def process_image(pil_image, values):
img = np.array(pil_image)
selected_channels = [
values["-OTSU RED CHANNEL-"], values["-OTSU GREEN CHANNEL-"],
values["-OTSU BLUE CHANNEL-"]
]
if np.where(selected_channels)[0].size == 1 and len(img.shape) == 2:
if values["-APPLY LOCAL OTSU-"]:
radius = values["-LOCAL OTSU SIZE-"]
local_mask = disk(
radius
) if values["-LOCAL OTSU SHAPE-"] == "Disk" else rectangle(
int(radius), int(radius))
otsu_img = img >= rank.otsu(img, local_mask)
else:
otsu_img = img >= threshold_otsu(img)
otsu_np_img = 255 * np.asarray(otsu_img, dtype=np.uint8)
if values["-OTSU OVERLAY WITH IMAGE-"]:
cnts = cv2.findContours(otsu_np_img, cv2.RETR_LIST,
cv2.CHAIN_APPROX_NONE)[0]
cv2.drawContours(img, cnts, -1, 255, 1)
otsu_np_img = img
ret_img = Image.fromarray(otsu_np_img)
elif np.where(selected_channels)[0].size == 1:
if values["-APPLY LOCAL OTSU-"]:
radius = values["-LOCAL OTSU SIZE-"]
local_mask = disk(
radius
) if values["-LOCAL OTSU SHAPE-"] == "Disk" else rectangle(
int(radius), int(radius))
otsu_img = img[...,
np.where(selected_channels)[0][0]] >= rank.otsu(
img[..., np.where(selected_channels)[0][0]],
local_mask)
else:
threshold_global_otsu = threshold_otsu(
img[..., np.where(selected_channels)[0][0]])
otsu_img = img[..., np.where(selected_channels
)[0][0]] >= threshold_global_otsu
otsu_np_img = 255 * np.asarray(otsu_img, dtype=np.uint8)
if values["-OTSU OVERLAY WITH IMAGE-"]:
cnts = cv2.findContours(otsu_np_img, cv2.RETR_LIST,
cv2.CHAIN_APPROX_NONE)[0]
cv2.drawContours(img, cnts, -1, 255, 1)
otsu_np_img = img
ret_img = Image.fromarray(otsu_np_img)
else:
ret_img = pil_image
return ret_img
def robust_binarize(base_image,
_dilation=0,
heterogeity_size=10,
feature_size=50):
"""
Robust binarization algorithm based off random walker clustering
:param base_image:
:param _dilation: if set to anything other than 0, would perform a morphological dilation using this parameter value as size
:param heterogeity_size: size of the feature (px) that the method will try to eliminate by smoothing
:param feature_size: size of the feature (px) that the method will try to segment out
:return: binary_labels
"""
if np.percentile(base_image, 99) < 0.20:
if np.percentile(base_image, 99) > 0:
mult = 0.20 / np.percentile(
base_image, 99) # poissonean background assumptions
else:
mult = 1000. / np.sum(base_image)
base_image = base_image * mult
base_image[base_image > 1] = 1
clustering_markers = np.zeros(base_image.shape, dtype=np.uint8)
selem = disk(heterogeity_size)
smooth = gaussian_filter(base_image, heterogeity_size, mode='constant')
smooth_median = median(smooth, selem)
uniform_median = median(base_image, selem)
selem2 = disk(feature_size)
local_otsu = rank.otsu(smooth_median, selem2)
uniform_median_otsu = rank.otsu(uniform_median, selem2)
clustering_markers[smooth_median < local_otsu * 0.9] = 1
clustering_markers[smooth_median > local_otsu * 1.1] = 2
# dbg.random_walker_debug(smooth_median, clustering_markers)
# dbg.robust_binarize_debug(base_image, smooth_median, smooth_median, local_otsu, clustering_markers,
# 0, uniform_median, uniform_median_otsu)
binary_labels = random_walker(
smooth_median, clustering_markers, beta=10, mode='bf') - 1
if _dilation:
selem = disk(_dilation)
binary_labels = dilation(binary_labels, selem)
# dbg.robust_binarize_debug(binary_labels, base_image)
# dbg.voronoi_debug(binary_labels, local_maxi, dist, segmented_cells_labels)
# dbg.Kristen_robust_binarize(binary_labels, base_image)
return binary_labels
