSE: print "exists, so breaking: #"+str(imName)+" in "+str(imageclass) return str(imName) x, y = im.size x1=0 y1=0 means=[] while y1<=y-480: while x1<=x-640: ims = im.crop((x1, y1, x1+640, y1+480)) mean1 = mean(np.array(ims)[:,:,1], disk(700)) means.append(((x1,y1),int(mean1[0][0]))) x1 = x1+160 x1=0 y1 = y1+120 zoomNRC(imName, img, imageclass, conf, conf.mean_threshold, means, im) return str(imName)
def watershed(image):
hsv_image = color.rgb2hsv(image)
low_res_image = rescale(hsv_image[:, :, 0], SCALE)
local_mean = mean(low_res_image, disk(50))
local_minimum_flat = np.argmin(local_mean)
local_minimum = np.multiply(np.unravel_index(local_minimum_flat, low_res_image.shape), round(1 / SCALE))
certain_bone_pixels = np.full_like(hsv_image[:, :, 0], False, bool)
certain_bone_pixels[
local_minimum[0] - INITIAL_WINDOW_SIZE/2:local_minimum[0]+INITIAL_WINDOW_SIZE/2,
local_minimum[1] - INITIAL_WINDOW_SIZE/2:local_minimum[1]+INITIAL_WINDOW_SIZE/2
] = True
certain_non_bone_pixels = np.full_like(hsv_image[:, :, 0], False, bool)
certain_non_bone_pixels[0:BORDER_SIZE, :] = True
certain_non_bone_pixels[-BORDER_SIZE:-1, :] = True
certain_non_bone_pixels[:, 0:BORDER_SIZE] = True
certain_non_bone_pixels[:, -BORDER_SIZE:-1] = True
smoothed_hsv = median(hsv_image[:, :, 0], disk(50))
threshold = MU * np.median(smoothed_hsv[certain_bone_pixels])
possible_bones = np.zeros_like(hsv_image[:, :, 0])
possible_bones[smoothed_hsv < threshold] = 1
markers = np.zeros_like(possible_bones)
markers[certain_bone_pixels] = 1
markers[certain_non_bone_pixels] = 2
labels = morphology.watershed(-possible_bones, markers)
return labels
def skmean(image):
from skimage.filters.rank import mean
mean_filtered = mean(image, disk(30))
print mean_filtered.min(), mean_filtered.max()
return mean_filtered
def test_smallest_selem16():
# check that min, max and mean returns identity if structuring element
# contains only central pixel
image = np.zeros((5, 5), dtype=np.uint16)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[1]], dtype=np.uint8)
rank.mean(image=image, selem=elem, out=out, mask=mask, shift_x=0, shift_y=0)
assert_equal(image, out)
rank.minimum(image=image, selem=elem, out=out, mask=mask, shift_x=0, shift_y=0)
assert_equal(image, out)
rank.maximum(image=image, selem=elem, out=out, mask=mask, shift_x=0, shift_y=0)
assert_equal(image, out)
def substract_mean(self, radius_disk):
circle = disk(radius_disk)
for i_rot in np.arange(self.stack_height):
stack_slice = self.score_stack[:,:,i_rot]
norm_factor = max(stack_slice.min(), stack_slice.max(), key=abs)
stack_slice *= 1./norm_factor
stack_slice = np.array(rank.mean(stack_slice, selem=circle), dtype=np.float32)
stack_slice *= norm_factor
self.score_stack[:,:,i_rot] = self.score_stack[:,:,i_rot]-stack_slice
def test_16bit():
image = np.zeros((21, 21), dtype=np.uint16)
selem = np.ones((3, 3), dtype=np.uint8)
for bitdepth in range(17):
value = 2 ** bitdepth - 1
image[10, 10] = value
assert rank.minimum(image, selem)[10, 10] == 0
assert rank.maximum(image, selem)[10, 10] == value
assert rank.mean(image, selem)[10, 10] == int(value / selem.size)
def smooth(self):
# TODO: there is non nan in the ff img, or?
mask = self.flatField == 0
from skimage.filters.rank import median, mean
from skimage.morphology import disk
ff = mean(median(self.flatField, disk(5), mask=~mask),
disk(13), mask=~mask)
return ff.astype(float) / ff.max(), mask
def _coarsenImage(image, f):
'''
seems to be a more precise (but slower)
way to down-scale an image
'''
from skimage.morphology import square
from skimage.filters import rank
from skimage.transform._warps import rescale
selem = square(f)
arri = rank.mean(image, selem=selem)
return rescale(arri, 1 / f, order=0)
def test_trivial_selem8():
# check that min, max and mean returns identity if structuring element
# contains only central pixel
image = np.zeros((5, 5), dtype=np.uint8)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[0, 0, 0], [0, 1, 0], [0, 0, 0]], dtype=np.uint8)
rank.mean(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_equal(image, out)
rank.geometric_mean(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_equal(image, out)
rank.minimum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_equal(image, out)
rank.maximum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_equal(image, out)
def binary_BF(image,
meanse=disk(10),
edgefilt='prewitt',
opense=disk(10),
fill_first=False,
bi_thresh=0.000025,
tophatse=disk(20)):
#convertim = img_as_ubyte(image)
meanim = rank.mean(image, meanse)
if edgefilt is 'prewitt':
edgeim = prewitt(meanim)
elif edgefilt is 'sobel':
edgeim = sobel(meanim)
elif edgefilt is 'scharr':
edgeim = scharr(meanim)
elif edgefilt is 'roberts':
edgeim = roberts(meanim)
closeim = closing(edgeim, opense)
openim = opening(closeim, opense)
if fill_first:
seed = np.copy(openim)
seed[1:-1, 1:-1] = openim.max()
mask = openim
filledim = reconstruction(seed, mask, method='erosion')
binarim = filledim > bi_thresh
else:
binarim = openim > bi_thresh * np.mean(openim)
seed = np.copy(binarim)
seed[1:-1, 1:-1] = binarim.max()
mask = binarim
filledim = reconstruction(seed, mask, method='erosion')
tophim = filledim - closing(white_tophat(filledim, tophatse),
opense) > 0.01
fig, ax = plt.subplots(nrows=2, ncols=4, figsize=(16, 8))
ax[0][0].imshow(image, cmap='gray')
ax[0][1].imshow(meanim, cmap='gray')
ax[0][2].imshow(edgeim, cmap='gray', vmax=4 * np.mean(edgeim))
ax[0][3].imshow(closeim, cmap='gray', vmax=4 * np.mean(closeim))
ax[1][0].imshow(openim, cmap='gray', vmax=4 * np.mean(openim))
ax[1][1].imshow(binarim, cmap='gray')
ax[1][2].imshow(filledim, cmap='gray')
ax[1][3].imshow(tophim, cmap='gray')
for axes in ax:
for axe in axes:
axe.axis('off')
fig.tight_layout()
return tophim
def _compute_local_cloudiness(self) -> None:
"""
Computes the local mean cloudiness from binary cloud masks.
Returns:
None
"""
# k = np.ones([self.cloud_window_size, self.cloud_window_size])
# s = convolve(self.cloudy.astype(int), k, mode='constant', cval=0.0)
# count = convolve(np.ones(self.cloudy.shape), k, mode='constant', cval=0.0)
# self.local_cloudiness = s/count
selem = square(self.cloud_window_size)
self.local_cloudiness = rank.mean(self.cloudy.astype(int), selem)
def blur_img_in_folder(path):
if not os.path.exists(os.path.join(path, "B")):
os.mkdir(os.path.join(path, "B"))
for file_name in get_file_list_in_dir(path):
image = io.imread(os.path.join(path, file_name))
selem = disk(20)
color_array = [
rank.mean(image[:, :, dim],
selem=selem).reshape(*image.shape[:2], 1)
for dim in range(3)
]
result = np.concatenate(color_array, axis=2)
io.imsave(os.path.join(path, "B", file_name), result)
def fix():
#png_files = [f for f in listdir(depth_folder) if isfile(join(depth_folder, f))]
#Parallel(n_jobs=4)(delayed(processInput)(i) for i in range (0, len(png_files)))
for i in range(0, len(png_files)):
depth = imread(depth_folder + "/" + png_files[i])
depth = rank.mean(depth, rectangle(3, 3), mask=depth != 0)
imsave("/Data2TB/FastFood/S1/depth_fixed/" + png_files[i], depth)
#dcv = cv2.imread("/Data2TB/FastFood/S1/depth_fixed/" + png_files[i], -1)
dcv = (depth / 256).astype('uint8')
#dcv = np.zeros((480,640,3), np.uint8)
#dcv = cv2.cvtColor(depth,cv2.COLOR_GRAY2RGB,)
cv2.imwrite(
"/Data2TB/FastFood/S1/depth_paletted_fixed/" + png_files[i], dcv)
def test_empty_selem():
# check that min, max and mean returns zeros if structuring element is
# empty
image = np.zeros((5, 5), dtype=np.uint16)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
res = np.zeros_like(image)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[0, 0, 0], [0, 0, 0]], dtype=np.uint8)
rank.mean(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_equal(res, out)
rank.minimum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_equal(res, out)
rank.maximum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_equal(res, out)
def bleach_location(pre_pixels: np.array,
post_pixels: np.array,
expected_position=DEFAULT,
half_roi_size=DEFAULT):
"""
Finds the location of a bright spot in the post_pixels image
The pre_pixel image will be subtracted from the pos_pixel image (after adding
an offset to account for noise), mean filtered, and the position of the maximum in the image will
be returned. To speed up finding the location provide the estimated location and an roi
within which the real maximum should be located
:param pre_pixels:
:param post_pixels:
:param expected_position: tuple[int, int] with expected position
:param half_roi_size: tuple[int, int] area around expected_position to be searched for spot
:return:
"""
# assume pre and post are the same size
if expected_position == DEFAULT or half_roi_size == DEFAULT:
pre_roi = pre_pixels
post_roi = post_pixels
else:
if (expected_position[0] - half_roi_size[0] < 0) or \
(expected_position[1] - half_roi_size[1] < 0) or \
(expected_position[0] + half_roi_size[0] > post_pixels.shape[0]) or \
(expected_position[1] + half_roi_size[1] > post_pixels.shape[1]):
pre_roi = pre_pixels
post_roi = post_pixels
else:
cc = post_pixels.shape[1] - expected_position[1]
ep_rc = [expected_position[0], cc]
pre_roi = pre_pixels[ep_rc[0] - half_roi_size[0]:ep_rc[0] +
half_roi_size[0], ep_rc[1] -
half_roi_size[1]:ep_rc[1] + half_roi_size[1]]
post_roi = post_pixels[ep_rc[0] - half_roi_size[0]:ep_rc[0] +
half_roi_size[0],
ep_rc[1] - half_roi_size[1]:ep_rc[1] +
half_roi_size[1]]
subtracted = post_roi + 100 - pre_roi
selem = disk(2)
subtracted_mean = rank.mean(subtracted, selem=selem)
peaks_rc_roi = peak_local_max(subtracted_mean,
min_distance=20,
threshold_rel=0.6,
num_peaks=1,
indices=True)
peaks_rc = peaks_rc_roi + [
ep_rc[0] - half_roi_size[0], ep_rc[1] - half_roi_size[1]
]
peaks = [peaks_rc[0][0], post_pixels.shape[1] - peaks_rc[0][1]]
return peaks
def smooth(image_in, smooth_type, smooth_size, contrast=False):
# smoothed = rank.median(np.copy(image_in), disk(smooth_size))
if smooth_type == 'mean':
print('running a mean filter')
return rank.mean(np.copy(image_in), disk(smooth_size))
if smooth_type == 'median':
print('running a median filter')
return rank.median(np.copy(image_in), disk(smooth_size))
if smooth_type == 'gaussian':
print('running a Gaussian filter')
return gaussian(image_in, smooth_size)
if smooth_type == 'none':
print('not running a filter')
return np.copy(image_in)
def test_16bit():
image = np.zeros((21, 21), dtype=np.uint16)
selem = np.ones((3, 3), dtype=np.uint8)
for bitdepth in range(17):
value = 2 ** bitdepth - 1
image[10, 10] = value
if bitdepth > 11:
expected = ['Bitdepth of %s' % (bitdepth - 1)]
else:
expected = []
with expected_warnings(expected):
assert rank.minimum(image, selem)[10, 10] == 0
assert rank.maximum(image, selem)[10, 10] == value
assert rank.mean(image, selem)[10, 10] == int(value / selem.size)
def test_16bit():
image = np.zeros((21, 21), dtype=np.uint16)
selem = np.ones((3, 3), dtype=np.uint8)
for bitdepth in range(17):
value = 2**bitdepth - 1
image[10, 10] = value
if bitdepth > 11:
expected = ['Bitdepth of %s' % (bitdepth - 1)]
else:
expected = []
with expected_warnings(expected):
assert rank.minimum(image, selem)[10, 10] == 0
assert rank.maximum(image, selem)[10, 10] == value
assert rank.mean(image, selem)[10, 10] == int(value / selem.size)
def _segment_edge_areas(self, edges, disk_size, mean_threshold, min_object_size):
"""
Takes a greyscale image (with brighter colors corresponding to edges) and returns a
binary image where white indicates an area with high edge density and black indicates low density.
"""
# Convert the greyscale edge information into black and white (ie binary) image
threshold = threshold_otsu(edges)
# Filter out the edge data below the threshold, effectively removing some noise
raw_channel_areas = edges <= threshold
# Smooth out the data
channel_areas = rank.mean(raw_channel_areas, disk(disk_size)) < mean_threshold
# Remove specks and blobs that are the result of artifacts
clean_channel_areas = remove_small_objects(channel_areas, min_size=min_object_size)
# Fill in any areas that are completely surrounded by the areas (hopefully) covering the channels
return ndimage.binary_fill_holes(clean_channel_areas)
def ski_uniform_filter(img, myfilter, kernel):
# applies a filter to an image
# skiimage has different ways to define the kernel
# this a function compensates for it
if myfilter == "Median":
kernel2d = np.ones((kernel, kernel), dtype=bool)
result = skimage.filters.median(img, selem=kernel2d)
elif myfilter == "Gaussian":
result = skimage.filters.gaussian(img, kernel)
elif myfilter == "Mean":
selem = disk(kernel)
result = rank.mean(img, selem=selem)
elif myfilter == "None":
result = img
return result
def test_16bit(self):
image = np.zeros((21, 21), dtype=np.uint16)
footprint = np.ones((3, 3), dtype=np.uint8)
for bitdepth in range(17):
value = 2**bitdepth - 1
image[10, 10] = value
if bitdepth >= 11:
expected = ['Bad rank filter performance']
else:
expected = []
with expected_warnings(expected):
assert rank.minimum(image, footprint)[10, 10] == 0
assert rank.maximum(image, footprint)[10, 10] == value
mean_val = rank.mean(image, footprint)[10, 10]
assert mean_val == int(value / footprint.size)
def test_random_sizes(self):
# make sure the size is not a problem
elem = np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]], dtype=np.uint8)
for m, n in np.random.randint(1, 101, size=(10, 2)):
mask = np.ones((m, n), dtype=np.uint8)
image8 = np.ones((m, n), dtype=np.uint8)
out8 = np.empty_like(image8)
rank.mean(image=image8, selem=elem, mask=mask, out=out8,
shift_x=0, shift_y=0)
assert_equal(image8.shape, out8.shape)
rank.mean(image=image8, selem=elem, mask=mask, out=out8,
shift_x=+1, shift_y=+1)
assert_equal(image8.shape, out8.shape)
rank.geometric_mean(image=image8, selem=elem, mask=mask, out=out8,
shift_x=0, shift_y=0)
assert_equal(image8.shape, out8.shape)
rank.geometric_mean(image=image8, selem=elem, mask=mask, out=out8,
shift_x=+1, shift_y=+1)
assert_equal(image8.shape, out8.shape)
image16 = np.ones((m, n), dtype=np.uint16)
out16 = np.empty_like(image8, dtype=np.uint16)
rank.mean(image=image16, selem=elem, mask=mask, out=out16,
shift_x=0, shift_y=0)
assert_equal(image16.shape, out16.shape)
rank.mean(image=image16, selem=elem, mask=mask, out=out16,
shift_x=+1, shift_y=+1)
assert_equal(image16.shape, out16.shape)
rank.geometric_mean(image=image16, selem=elem, mask=mask, out=out16,
shift_x=0, shift_y=0)
assert_equal(image16.shape, out16.shape)
rank.geometric_mean(image=image16, selem=elem, mask=mask, out=out16,
shift_x=+1, shift_y=+1)
assert_equal(image16.shape, out16.shape)
rank.mean_percentile(image=image16, mask=mask, out=out16,
selem=elem, shift_x=0, shift_y=0, p0=.1, p1=.9)
assert_equal(image16.shape, out16.shape)
rank.mean_percentile(image=image16, mask=mask, out=out16,
selem=elem, shift_x=+1, shift_y=+1, p0=.1, p1=.9)
assert_equal(image16.shape, out16.shape)
def _segment_edge_areas(self, edges, disk_size, mean_threshold,
min_object_size):
"""
Takes a greyscale image (with brighter colors corresponding to edges) and returns a
binary image where white indicates an area with high edge density and black indicates low density.