def load_edge2(self, img, low_rate=False):
radius = 15
selem = disk(radius)
if (low_rate == False):
img_blur = skimage.filters.gaussian(img, sigma=1)
#thresh = threshold_yen(img_blur)
#binary = img_blur > thresh
binary = rank.otsu(img_blur, selem)
else:
#thresh = threshold_yen(img)
#binary = img > thresh
binary = rank.otsu(img, selem)
canny_img = canny(img.astype(np.float), sigma=self.sigma)
return np.bitwise_and(canny_img, binary).astype(np.float)
def get_local_otsu(img):
radius = 5
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
# blur = cv2.GaussianBlur(img, (5, 5), 0)
# ret, th = cv2.threshold(blur, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
return img > local_otsu
def binarize_image(base_image, _dilation=0, feature_size=2):
'''
Binarizes an image using local otsu and random walker
Borrowed from Andrei's Imagepipe
:param base_image: [np.ndarray] input image
:param _dilation: [float] amount of dilation to implement in Binarization
:param feature_size: [float] size of the structuring disk for random Walker
:return: [np.ndarray] binarized image
'''
print "> Binarizing Image..."
if np.percentile(base_image, 99) < 0.20:
if np.percentile(base_image, 99) > 0:
mult = 0.20 / np.percentile(
base_image, 99) # poissonean background assumptions
else:
mult = 1000. / np.sum(base_image)
base_image = base_image * mult
base_image[base_image > 1] = 1
clustering_markers = np.zeros(base_image.shape, dtype=np.uint8)
selem2 = disk(feature_size)
print '> Performing Local Otsu'
local_otsu = rank.otsu(base_image, selem2)
# view_2d_img(local_otsu)
clustering_markers[base_image < local_otsu * 0.9] = 1
clustering_markers[base_image > local_otsu * 1.1] = 2
print "> Performing Random Walker Binarization"
binary_labels = random_walker(
base_image, clustering_markers, beta=10, mode='bf') - 1
if _dilation:
selem = disk(_dilation)
binary_labels = dilation(binary_labels, selem)
return binary_labels
def autoThresholding(image2d, method='triangle', radius=10, value=50):
"""Autothreshold an 2D intensity image which is calculated using:
binary = image2d >= thresh
:param image2d: input image for thresholding
:type image2d: NumPy.Array
:param method: choice of thresholding method, defaults to 'triangle'
:type method: str, optional
:param radius: radius of disk when using local Otsu threshold, defaults to 10
:type radius: int, optional
:param value: manual threshold value, defaults to 50
:type value: int, optional
:return: binary - binary mask from thresholding
:rtype: NumPy.Array
"""
# calculate global Otsu threshold
if method == 'global_otsu':
thresh = threshold_otsu(image2d)
# calculate local Otsu threshold
if method == 'local_otsu':
thresh = rank.otsu(image2d, disk(radius))
if method == 'value_based':
thresh = value
if method == 'triangle':
thresh = threshold_triangle(image2d)
binary = image2d >= thresh
return binary
def threshold_img(img, method='global_otsu', radius=50):
""" Given a gray scale image return a thresholded binary image using Otsu's thresholding method.
img: A gray scale numpy array.
method:
- 'global_otsu' computes a global threshold value for the whole image and uses this to binarize the
input image. (default)
- 'local_otsu' computes a local threshols value for each pixel (threshold is computed within a neighborhood of a radius).
radius: The 2D neighborhood to compute local thresholds in local_otsu method
Returns:
img_binary: A binary image (same size as input img).
threshold: Threshold value used to binarize the image.