"""
# Convert the greyscale edge information into black and white (ie binary) image
threshold = threshold_otsu(edges)
# Filter out the edge data below the threshold, effectively removing some noise
raw_channel_areas = edges <= threshold
# Smooth out the data
channel_areas = rank.mean(raw_channel_areas,
disk(disk_size)) < mean_threshold
# Remove specks and blobs that are the result of artifacts
clean_channel_areas = remove_small_objects(channel_areas,
min_size=min_object_size)
# Fill in any areas that are completely surrounded by the areas (hopefully) covering the channels
return ndimage.binary_fill_holes(clean_channel_areas)
def color_adjustment(self, img, mask=None, gaussian_std=.0, gamma=1.0, contrast = 1.0, brightness = 0, mult_rgb = np.array([1.0, 1.0, 1.0]), blur_radius = 0):
img **= gamma
img *= contrast
img += np.random.randn(*img.shape).astype('float32') * gaussian_std
img += brightness
img *= mult_rgb
np.clip(img, 0.0, 1.0, img)
blur_mask = None
if mask is not None:
blur_mask = random.choice([mask,1-mask,np.ones_like(mask)])
if blur_radius > 0:
selem = disk(blur_radius)
tmp_img = img.copy()
for i in range(img.shape[2]):
img[:, :, i] = rank.mean(img[:, :, i], selem=selem,mask=blur_mask) / 255.0
img[np.where(blur_mask == 0)] = tmp_img[np.where(blur_mask==0)]
return img
def mask_gen(img_filepath):
# Open image
img = io.imread(img_filepath)
converted_img = img_as_float(img)
# bilateral smoothing to preserve borders
img_smooth = mean(converted_img, morphology.disk(10))
# Equalize histogram of input image
img_histeq = exposure.equalize_adapthist(img_smooth)
# Highpass filter for image
img_otsu = img_histeq >= filters.threshold_otsu(img_histeq)
# generate mask
# edges = feature.canny(filters.gaussian(img_histeq),
# sigma=1,
# # low_threshold=0.01*((2**16)-1),
# # high_threshold=0.1*((2**16)-1)
# )
# mask = ndi.binary_fill_holes(edges)
# mask = morphology.binary_dilation(mask)
# mask = ndi.binary_fill_holes(mask)
# mask = morphology.binary_opening(mask)
# mask = ndi.binary_fill_holes(mask)
final_mask = ndi.binary_fill_holes(img_otsu)
# remove blobs touching border
cleared_mask = segmentation.clear_border(final_mask)
label_mask = img_labeler(cleared_mask)
mask_centroids = centroids(label_mask)
# TODO: test blob removal
distances = []
for centroid in mask_centroids:
distances.append(ruler(*centroid, len(img) - 1, len(img) - 1))
# Minimum distance centroid from bottom right
try:
min_idx = distances.index(min(distances))
# print("southeast-most centroid index: " + str(min_idx))
# remove labeled regions in for loop
for idx, region in enumerate(measure.regionprops(label_mask)):
if idx != min_idx:
for region_coord in region.coords:
x = region_coord[0]
y = region_coord[1]
cleared_mask[x, y] = 0
except ValueError:
raise ValueError("Couldn't segment", img_filepath)
return (img, img_smooth, img_otsu, final_mask, cleared_mask)
def check_all():
np.random.seed(0)
image = np.random.rand(25, 25)
selem = morphology.disk(1)
refs = np.load(os.path.join(skimage.data_dir, "rank_filter_tests.npz"))
assert_equal(refs["autolevel"], rank.autolevel(image, selem))
assert_equal(refs["autolevel_percentile"],
rank.autolevel_percentile(image, selem))
assert_equal(refs["bottomhat"], rank.bottomhat(image, selem))
assert_equal(refs["equalize"], rank.equalize(image, selem))
assert_equal(refs["gradient"], rank.gradient(image, selem))
assert_equal(refs["gradient_percentile"],
rank.gradient_percentile(image, selem))
assert_equal(refs["maximum"], rank.maximum(image, selem))
assert_equal(refs["mean"], rank.mean(image, selem))
assert_equal(refs["geometric_mean"], rank.geometric_mean(image, selem)),
assert_equal(refs["mean_percentile"], rank.mean_percentile(image, selem))
assert_equal(refs["mean_bilateral"], rank.mean_bilateral(image, selem))
assert_equal(refs["subtract_mean"], rank.subtract_mean(image, selem))
assert_equal(refs["subtract_mean_percentile"],
rank.subtract_mean_percentile(image, selem))
assert_equal(refs["median"], rank.median(image, selem))
assert_equal(refs["minimum"], rank.minimum(image, selem))
assert_equal(refs["modal"], rank.modal(image, selem))
assert_equal(refs["enhance_contrast"], rank.enhance_contrast(image, selem))
assert_equal(refs["enhance_contrast_percentile"],
rank.enhance_contrast_percentile(image, selem))
assert_equal(refs["pop"], rank.pop(image, selem))
assert_equal(refs["pop_percentile"], rank.pop_percentile(image, selem))
assert_equal(refs["pop_bilateral"], rank.pop_bilateral(image, selem))
assert_equal(refs["sum"], rank.sum(image, selem))
assert_equal(refs["sum_bilateral"], rank.sum_bilateral(image, selem))
assert_equal(refs["sum_percentile"], rank.sum_percentile(image, selem))
assert_equal(refs["threshold"], rank.threshold(image, selem))
assert_equal(refs["threshold_percentile"],
rank.threshold_percentile(image, selem))
assert_equal(refs["tophat"], rank.tophat(image, selem))
assert_equal(refs["noise_filter"], rank.noise_filter(image, selem))
assert_equal(refs["entropy"], rank.entropy(image, selem))
assert_equal(refs["otsu"], rank.otsu(image, selem))
assert_equal(refs["percentile"], rank.percentile(image, selem))
assert_equal(refs["windowed_histogram"],
rank.windowed_histogram(image, selem))
def pyramid_decomposition(image):
"""
Разложение начинается с масштаба исходного изображения. Оно делится на
непересекающиеся квадраты размером 2х2 пикселя, в каждом из которых мы
получаем значения минимума, максимума и среднего из 4-х пикселей, его
составляющих. Далее из этих значений формируем три изображения:
минимумов, максимумов и средних, которые уменьшены в 2 раза по
горизонтали и вертикали относительно исходного. Повторяем процедуру и
раскладываем полученные изображения в пирамиды до уровня, на котором
размер ещё составляет не менее 2 пикселей по горизонтали и вертикали.
:param image:
:return:
"""
width, height = image.shape
factor = 2
max_list, min_list, mean_list = [], [], []
image_2_map = image.copy()
map_max = maximum_filter(image_2_map, factor)
map_min = minimum_filter(image_2_map, factor)
map_mean = mean_percentile(image_2_map, np.ones((2, 2))) / 255.
while min(width, height) > 3:
width, height = int(width / factor), int(height / factor)
map_max = resize(map_max, (width, height))
map_min = resize(map_min, (width, height))
map_mean = resize(map_mean, (width, height))
width, height = map_max.shape
max_list.append(map_max)
min_list.append(map_min)
mean_list.append(map_mean)
map_max = maximum_filter(map_max, factor)
map_min = minimum_filter(map_min, factor)
map_mean = mean(map_mean, np.ones((2, 2)))
return max_list, min_list, mean_list
def merge(self, ori_img, mask_img, fil_light=True):
img = ori_img.copy()
img_s = cv2.split(img)
if not self.if_set_border:
print("merge base circle")
# hough圆范围矩阵
border = np.fromfunction(self.func2, mask_img.shape)
else:
print("merge base border")
self.border_mask = cv2.fillConvexPoly(self.border_mask,
self.border_cnt, 0)
cv2.imwrite("out.jpg", self.border_mask)
mask = cv2.resize(self.border_mask,
(ori_img.shape[1], ori_img.shape[0]),
cv2.INTER_NEAREST)
# 手选范围矩阵
border = np.where(mask == 0, True, False)
# 计算总面积
self.all_area = np.sum(border == True)
# 叠加检测结果矩阵
border = np.where(mask_img > 0, border, False)
# 叠加局部细纹合并矩阵（局部细纹大于30%认定整个区域为杂质区域）
bad = sfr.mean(border, disk(15))
border = np.where(bad > 255 * 0.30, True, border) # 原0.25
border = np.where(bad < 255 * 0.08, False, border) # 原0.08
if fil_light: # 叠加过滤光斑矩阵
light = sfr.maximum(self.orig_gray, disk(15))
# light_mean = sfr.mean(self.orig_gray, disk(15))
# light=np.where(light_mean>255*0.9,light,self.orig_gray)
border = np.where(light < 230, border, False)
mask = np.where(border, mask_img, 0)
img_s[0] = np.where(border, 255, img_s[0])
img_s[1] = np.where(border, 0, img_s[1])
img_s[2] = np.where(border, 0, img_s[2])
img = cv2.merge(img_s)
# 计算杂质面积
self.dirt_area = np.sum(border == True)
return img, mask
def meanFilter(self, m=3, array=numpy.empty(0)):
"""
Mean filtering, replaces the intensity value, by the average
intensity of a pixels neighbours including itself.
m is the size of the filter, default is 3x3
@method meanFilter
@param m {int} The width and height of the m x m filtering matrix,
default is 3.
@param array {numpy array} the array which the operation is carried
out on.
"""
self.__printStatus("Mean filtering " + str(m) + "x" + str(m) + "...")
if not array.any():
array = self.image_array
if array.dtype not in ["uint8", "uint16"]:
array = numpy.uint8(array)
mean3x3filter = rank.mean(array, square(m), mask=self.mask)
self.image_array = mean3x3filter * self.mask
self.__printStatus("[done]", True)
return self
def create_markers(im, min_size = 3, connectivity=2):
im = rank.mean(im, np.ones((3,3)))
im = im > threshold_li(im)
im = erosion(im, np.ones((3,3)))
labels = measure.label(im, connectivity=connectivity)
labels_flat = labels.ravel()
labels_count = np.bincount(labels_flat)
index = np.argsort(labels_flat)[labels_count[0]:]
coordinates = np.column_stack(np.unravel_index(index, im.shape))
lab = np.cumsum(labels_count[1:])
im = np.zeros(im.shape, np.uint8)
it = dict(enumerate(np.split(coordinates, lab), start=1))
for _, indexes in it.items():
if len(indexes) < min_size:
continue
center = np.mean(indexes, axis=0)
y, x = int(center[0]), int(center[1])
im[y,x] = 255
return im
def background_subtraction(phase_contrast, diameter=19):
"""Local mean subtraction with clipping.
Parameters
-----------
phase_contrast : numpy.ndarray
Returns
--------
Tuple of numpy.ndarray
"""
# compute local average image
selem = disk(diameter)
background = mean((phase_contrast * 255).astype('uint8'), selem) / 255.
# build difference and clip
segmentation = np.maximum(background - phase_contrast, 0)
return background, segmentation
def meanFilter(self, m=3, array=numpy.empty(0)):
"""
Mean filtering, replaces the intensity value, by the average
intensity of a pixels neighbours including itself.
m is the size of the filter, default is 3x3
@method meanFilter
@param m {int} The width and height of the m x m filtering matrix,
default is 3.
@param array {numpy array} the array which the operation is carried
out on.
"""
self.__printStatus("Mean filtering " + str(m) + "x" + str(m) + "...")