"""
if len(img.shape) > 2:
img = rgb2gray(img)
if method == 'global_otsu':
threshold = threshold_otsu(img)
img_binary = img >= threshold
elif method == 'local_otsu':
selem = disk(radius)
threshold = rank.otsu(img, selem)
img_binary = img >= threshold
return np.uint8(img_binary), threshold
def threshold(im, binary=False, local=False):
'''
im: array
TODO:
- noise filtering
- use local otsu: rank.otsu
'''
#im = histeq(im)
#im = contrast(im)
#imshow(im)
minval, maxval = 0, 255
im_gray = im.copy()
if is_colored(im):
im_gray = cv2.cvtColor(im, cv2.COLOR_RGB2GRAY)
#im_gray = cv2.normalize(im_gray, None, alpha=minval, beta=maxval, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_8UC1)
if binary:
minval = 5
thresh_type = cv2.THRESH_BINARY
retval, im_thresh = cv2.threshold(im_gray,minval,maxval,thresh_type)
elif local == False:
#thresh_type = cv2.THRESH_BINARY+cv2.THRESH_OTSU
thresh = filters.threshold_otsu(im_gray)
im_thresh = (im_gray > thresh).astype('uint8')*255
else:
im_thresh = rank.otsu(im_gray, morphology.disk(5))
im_thresh = (im_gray >= im_thresh).astype('uint8')*255
return im_thresh
def binarize_2d(float_surface, cutoff_type='static', mcc_cutoff=None):
"""
Performs a 2d binarization based on several possible methods
:param float_surface:
:param cutoff_type: ['otsu', 'local_otsu', 'static', 'log-otsu"]. Local Otsu is done with 5px mask
:param mcc_cutoff: is cutoff_type is 'static', this will be the cutoff threshold
:return: binary labels
"""
if cutoff_type == 'otsu':
mcc_cutoff = threshold_otsu(float_surface)
elif cutoff_type == 'local otsu':
selem = disk(5)
mcc_cutoff = rank.otsu(float_surface, selem)
elif cutoff_type == 'static':
pass
elif cutoff_type == 'log-otsu':
mcc_cutoff = threshold_otsu(
np.log(float_surface + np.min(float_surface[float_surface > 0])))
else:
raise PipeArgError('unknown cutoff type')
binary_stack = np.zeros_like(float_surface).astype(np.bool)
binary_stack[float_surface > mcc_cutoff] = 1
return binary_stack
def __otsu_method(
image: Union[np.ndarray, Iterable, np.uint8]) -> np.ndarray:
selem = disk(20)
t_otsu = otsu(image, selem=selem)
print(t_otsu)
imshow(t_otsu)
# th_motsu = threshold_multiotsu(image, classes=2)
# im = np.digitize(image, bins=th_motsu)
# imshow(im)
plt.show()
test = (image * 255 + 15) <= t_otsu
result = np.zeros(image.shape, dtype=np.uint8)
for i, l in enumerate(test):
for j, v in enumerate(l):
if v:
result[i, j] = 255
imshow(result)
plt.show()
# result = gaussian(gaussian(result, 7), 7)
result = gaussian(result, 7)
imshow(result)
plt.show()
result = minimum(maximum(result, disk(5)), disk(12))
imshow(result)
plt.show()
result = gaussian(result, 3)
imshow(result)
plt.show()
# return self.__ending(gaussian(self.__ending(result), 7))
# return self.__ending(result)
return result
def local_otsu(image, radius=15):
# radius = 15
selem = disk(radius)
local_otsu = rank.otsu(image, selem)
return (image >= local_otsu) * 255
def getIntensityThresholdOtsu(s, params):
logging.info(
f"{s['filename']} - \tLightDarkModule.getIntensityThresholdOtsu")
name = "otsu"
local = strtobool(params.get("local", "False"))
radius = float(params.get("radius", 15))