if not array.any():
array = self.image_array
if array.dtype not in ["uint8", "uint16"]:
array = numpy.uint8(array)
mean3x3filter = rank.mean(array, square(m), mask=self.mask)
self.image_array = mean3x3filter * self.mask
self.__printStatus("[done]", True)
return self
def apply_filter(img, v=1):
if v == 0:
return img[:, :, 0]
elif v == 1:
return remove_small_blobs(img[:, :, 0], background=255)
elif v == 2:
selem = disk(1.4)
dilatado = dilation(
remove_small_blobs(img[:, :, 0], background=255, min_area=10),
selem)
unblobbed2 = remove_small_blobs(erosion(dilatado, selem),
background=255,
min_area=15)
return rank.mean(unblobbed2, selem=selem)
elif v == 3:
unblobbed = remove_small_blobs(img[:, :, 0], background=255)
selem = disk(1.4)
return remove_small_blobs(dilation(unblobbed, selem),
background=255,
min_area=10)
else:
pass
def check_all():
np.random.seed(0)
image = np.random.rand(25, 25)
selem = morphology.disk(1)
refs = np.load(os.path.join(skimage.data_dir, "rank_filter_tests.npz"))
assert_equal(refs["autolevel"], rank.autolevel(image, selem))
assert_equal(refs["autolevel_percentile"], rank.autolevel_percentile(image, selem))
assert_equal(refs["bottomhat"], rank.bottomhat(image, selem))
assert_equal(refs["equalize"], rank.equalize(image, selem))
assert_equal(refs["gradient"], rank.gradient(image, selem))
assert_equal(refs["gradient_percentile"], rank.gradient_percentile(image, selem))
assert_equal(refs["maximum"], rank.maximum(image, selem))
assert_equal(refs["mean"], rank.mean(image, selem))
assert_equal(refs["mean_percentile"], rank.mean_percentile(image, selem))
assert_equal(refs["mean_bilateral"], rank.mean_bilateral(image, selem))
assert_equal(refs["subtract_mean"], rank.subtract_mean(image, selem))
assert_equal(refs["subtract_mean_percentile"], rank.subtract_mean_percentile(image, selem))
assert_equal(refs["median"], rank.median(image, selem))
assert_equal(refs["minimum"], rank.minimum(image, selem))
assert_equal(refs["modal"], rank.modal(image, selem))
assert_equal(refs["enhance_contrast"], rank.enhance_contrast(image, selem))
assert_equal(refs["enhance_contrast_percentile"], rank.enhance_contrast_percentile(image, selem))
assert_equal(refs["pop"], rank.pop(image, selem))
assert_equal(refs["pop_percentile"], rank.pop_percentile(image, selem))
assert_equal(refs["pop_bilateral"], rank.pop_bilateral(image, selem))
assert_equal(refs["sum"], rank.sum(image, selem))
assert_equal(refs["sum_bilateral"], rank.sum_bilateral(image, selem))
assert_equal(refs["sum_percentile"], rank.sum_percentile(image, selem))
assert_equal(refs["threshold"], rank.threshold(image, selem))
assert_equal(refs["threshold_percentile"], rank.threshold_percentile(image, selem))
assert_equal(refs["tophat"], rank.tophat(image, selem))
assert_equal(refs["noise_filter"], rank.noise_filter(image, selem))
assert_equal(refs["entropy"], rank.entropy(image, selem))
assert_equal(refs["otsu"], rank.otsu(image, selem))
assert_equal(refs["percentile"], rank.percentile(image, selem))
assert_equal(refs["windowed_histogram"], rank.windowed_histogram(image, selem))
def background_subtraction(self, img, method='avg'):
#width, height = img.shape
if method=='avg':
# vigra
#kernel = vigra.filters.averagingKernel(radius)
#bgsub = img - vigra.filters.convolve(self.ut.to_float(img), kernel)
# with skimage
se = disk(self.settings.background_subtraction['radius'])
bgsub = img.astype(np.dtype('float')) - rank.mean(img, se)
bgsub[bgsub < 0] = 0
bgsub = bgsub.astype(img.dtype)
if method=='med':
# vigra
#kernel = vigra.filters.averagingKernel(radius)
#bgsub = img - vigra.filters.convolve(self.ut.to_float(img), kernel)
# with skimage
se = disk(self.settings.background_subtraction['radius'])
bgsub = img.astype(np.dtype('float')) - rank.median(img, se)
bgsub[bgsub < 0] = 0
bgsub = bgsub.astype(img.dtype)
elif method=='constant_median':
# vigra
#bgsub = img - np.median(np.array(img))
# with skimage
bgsub = img - np.median(img)
bgsub[bgsub < 0] = 0
bgsub = bgsub.astype(img.dtype)
return bgsub
def mean_filter(image, kernel_shape, kernel_size):
"""Apply a mean filter to a 2-d image.
Parameters
----------
image : np.ndarray, np.uint
Image with shape (y, x).
kernel_shape : str
Shape of the kernel used to compute the filter ('diamond', 'disk',
'rectangle' or 'square').
kernel_size : int or Tuple(int)
The size of the kernel. For the rectangle we expect two integers
(height, width).
Returns
-------
image_filtered : np.ndarray, np.uint
Filtered 2-d image with shape (y, x).
"""
# check parameters
check_array(image,
ndim=2,
dtype=[np.uint8, np.uint16])
check_parameter(kernel_shape=str,
kernel_size=(int, tuple, list))
# get kernel
kernel = _define_kernel(shape=kernel_shape,
size=kernel_size,
dtype=image.dtype)
# apply filter
image_filtered = rank.mean(image, kernel)
return image_filtered
unique = np.unique(R)
centroid = ndimage.measurements.center_of_mass(gel, R, unique)
# finding the intensity and priting results:
for i in range(len(centroid)):
print 'Spot %d x: %f y: %f intensity: %d' % (i+1, centroid[i][0], centroid[i][1], gel[int(centroid[i][0]), int(centroid[i][1])])
colored = label2rgb(R, gel, bg_label=0)
for i in range(len(centroid)):
rr, cc = circle(centroid[i][0], centroid[i][1], 2)
colored[rr, cc] = (1,0,0)
io.imsave(argv[2], colored)
print "Smoothing the image before running watershed..."
loc_mean = mean(gel, disk(1))
smooth_M = watershed(loc_mean, ' ')
print "Number of spots found on the smoothed image without any post process is:"
print len(np.unique(smooth_M))
R = morphology.remove_small_objects(smooth_M.astype(int), 6)
colored = label2rgb(R, gel, bg_label=0)
io.imsave('smooth_cleaned.png', colored)
print "Number of spots found on the smoothed image after image processing is:"
print len(np.unique(R))
#############################
#Answering the question 1, using different edge operator methods to detect markers:
print 'The number of spots found using roberts gradient method is:'
M_roberts = watershed(gel, 'roberts')
R_roberts = morphology.remove_small_objects(M_roberts.astype(int), 64)
print len(np.unique(R_roberts))
def pipeline(filename):
# Report that the pipeline is being executed
print " Starting pipeline for", filename
# Import tif file
import skimage.io as io # Image file manipulation module
img = io.imread(filename) # Importing multi-color tif file
# Slicing: We only work on one channel for segmentation
green = img[0,:,:]
#------------------------------------------------------------------------------
# PREPROCESSING AND SIMPLE CELL SEGMENTATION:
# (I) SMOOTHING AND (II) ADAPTIVE THRESHOLDING
# -------
# Part I
# -------
# Gaussian smoothing
sigma = 3 # Smoothing factor for Gaussian
green_smooth = ndi.filters.gaussian_filter(green,sigma) # Perform smoothing
# -------
# Part II
# -------
# Create an adaptive background
struct = ((np.mgrid[:31,:31][0] - 15)**2 + (np.mgrid[:31,:31][1] - 15)**2) <= 15**2 # Create a disk-shaped structural element
from skimage.filters import rank # Import module containing mean filter function
bg = rank.mean(green_smooth, selem=struct) # Run a mean filter over the image using the disc
# Threshold using created background
green_mem = green_smooth >= bg
# Clean by morphological hole filling
green_mem = ndi.binary_fill_holes(np.logical_not(green_mem))
#------------------------------------------------------------------------------
# IMPROVED CELL SEGMENTATION BY SEEDING AND EXPANSION:
# (I) SEEDING BY DISTANCE TRANSFORM
# (II) EXPANSION BY WATERSHED
# -------
# Part I
# -------
# Distance transform on thresholded membranes
# Advantage of distance transform for seeding: It is quite robust to local
# "holes" in the membranes.
green_dt= ndi.distance_transform_edt(green_mem)
# Dilating (maximum filter) of distance transform improves results
green_dt = ndi.filters.maximum_filter(green_dt,size=10)
# Retrieve and label the local maxima
from skimage.feature import peak_local_max
green_max = peak_local_max(green_dt,indices=False,min_distance=10) # Local maximum detection
green_max = ndi.label(green_max)[0] # Labeling
# -------
# Part II
# -------
# Get the watershed function and run it
from skimage.morphology import watershed
green_ws = watershed(green_smooth,green_max)
#------------------------------------------------------------------------------
# IDENTIFICATION OF CELL EDGES
# Define the edge detection function
def edge_finder(footprint_values):
if (footprint_values == footprint_values[0]).all():
return 0
else:
return 1
# Iterate the edge finder over the segmentation
green_edges = ndi.filters.generic_filter(green_ws,edge_finder,size=3)
#------------------------------------------------------------------------------
# POSTPROCESSING: REMOVING CELLS AT THE IMAGE BORDER
# Create a mask for the image boundary pixels
boundary_mask = np.ones_like(green_ws) # Initialize with all ones
boundary_mask[1:-1,1:-1] = 0 # Set middle square to 0
# Iterate over all cells in the segmentation
current_label = 1
for cell_id in np.unique(green_ws):
# If the current cell touches the boundary, remove it
if np.sum((green_ws==cell_id)*boundary_mask) != 0:
green_ws[green_ws==cell_id] = 0
# This is to keep the labeling continuous, which is cleaner
else:
green_ws[green_ws==cell_id] = current_label
current_label += 1
#------------------------------------------------------------------------------
# MEASUREMENTS: SINGLE-CELL AND MEMBRANE READOUTS
# Initialize a dict for results of choice
results = {"cell_id":[], "green_mean":[], "red_mean":[],"green_membrane_mean":[],
"red_membrane_mean":[],"cell_size":[],"cell_outline":[]}
# Iterate over segmented cells
for cell_id in np.unique(green_ws)[1:]:
# Mask the pixels of the current cell
cell_mask = green_ws==cell_id
edge_mask = np.logical_and(cell_mask,green_edges)
# Get the current cell's values
# Note that the original raw data is used for quantification!
results["cell_id"].append(cell_id)
results["green_mean"].append(np.mean(img[0,:,:][cell_mask]))
results["red_mean"].append(np.mean(img[1,:,:][cell_mask]))
results["green_membrane_mean"].append(np.mean(img[0,:,:][edge_mask]))
results["red_membrane_mean"].append(np.mean(img[1,:,:][edge_mask]))
results["cell_size"].append(np.sum(cell_mask))
results["cell_outline"].append(np.sum(edge_mask))
#------------------------------------------------------------------------------
# REPORT PROGRESS AND RETURN RESULTS
print " Completed pipeline for", filename
return green_ws, results
# increasing, objects with bigger sizes are filtered as well, such as the
# camera tripod. The median filter is often used for noise removal because
# borders are preserved and e.g. salt and pepper noise typically does not
# distort the gray-level.
#
# Image smoothing
# ===============
#
# The example hereunder shows how a local **mean** filter smooths the camera
# man image.
from skimage.filters.rank import mean
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=[10, 7], sharex=True, sharey=True)
loc_mean = mean(noisy_image, disk(10))
ax1.imshow(noisy_image, vmin=0, vmax=255, cmap=plt.cm.gray)
ax1.set_title('Original')
ax1.axis('off')
ax1.set_adjustable('box-forced')
ax2.imshow(loc_mean, vmin=0, vmax=255, cmap=plt.cm.gray)
ax2.set_title('Local mean $r=10$')
ax2.axis('off')
ax2.set_adjustable('box-forced')
######################################################################
#
# One may be interested in smoothing an image while preserving important
# borders (median filters already achieved this), here we use the
noise = (df.at[0, 'noise'])[0]
adv_im = (df.at[0, 'adv_im'])[0]
adv_recon = (df.at[0, 'adv_recon'])[0]
if (sys.argv[2] == 'bin'):
adv_bin = adv_im.copy()
adv_bin = (adv_bin.reshape((-1, 784))).astype(np.float32)
adv_bin[adv_bin > 0.5] = 1
adv_bin[adv_bin <= 0.5] = 0
l_noise.b.set_value(np.zeros((784, )).astype(np.float32))
adv_bin_recon = adv_plot(mnist_input(adv_bin))[0]
adv_bin_recon = (adv_bin_recon / 255.0).astype(np.float32)
if (sys.argv[2] == 'mean_filter'):
radius = 1
adv_mean = mean(adv_im, disk(radius))
# adv_mean = (adv_mean.reshape((-1, 784))).astype(np.float32)
l_noise.b.set_value(np.zeros((784, )).astype(np.float32))
adv_mean_recon = adv_plot(mnist_input(adv_mean))[0]
adv_mean_recon = (adv_mean_recon / 255.0).astype(np.float32)
orig_mean = mean(orig.copy().reshape(28, 28), disk(radius))
#print("adv_bin shape: ", adv_bin.shape)
#adv_bin_recon = lasagne.layers.get_output(l_dec_x, adv_bin, deterministic = True)
#print("type of adv_bin_recon: ", type(adv_bin_recon))
fig = plt.figure(figsize=(10, 10))
img = orig
i = 1
title = "Original Image"
def TestSample(self): # Run pump, take samples and analyse
global currentPhoto
self.im1Count["text"] = "-" # Reset text fields
self.im2Count["text"] = "-"
self.im3Count["text"] = "-"
self.im1Average["text"] = "-"
self.im2Average["text"] = "-"
self.im3Average["text"] = "-"
self.imFinalCount["text"] = "-"
self.imFinalAverage["text"] = "-"
self.sizeAct["text"] = "-"
self.Confidence["text"] = "-"
self.ConfDisp["bg"] = "grey"
##'''
global camera
camera.stop_preview() # Quit preview if open
########################### Run pump and take Pictures ###############################
self.pump_On() # Turn on pump
self.update_idletasks() # Refresh Gui
for x in range(0, 25): # Wait 25 seconds
self.labelCurrentAction["text"] = "Pumping Liquid - %d" % (25 - x)
self.update_idletasks()
time.sleep(1)
self.pump_Off() # Turn off pump
for x in range(1, 4): # Take 3 images
self.pump_Off()
self.labelCurrentAction["text"] = "Powder Settle Time"
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction["text"] = "Capturing Image %d" % x
camera.hflip = True # Flip camera orientation appropriately
camera.vflip = True
camera.capture("/home/pi/PythonTempFolder/OrigPic" + str(x) + ".jpg") # Save image to default directory
self.update_idletasks()
time.sleep(2)
if x < 3:
self.pump_On() # Turn on pump
for y in range(0, 6): # Wait 6 seconds
self.labelCurrentAction["text"] = "Pumping Liquid - %d" % (6 - y)
self.update_idletasks()
time.sleep(1)
self.pump_Off() # Turn off pump
##'''
################################################################################################
########################### Analyse Pictures ###############################
for x in range(1, 4):
self.labelCurrentAction["text"] = "Loading image as greyscale - im %d" % x
self.update_idletasks()
image1 = io.imread(
"/home/pi/PythonTempFolder/OrigPic" + str(x) + ".jpg", as_grey=True
) # Load image as greyscale
##
##image1 = io.imread('/home/pi/SDP Project/PowderTests/PPIM169041/169041Pic' + str(x) + '.jpg', as_grey=True) ##Comment Out
##
self.labelCurrentAction["text"] = "Cropping" # Crop image
self.update_idletasks()
fromFile = np.asarray(image1, dtype=np.float32)
orig = fromFile[0:1080, 420:1500]
currentPhoto = orig
self.showCurrent()
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction["text"] = "Applying minimum filter" # Apply minimum filter
self.update_idletasks()
image2 = minimum(orig, disk(6))
currentPhoto = image2
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
self.labelCurrentAction["text"] = "Applying mean filter" # Apply mean filter
self.update_idletasks()
image3 = mean(image2, disk(22))
currentPhoto = image3
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
self.labelCurrentAction["text"] = "Applying maximum filter" # Apply maximum filter
self.update_idletasks()
image4 = maximum(image3, disk(6))
currentPhoto = image4
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction["text"] = "Normalising" # Subtract filtered image from original
self.update_idletasks()
new = np.asarray(image4, dtype=np.float32)
new[0:, 0:] = new[0:, 0:] / 255
sub = np.subtract(orig, new)
sub[0:, 0:] += 128 / 255 # Scale appropriately
imFinal = sub
currentPhoto = sub
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
time.sleep(1)
self.labelCurrentAction["text"] = "Thresholding (Otsu)" # Get Otsu threshold value from image
self.update_idletasks()
thresh = threshold_otsu(imFinal) ##Threshold
print("T - " + str(thresh))
intensity = float(self.entryIntensity.get()) # Get manual threshold value from text field
self.labelCurrentAction[
"text"
] = "Creating Binary Image" # Create binary image from threshold value (changed to manual - ignore otsu)
self.update_idletasks()
binary = sub <= intensity # 0.095 #(thresh+0.2)
scipy.misc.imsave(
"/home/pi/PythonTempFolder/binary" + str(x) + ".jpg", binary
) # Save binary image to default directory
currentPhoto = binary
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
labels = label(binary)
self.labelCurrentAction["text"] = "Analysing Particles"
self.update_idletasks()
counter = 0
areaCount = 0
Tmin = int(self.entryTmin.get()) # Get size thresholds from text input
Tmax = int(self.entryTmax.get())
################################################################################################
# Tmin = 10
# Tmax = 300
for region in regionprops(labels): # Iterate through particles in the binary image
if region.area <= Tmax and region.area >= Tmin:
counter = counter + 1 # Count number of particles found
areaCount = areaCount + region.area # Sum area of all particles
average = areaCount / counter # Calculate average area
if x == 1:
self.im1Count["text"] = counter
self.im1Average["text"] = round(average, 5) # Display average image 1
counter1 = counter
average1 = average
if x == 2:
self.im2Count["text"] = counter
self.im2Average["text"] = round(average, 5) # Display average image 2
counter2 = counter
average2 = average
if x == 3:
self.im3Count["text"] = counter
self.im3Average["text"] = round(average, 5) # Display average image 3
counter3 = counter
average3 = average
print(counter)
average = areaCount / counter
# print(average)
self.t.destroy()
self.update_idletasks()
finalCount = (counter1 + counter2 + counter3) / 3 # Calculate final count all images
finalAverage = (average1 + average2 + average3) / 3 # Calculate final average all images
self.imFinalCount["text"] = finalCount
self.imFinalAverage["text"] = round(finalAverage, 3)
microns = (math.sqrt((finalAverage * 113.0989232) / 3.14159265359)) * 2 # Size approximation
self.sizeAct["text"] = "~ " + str(round(microns, 3)) + " microns"
maxCount = max(counter1, counter2, counter3)
Conf = float(finalCount) / float(maxCount)
self.Confidence["text"] = str(round(Conf, 3)) + " %"
print(finalCount)
# print(maxCount)
print(Conf)
self.ConfDisp["bg"] = "red" # Change confidence colours
if Conf >= 0.84:
self.ConfDisp["bg"] = "yellow"
if Conf >= 0.93:
self.ConfDisp["bg"] = "green"
self.labelCurrentAction["text"] = "Complete!"
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction["text"] = "idle"
self.update_idletasks()
"""
import numpy as np
import matplotlib.pyplot as plt
from skimage import data
from skimage.morphology import disk
from skimage.filters import rank
image = (data.coins()).astype(np.uint16) * 16
selem = disk(20)
percentile_result = rank.mean_percentile(image, selem=selem, p0=0.1, p1=0.9)
bilateral_result = rank.mean_bilateral(image, selem=selem, s0=500, s1=500)
normal_result = rank.mean(image, selem=selem)
fig, axes = plt.subplots(nrows=3, figsize=(8, 10))
ax0, ax1, ax2 = axes
ax0.imshow(np.hstack((image, percentile_result)))
ax0.set_title("Percentile mean")
ax0.axis("off")
ax1.imshow(np.hstack((image, bilateral_result)))
ax1.set_title("Bilateral mean")
ax1.axis("off")
ax2.imshow(np.hstack((image, normal_result)))
ax2.set_title("Local mean")
sigma = 3 # Smoothing factor for Gaussian green_smooth = ndi.filters.gaussian_filter(green,sigma) # Perform smoothing # visualise plt.imshow(green_smooth,interpolation='none',cmap='gray') plt.show() # ------- # Part II # ------- # Create an adaptive background struct = ((np.mgrid[:31,:31][0] - 15)**2 + (np.mgrid[:31,:31][1] - 15)**2) <= 15**2 # Create a disk-shaped structural element from skimage.filters import rank # Import module containing mean filter function bg = rank.mean(green_smooth, selem=struct) # Run a mean filter over the image using the disc # Threshold using created background green_mem = green_smooth >= bg # Clean by morphological hole filling green_mem = ndi.binary_fill_holes(np.logical_not(green_mem)) # Show the result plt.imshow(green_mem,interpolation='none',cmap='gray') plt.show() #%% #------------------------------------------------------------------------------
def TestSample(self): #Run pump, take samples and analyse
global currentPhoto
self.im1Count["text"] = "-" #Reset text fields
self.im2Count["text"] = "-"
self.im3Count["text"] = "-"
self.im1Average["text"] = "-"
self.im2Average["text"] = "-"
self.im3Average["text"] = "-"
self.imFinalCount["text"] = "-"
self.imFinalAverage["text"] = "-"
self.sizeAct["text"] = "-"
self.Confidence["text"] = "-"
self.ConfDisp["bg"] = "grey"
##'''
global camera
camera.stop_preview() #Quit preview if open
########################### Run pump and take Pictures ###############################
self.pump_On() #Turn on pump
self.update_idletasks() #Refresh Gui
for x in range(0, 25): #Wait 25 seconds
self.labelCurrentAction["text"] = "Pumping Liquid - %d" % (25 - x)
self.update_idletasks()
time.sleep(1)
self.pump_Off() #Turn off pump
for x in range(1, 4): #Take 3 images
self.pump_Off()
self.labelCurrentAction["text"] = "Powder Settle Time"
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction["text"] = "Capturing Image %d" % x
camera.hflip = True #Flip camera orientation appropriately
camera.vflip = True
camera.capture('/home/pi/PythonTempFolder/OrigPic' + str(x) +
'.jpg') #Save image to default directory
self.update_idletasks()
time.sleep(2)
if (x < 3):
self.pump_On() #Turn on pump
for y in range(0, 6): #Wait 6 seconds
self.labelCurrentAction["text"] = "Pumping Liquid - %d" % (
6 - y)
self.update_idletasks()
time.sleep(1)
self.pump_Off() #Turn off pump
##'''
################################################################################################
########################### Analyse Pictures ###############################
for x in range(1, 4):
self.labelCurrentAction[
"text"] = "Loading image as greyscale - im %d" % x
self.update_idletasks()
image1 = io.imread('/home/pi/PythonTempFolder/OrigPic' + str(x) +
'.jpg',
as_grey=True) #Load image as greyscale
##
##image1 = io.imread('/home/pi/SDP Project/PowderTests/PPIM169041/169041Pic' + str(x) + '.jpg', as_grey=True) ##Comment Out
##
self.labelCurrentAction["text"] = "Cropping" #Crop image
self.update_idletasks()
fromFile = np.asarray(image1, dtype=np.float32)
orig = fromFile[0:1080, 420:1500]
currentPhoto = orig
self.showCurrent()
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction[
"text"] = "Applying minimum filter" #Apply minimum filter
self.update_idletasks()
image2 = minimum(orig, disk(6))
currentPhoto = image2
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
self.labelCurrentAction[
"text"] = "Applying mean filter" #Apply mean filter
self.update_idletasks()
image3 = mean(image2, disk(22))
currentPhoto = image3
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
self.labelCurrentAction[
"text"] = "Applying maximum filter" #Apply maximum filter
self.update_idletasks()
image4 = maximum(image3, disk(6))
currentPhoto = image4
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction[
"text"] = "Normalising" #Subtract filtered image from original
self.update_idletasks()
new = np.asarray(image4, dtype=np.float32)
new[0:, 0:] = new[0:, 0:] / 255
sub = np.subtract(orig, new)
sub[0:, 0:] += (128 / 255) #Scale appropriately
imFinal = sub
currentPhoto = sub
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
time.sleep(1)
self.labelCurrentAction[
"text"] = "Thresholding (Otsu)" #Get Otsu threshold value from image
self.update_idletasks()
thresh = threshold_otsu(imFinal) ##Threshold
print("T - " + str(thresh))
intensity = float(self.entryIntensity.get()
) #Get manual threshold value from text field
self.labelCurrentAction[
"text"] = "Creating Binary Image" #Create binary image from threshold value (changed to manual - ignore otsu)
self.update_idletasks()
binary = sub <= intensity #0.095 #(thresh+0.2)
scipy.misc.imsave('/home/pi/PythonTempFolder/binary' + str(x) +
'.jpg',
binary) #Save binary image to default directory
currentPhoto = binary
self.t.destroy()
self.update_idletasks()
self.showCurrent()
self.update_idletasks()
labels = label(binary)
self.labelCurrentAction["text"] = "Analysing Particles"
self.update_idletasks()
counter = 0
areaCount = 0
Tmin = int(
self.entryTmin.get()) #Get size thresholds from text input
Tmax = int(self.entryTmax.get())
################################################################################################
#Tmin = 10
#Tmax = 300
for region in regionprops(
labels): #Iterate through particles in the binary image
if (region.area <= Tmax and region.area >= Tmin):
counter = counter + 1 #Count number of particles found
areaCount = areaCount + region.area #Sum area of all particles
average = areaCount / counter #Calculate average area
if (x == 1):
self.im1Count["text"] = counter
self.im1Average["text"] = round(average,
5) #Display average image 1
counter1 = counter
average1 = average
if (x == 2):
self.im2Count["text"] = counter
self.im2Average["text"] = round(average,
5) #Display average image 2
counter2 = counter
average2 = average
if (x == 3):
self.im3Count["text"] = counter
self.im3Average["text"] = round(average,
5) #Display average image 3
counter3 = counter
average3 = average
print(counter)
average = areaCount / counter
#print(average)
self.t.destroy()
self.update_idletasks()
finalCount = (counter1 + counter2 +
counter3) / 3 #Calculate final count all images
finalAverage = (average1 + average2 +
average3) / 3 #Calculate final average all images
self.imFinalCount["text"] = finalCount
self.imFinalAverage["text"] = round(finalAverage, 3)
microns = (math.sqrt((finalAverage * 113.0989232) /
3.14159265359)) * 2 #Size approximation
self.sizeAct["text"] = "~ " + str(round(microns, 3)) + " microns"
maxCount = max(counter1, counter2, counter3)
Conf = float(finalCount) / float(maxCount)
self.Confidence["text"] = str(round(Conf, 3)) + " %"
print(finalCount)
#print(maxCount)
print(Conf)
self.ConfDisp["bg"] = "red" #Change confidence colours
if (Conf >= 0.84):
self.ConfDisp["bg"] = "yellow"
if (Conf >= 0.93):
self.ConfDisp["bg"] = "green"
self.labelCurrentAction["text"] = "Complete!"
self.update_idletasks()
time.sleep(2)
self.labelCurrentAction["text"] = "idle"
self.update_idletasks()
def prefilter(self, img, method='median'):
ps = self.settings.prefilter_settings[method]
print
print 'prefiltering :', method
if method=='median':
radius = ps['median_size']
# with vigra
#filtered= vigra.filters.discMedian(img, radius)
# with skimage
pref = rank.median(img, disk(radius))
elif method=='avg':
# with skimage
se = disk(ps['avg_size'])
pref = rank.mean(img, se)
elif method=='bilateral':
# with skimage
se = disk(ps['bil_radius'])
pref = rank.mean_bilateral(img, se,
s0=ps['bil_lower'],
s1=ps['bil_upper'])
elif method=='denoise_bilateral':
#skimage.filters.denoise_bilateral(image, win_size=5, sigma_range=None, sigma_spatial=1,
pref = restoration.denoise_bilateral(img, ps['win_size'], ps['sigma_signal'], ps['sigma_space'], ps['bins'],
mode='constant', cval=0, multichannel=False)
elif method=='close_rec':
se = disk(ps['close_size'])
dil = morphology.dilation(img, se)
rec = morphology.reconstruction(dil, img, method='erosion')
# reconstruction gives back a float image (for whatever reason).
pref = rec.astype(dil.dtype)
elif method=='denbi_clorec':
temp = restoration.denoise_bilateral(img, ps['win_size'], ps['sigma_signal'], ps['sigma_space'], ps['bins'],
mode='constant', cval=0, multichannel=False)
temp = 255 * temp
temp = temp.astype(img.dtype)
se = disk(ps['close_size'])
dil = morphology.dilation(temp, se)
rec = morphology.reconstruction(dil, temp, method='erosion')
# reconstruction gives back a float image (for whatever reason).
pref = rec.astype(img.dtype)
elif method=='denbi_asfrec':
temp = restoration.denoise_bilateral(img, ps['win_size'], ps['sigma_signal'], ps['sigma_space'], ps['bins'],
mode='constant', cval=0, multichannel=False)
temp = 255 * temp
temp = temp.astype(img.dtype)
se = disk(ps['close_size'])
dil = morphology.dilation(temp, se)
rec = morphology.reconstruction(dil, temp, method='erosion')
se = disk(ps['open_size'])
ero = morphology.erosion(rec, se)
rec2 = morphology.reconstruction(ero, rec, method='dilation')
# reconstruction gives back a float image (for whatever reason).
pref = rec2.astype(img.dtype)
elif method=='med_denbi_asfrec':
if ps['median_size'] > 1:
radius = ps['median_size']
pref = rank.median(img, disk(radius))
else:
pref = img
temp = restoration.denoise_bilateral(pref, ps['win_size'], ps['sigma_signal'], ps['sigma_space'], ps['bins'],
mode='constant', cval=0, multichannel=False)
temp = 255 * temp
temp = temp.astype(img.dtype)
if ps['close_size'] > 0 :
se = disk(ps['close_size'])
dil = morphology.dilation(temp, se)
rec = morphology.reconstruction(dil, temp, method='erosion')
else:
rec = temp
if ps['open_size'] > 0:
se = disk(ps['open_size'])
ero = morphology.erosion(rec, se)
rec2 = morphology.reconstruction(ero, rec, method='dilation')
else:
rec2 = rec
# reconstruction gives back a float image (for whatever reason).
pref = rec2.astype(img.dtype)
return pref
camera1 = exposure.equalize_adapthist(camera1) camera1 = exposure.rescale_intensity(camera1) #camera1 = exposure.adjust_gamma(camera1) camera1 = exposure.adjust_sigmoid(camera1) #camera1 = exposure.adjust_log(camera1) #noise = np.random.random(camera1.shape) #noisy_image = camera1 #noisy_image[noise > 0.98] = 1 #noisy_image[noise < 0.02] = 0 #camera1 = median(noisy_image, disk(1)) #selem = disk(30.0) #camera1 = rank.equalize(camera1, selem=selem) #plt.imshow(camera1, cmap='gray', interpolation='nearest') camera = rgb2gray(camera1) camera = mean(camera, disk(1)) #camera = mean_bilateral(camera, disk(10)) camera = median(camera, disk(1)) from scipy.misc import imsave print(camera) val = filters.threshold_otsu(camera) camera = closing(camera > val, square(3)) camera = opening(camera, square(2)) #camera = closing(camera, square(3)) #camera = opening(camera, square(2)) #camera = opening(camera, square(2)) #camera = mean(camera, disk(1)) #plt.imshow(camera, cmap='gray', interpolation='nearest')
import skimage
import matplotlib.pyplot as plt
from skimage import io
from skimage.exposure import histogram, equalize_hist
from skimage.util import random_noise
import numpy as np
from AMF import AMF
from skimage.filters import rank, median
from skimage.morphology import disk
noise_org = io.imread("../pic/NOISE.bmp", as_gray=True)
noise_roi = noise_org[100:200, 100:200]
selem = disk(3)
noise_mean = rank.mean(noise_roi, selem=selem)
hist, hist_centers = histogram(noise_org, nbins=256, normalize=True)
noise_median = median(noise_roi, selem=selem)
fig, ax = plt.subplots(ncols=3, nrows=2, figsize=(10, 5))
ax[0, 0].imshow(noise_org, cmap=plt.cm.gray)
ax[0, 0].axis('off')
ax[0, 0].set_title("original")
ax[0, 1].imshow(noise_roi, cmap=plt.cm.gray)
ax[0, 1].axis('off')
ax[0, 1].set_title("ROI")
ax[0, 2].plot(hist_centers, hist, lw=2)
from skimage.io import imread
from skimage.io import imshow
from skimage.io import imsave
from skimage.io import show
from skimage.filters import rank
from skimage.morphology import disk
from skimage.color import rgb2gray
if __name__ == '__main__':
selem = disk(20)
mon_image = imread("./test_ng.png")
mon_image_nv = rgb2gray(mon_image)
im_mean = rank.mean(mon_image_nv, selem=selem)
imshow(im_mean)
show()
imsave("./mean_sk.png", im_mean)
frequencies remain untouched.
"""
import numpy as np
import matplotlib.pyplot as plt
from skimage import data
from skimage.morphology import disk
from skimage.filters import rank
image = (data.coins()).astype(np.uint16) * 16
selem = disk(20)
percentile_result = rank.mean_percentile(image, selem=selem, p0=.1, p1=.9)
bilateral_result = rank.mean_bilateral(image, selem=selem, s0=500, s1=500)
normal_result = rank.mean(image, selem=selem)
fig, axes = plt.subplots(nrows=2,
ncols=2,
figsize=(8, 10),
sharex=True,
sharey=True)
ax = axes.ravel()
titles = ['Original', 'Percentile mean', 'Bilateral mean', 'Local mean']
imgs = [image, percentile_result, bilateral_result, normal_result]
for n in range(0, len(imgs)):
ax[n].imshow(imgs[n])
ax[n].set_title(titles[n])
ax[n].set_adjustable('box-forced')
ax[n].axis('off')
def compute_local_features(retinal_image):
red_channel = retinal_image.preprocessed_image[:, :, 0]
green_channel = retinal_image.preprocessed_image[:, :, 1]
blue_channel = retinal_image.preprocessed_image[:, :, 2]
hue_channel = color.rgb2hsv(retinal_image.preprocessed_image)[:, :, 0]
saturation_channel = color.rgb2hsv(retinal_image.preprocessed_image)[:, :,
1]
value_channel = color.rgb2hsv(retinal_image.preprocessed_image)[:, :, 2]
#mean- large
mean_red_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_blue_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_green_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_hue_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_saturation_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_value_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
#mean- small
mean_red_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_green_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_blue_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_hue = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_saturation = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_value = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
#minimum- large
minimum_red_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_green_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_blue_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_hue_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_saturation_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_value_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
#minimum- small
minimum_red_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_green_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_blue_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_hue = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_saturation = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
minimum_value = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
#maximum- large
maximum_red_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_green_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_blue_intensity_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_hue_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_saturation_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_value_large = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
#maximum- small
maximum_red_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_green_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_blue_intensity = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_hue = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_saturation = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
maximum_value = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
# std- large
mean_red_intensity_large1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_red_intensity_large_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_green_intensity_large1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_green_intensity_large_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_blue_intensity_large1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_blue_intensity_large_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_hue_large1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_hue_large_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_saturation_large1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_saturation_large_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_value_large1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_value_large_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
# std- small
mean_red_intensity_1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_red_intensity_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_green_intensity_1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_green_intensity_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_blue_intensity_1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_blue_intensity_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_hue_1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_hue_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_saturation_1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_saturation_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_value_1 = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
mean_value_potency = np.zeros(
(retinal_image.labels.shape[0], retinal_image.labels.shape[1]))
max_labels = np.amax(retinal_image.labels)
distanceTransform = ndimage.distance_transform_edt(retinal_image.vessels)
diameter = distanceTransform * retinal_image.skeletonWithoutCrossings
meanDiameterInRegion = np.zeros(np.max(retinal_image.labels))
for i in range(1, max_labels + 1):
meanDiameterInRegion[i - 1] = np.mean(
diameter[retinal_image.labels == (i)])
disk_diameter = meanDiameterInRegion[i - 1]
# disk_diameter=2;
disk_diameter_large = 2 * disk_diameter
labels_points = (retinal_image.labels == i)
labels_points_indexes = np.nonzero(labels_points)
labels_points_indexes = list(labels_points_indexes)
rows = (labels_points_indexes)[0]
cols = (labels_points_indexes)[1]
#labels_points_int=labels_points.astype(int)
#mean_intensity[rows,cols]=mean(img_rgb[labels_points==True], disk(disk_diameter))
#mean_intensity[rows,cols]=mean(red_channel[rows,cols], disk(disk_diameter))
#mean- large
mean_red_intensity_large_iteration = mean(red_channel,
disk(disk_diameter_large))
mean_red_intensity_large[
rows, cols] = mean_red_intensity_large_iteration[rows, cols]
mean_green_intensity_large_iteration = mean(green_channel,
disk(disk_diameter_large))
mean_green_intensity_large[
rows, cols] = mean_green_intensity_large_iteration[rows, cols]
mean_blue_intensity_large_iteration = mean(blue_channel,
disk(disk_diameter_large))
mean_blue_intensity_large[
rows, cols] = mean_blue_intensity_large_iteration[rows, cols]
mean_hue_large_iteration = mean(hue_channel, disk(disk_diameter_large))
mean_hue_large[rows, cols] = mean_hue_large_iteration[rows, cols]
mean_saturation_large_iteration = mean(saturation_channel,
disk(disk_diameter_large))
mean_saturation_large[rows,
cols] = mean_saturation_large_iteration[rows,
cols]
mean_value_large_iteration = mean(value_channel,
disk(disk_diameter_large))
mean_value_large[rows, cols] = mean_value_large_iteration[rows, cols]
#mean- small
mean_red_intensity_iteration = mean(red_channel, disk(disk_diameter))
mean_red_intensity[rows, cols] = mean_red_intensity_iteration[rows,
cols]
mean_green_intensity_iteration = mean(green_channel,
disk(disk_diameter))
mean_green_intensity[rows, cols] = mean_green_intensity_iteration[rows,
cols]
mean_blue_intensity_iteration = mean(blue_channel, disk(disk_diameter))
mean_blue_intensity[rows, cols] = mean_blue_intensity_iteration[rows,
cols]
mean_hue_iteration = mean(hue_channel, disk(disk_diameter))
mean_hue[rows, cols] = mean_hue_iteration[rows, cols]
mean_saturation_iteration = mean(saturation_channel,
disk(disk_diameter))
mean_saturation[rows, cols] = mean_saturation_iteration[rows, cols]
mean_value_iteration = mean(value_channel, disk(disk_diameter))
mean_value[rows, cols] = mean_value_iteration[rows, cols]
#minimum- large
minimum_red_intensity_iteration = minimum(red_channel,
disk(disk_diameter))
minimum_red_intensity[rows,
cols] = minimum_red_intensity_iteration[rows,
cols]
minimum_green_intensity_iteration = minimum(green_channel,
disk(disk_diameter))
minimum_green_intensity[rows,
cols] = minimum_green_intensity_iteration[rows,
cols]
minimum_blue_intensity_iteration = minimum(blue_channel,
disk(disk_diameter))
minimum_blue_intensity[rows,
cols] = minimum_blue_intensity_iteration[rows,
cols]
minimum_hue_iteration = minimum(hue_channel, disk(disk_diameter))
minimum_hue[rows, cols] = minimum_hue_iteration[rows, cols]
minimum_saturation_iteration = minimum(saturation_channel,
disk(disk_diameter))
minimum_saturation[rows, cols] = minimum_saturation_iteration[rows,
cols]
minimum_value_iteration = minimum(value_channel, disk(disk_diameter))
minimum_value[rows, cols] = minimum_value_iteration[rows, cols]
#minimum- small
minimum_red_intensity_large_iteration = minimum(
red_channel, disk(disk_diameter_large))
minimum_red_intensity_large[
rows, cols] = minimum_red_intensity_large_iteration[rows, cols]
minimum_green_intensity_large_iteration = minimum(
green_channel, disk(disk_diameter_large))
minimum_green_intensity_large[
rows, cols] = minimum_green_intensity_large_iteration[rows, cols]
minimum_blue_intensity_large_iteration = minimum(
blue_channel, disk(disk_diameter_large))
minimum_blue_intensity_large[
rows, cols] = minimum_blue_intensity_large_iteration[rows, cols]
minimum_hue_large_iteration = minimum(hue_channel,
disk(disk_diameter_large))
minimum_hue_large[rows, cols] = minimum_hue_large_iteration[rows, cols]
minimum_saturation_large_iteration = minimum(saturation_channel,
disk(disk_diameter_large))
minimum_saturation_large[
rows, cols] = minimum_saturation_large_iteration[rows, cols]
minimum_value_large_iteration = minimum(value_channel,
disk(disk_diameter_large))
minimum_value_large[rows, cols] = minimum_value_large_iteration[rows,
cols]
#maximum- large
maximum_red_intensity_large_iteration = maximum(
red_channel, disk(disk_diameter_large))
maximum_red_intensity_large[
rows, cols] = maximum_red_intensity_large_iteration[rows, cols]
maximum_green_intensity_large_iteration = maximum(
green_channel, disk(disk_diameter_large))
maximum_green_intensity_large[
rows, cols] = maximum_green_intensity_large_iteration[rows, cols]
maximum_blue_intensity_large_iteration = maximum(
blue_channel, disk(disk_diameter_large))
maximum_blue_intensity_large[
rows, cols] = maximum_blue_intensity_large_iteration[rows, cols]
maximum_hue_large_iteration = maximum(hue_channel,
disk(disk_diameter_large))
maximum_hue_large[rows, cols] = maximum_hue_large_iteration[rows, cols]
maximum_saturation_large_iteration = maximum(saturation_channel,
disk(disk_diameter_large))
maximum_saturation_large[
rows, cols] = maximum_saturation_large_iteration[rows, cols]
maximum_value_large_iteration = maximum(value_channel,
disk(disk_diameter_large))
maximum_value_large[rows, cols] = maximum_value_large_iteration[rows,
cols]
#maximum- small
maximum_red_intensity_iteration = maximum(red_channel,
disk(disk_diameter))
maximum_red_intensity[rows,
cols] = maximum_red_intensity_iteration[rows,
cols]
maximum_green_intensity_iteration = maximum(green_channel,
disk(disk_diameter))
maximum_green_intensity[rows,
cols] = maximum_green_intensity_iteration[rows,
cols]
maximum_blue_intensity_iteration = maximum(blue_channel,
disk(disk_diameter))
maximum_blue_intensity[rows,
cols] = maximum_blue_intensity_iteration[rows,
cols]
maximum_hue_iteration = maximum(hue_channel, disk(disk_diameter))
maximum_hue[rows, cols] = maximum_hue_iteration[rows, cols]
maximum_saturation_iteration = maximum(saturation_channel,
disk(disk_diameter))
maximum_saturation[rows, cols] = maximum_saturation_iteration[rows,
cols]
maximum_value_iteration = maximum(value_channel, disk(disk_diameter))
maximum_value[rows, cols] = maximum_value_iteration[rows, cols]
#std-large
#std red
mean_red_intensity_large_iteration1 = mean(red_channel**2,
disk(disk_diameter_large))
mean_red_intensity_large1[
rows, cols] = mean_red_intensity_large_iteration1[rows, cols]
mean_red_intensity_large_potency_iteration = mean(
red_channel, disk(disk_diameter_large))
mean_red_intensity_large_potency[
rows, cols] = mean_red_intensity_large_potency_iteration[rows,
cols]**2
std_red = mean_red_intensity_large_potency - mean_red_intensity_large1
std_red = np.abs(std_red)
std_red_final = np.sqrt(std_red)
#std green
mean_green_intensity_large_iteration1 = mean(green_channel**2,
disk(disk_diameter_large))
mean_green_intensity_large1[
rows, cols] = mean_green_intensity_large_iteration1[rows, cols]
mean_green_intensity_large_potency_iteration = mean(
green_channel, disk(disk_diameter_large))
mean_green_intensity_large_potency[
rows, cols] = mean_green_intensity_large_potency_iteration[rows,
cols]**2
std_green = mean_green_intensity_large_potency - mean_green_intensity_large1
std_green = np.abs(std_green)
std_green_final = np.sqrt(std_green)
#std Blue
mean_blue_intensity_large_iteration1 = mean(blue_channel**2,
disk(disk_diameter_large))
mean_blue_intensity_large1[
rows, cols] = mean_blue_intensity_large_iteration1[rows, cols]
mean_blue_intensity_large_potency_iteration = mean(
blue_channel, disk(disk_diameter_large))
mean_blue_intensity_large_potency[
rows, cols] = mean_blue_intensity_large_potency_iteration[rows,
cols]**2
std_blue = mean_blue_intensity_large_potency - mean_blue_intensity_large1
std_blue = np.abs(std_blue)
std_blue_final = np.sqrt(std_blue)
#std hue
mean_hue_large_iteration1 = mean(hue_channel**2,
disk(disk_diameter_large))
mean_hue_large1[rows, cols] = mean_hue_large_iteration1[rows, cols]
mean_hue_large_potency_iteration = mean(hue_channel,
disk(disk_diameter_large))
mean_hue_large_potency[rows, cols] = mean_hue_large_potency_iteration[
rows, cols]**2
std_hue = mean_hue_large_potency - mean_hue_large1
std_hue = np.abs(std_hue)
std_hue_final = np.sqrt(std_hue)
#std saturation
mean_saturation_large_iteration1 = mean(saturation_channel**2,
disk(disk_diameter_large))
mean_saturation_large1[rows,
cols] = mean_saturation_large_iteration1[rows,
cols]
mean_saturation_large_potency_iteration = mean(
saturation_channel, disk(disk_diameter_large))
mean_saturation_large_potency[
rows, cols] = mean_saturation_large_potency_iteration[rows,
cols]**2
std_saturation = mean_saturation_large_potency - mean_saturation_large1
std_saturation = np.abs(std_saturation)
std_saturation_final = np.sqrt(std_saturation)
#std Value
mean_value_large_iteration1 = mean(value_channel**2,
disk(disk_diameter_large))
mean_value_large1[rows, cols] = mean_value_large_iteration1[rows, cols]
mean_value_large_potency_iteration = mean(value_channel,
disk(disk_diameter_large))
mean_value_large_potency[
rows, cols] = mean_value_large_potency_iteration[rows, cols]**2
std_value = mean_value_large_potency - mean_value_large1
std_value = np.abs(std_value)
std_value_final = np.sqrt(std_value)
#std-small
#std red
mean_red_intensity_iteration1 = mean(red_channel**2,
disk(disk_diameter))
mean_red_intensity_1[rows, cols] = mean_red_intensity_iteration1[rows,
cols]
mean_red_intensity_potency_iteration = mean(red_channel,
disk(disk_diameter))
mean_red_intensity_potency[
rows, cols] = mean_red_intensity_potency_iteration[rows, cols]**2
std_red_small = mean_red_intensity_potency - mean_red_intensity_1
std_red_small = np.abs(std_red_small)
std_red_final_small = np.sqrt(std_red_small)
#std green
mean_green_intensity_iteration1 = mean(green_channel**2,
disk(disk_diameter))
mean_green_intensity_1[rows,
cols] = mean_green_intensity_iteration1[rows,
cols]
mean_green_intensity_potency_iteration = mean(green_channel,
disk(disk_diameter))
mean_green_intensity_potency[
rows, cols] = mean_green_intensity_potency_iteration[rows, cols]**2
std_green_small = mean_green_intensity_potency - mean_green_intensity_1
std_green_small = np.abs(std_green_small)
std_green_final_small = np.sqrt(std_green_small)
#std Blue
mean_blue_intensity_iteration1 = mean(blue_channel**2,
disk(disk_diameter))
mean_blue_intensity_1[rows,
cols] = mean_blue_intensity_iteration1[rows,
cols]
mean_blue_intensity_potency_iteration = mean(blue_channel,
disk(disk_diameter))
mean_blue_intensity_potency[
rows, cols] = mean_blue_intensity_potency_iteration[rows, cols]**2
std_blue_small = mean_blue_intensity_potency - mean_blue_intensity_1
std_blue_small = np.abs(std_blue_small)
std_blue_final_small = np.sqrt(std_blue_small)
#std hue
mean_hue_iteration1 = mean(hue_channel**2, disk(disk_diameter))
mean_hue_1[rows, cols] = mean_hue_iteration1[rows, cols]
mean_hue_potency_iteration = mean(hue_channel, disk(disk_diameter))
mean_hue_potency[rows, cols] = mean_hue_potency_iteration[rows,
cols]**2
std_hue_small = mean_hue_potency - mean_hue_1
std_hue_small = np.abs(std_hue_small)
std_hue_final_small = np.sqrt(std_hue_small)
#std saturation
mean_saturation_iteration1 = mean(saturation_channel**2,
disk(disk_diameter))
mean_saturation_1[rows, cols] = mean_saturation_iteration1[rows, cols]
mean_saturation_potency_iteration = mean(saturation_channel,
disk(disk_diameter))
mean_saturation_potency[
rows, cols] = mean_saturation_potency_iteration[rows, cols]**2
std_saturation_small = mean_saturation_potency - mean_saturation_1
std_saturation_small = np.abs(std_saturation_small)
std_saturation_final_small = np.sqrt(std_saturation_small)
#std Value
mean_value_iteration1 = mean(value_channel**2, disk(disk_diameter))
mean_value_1[rows, cols] = mean_value_iteration1[rows, cols]
mean_value_potency_iteration = mean(value_channel, disk(disk_diameter))
mean_value_potency[rows, cols] = mean_value_potency_iteration[rows,
cols]**2
std_value_small = mean_value_potency - mean_value_1
std_value_small = np.abs(std_value_small)
std_value_final_small = np.sqrt(std_value_small)
#print(mean_intensity)
print(i, ':', disk_diameter)
return mean_red_intensity_large, mean_green_intensity_large, mean_blue_intensity_large, mean_hue_large, mean_saturation_large, mean_value_large, mean_red_intensity, mean_green_intensity, mean_blue_intensity, mean_hue, mean_saturation, mean_value, minimum_red_intensity_large, minimum_green_intensity_large, minimum_blue_intensity_large, minimum_hue_large, minimum_saturation_large, minimum_value_large, minimum_red_intensity, minimum_green_intensity, minimum_blue_intensity, minimum_hue, minimum_saturation, minimum_value, maximum_red_intensity_large, maximum_green_intensity_large, maximum_blue_intensity_large, maximum_hue_large, maximum_saturation_large, maximum_value_large, maximum_red_intensity, maximum_green_intensity, maximum_blue_intensity, maximum_hue, maximum_saturation, maximum_value, std_red_final, std_green_final, std_blue_final, std_hue_final, std_saturation_final, std_value_final, std_red_final_small, std_green_final_small, std_blue_final_small, std_hue_final_small, std_saturation_final_small, std_value_final_small