selem = disk(radius)
img = s.getImgThumb(s["image_work_size"])
img = color.rgb2gray(img)
if local:
thresh = rank.otsu(img, selem)
name += "local"
else:
thresh = threshold_otsu(img)
map = img < thresh
s.addToPrintList(name, str(map.mean()))
io.imsave(s["outdir"] + os.sep + s["filename"] + "_" + name + ".png",
map * 255)
s["img_mask_" + name] = (map * 255) > 0
if strtobool(params.get("invert", "False")):
s["img_mask_use"] = s["img_mask_use"] & ~s["img_mask_" + name]
else:
s["img_mask_use"] = s["img_mask_use"] & s["img_mask_" + name]
return
def estimate_background(_img):
*extrem, _img = gaussian_normalize(_img)
local_otsu = rank.otsu(_img, disk(otsu_disk_radii))
ub_background = rank.mean(_img,
disk(mean_disk_radii),
mask=_img <= local_otsu)
return anti_gaussian_normalize(ub_background / 256., *extrem)
def otsu_binarize(img):
radius = 13
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
threshold_global_otsu = threshold_otsu(img)
global_otsu = img >= threshold_global_otsu
# fig, ax = plt.subplots(2, 2, figsize=(8, 5))
# ax1, ax2, ax3, ax4 = ax.ravel()
#
# fig.colorbar(ax1.imshow(img, cmap=plt.cm.gray),
# ax=ax1, orientation='horizontal')
# ax1.set_title('Original')
# ax1.axis('off')
#
# fig.colorbar(ax2.imshow(local_otsu, cmap=plt.cm.gray),
# ax=ax2, orientation='horizontal')
# ax2.set_title('Local Otsu (radius=%d)' % radius)
# ax2.axis('off')
#
# ax3.imshow(img >= local_otsu, cmap=plt.cm.gray)
# ax3.set_title('Original >= Local Otsu' % threshold_global_otsu)
# ax3.axis('off')
#
# ax4.imshow(global_otsu, cmap=plt.cm.gray)
# ax4.set_title('Global Otsu (threshold = %d)' % threshold_global_otsu)
# ax4.axis('off')
#
# plt.show()
return local_otsu
def threshold(data, process_param):
if process_param["threshold"] == "otsu":
thresh = threshold_otsu(data)
if process_param["threshold"] == "mean":
thresh = threshold_mean(data)
if process_param["threshold"] == "minimum":
thresh = threshold_minimum(data)
if process_param["threshold"] == "yen":
thresh = threshold_yen(data)
if process_param["threshold"] == "isodata":
thresh = threshold_isodata(data)
if process_param["threshold"] == "li":
thresh = threshold_li(data)
if process_param["threshold"] == "local":
thresh = threshold_local(data, process_param["local_size"])
if process_param["threshold"] == "local_otsu":
selem = disk(process_param["local_size"])
data = data.astype(np.float64)
data = data - np.min(data)
data = np.uint8(255 * data / np.max(data))
thresh = rank.otsu(data, selem)
if process_param["threshold"] == "lg_otsu":
selem = disk(process_param["local_size"])
data = data.astype(np.float64)
data = data - np.min(data)
data = np.uint8(255 * data / np.max(data))
threshl = rank.otsu(data, selem)
threshg = threshold_otsu(data)
if process_param["threshold"] == "niblack":
thresh = threshold_niblack(data, process_param["local_size"])
mask = data > thresh
if process_param["threshold"] == "sauvola":
thresh = threshold_sauvola(data, process_param["local_size"])
mask = data > thresh
if process_param["threshold"] == "lg_otsu":
mask1 = data >= threshl
mask2 = data > threshg
mask = mask1 * mask2
elif process_param["threshold"] == "local_otsu":
mask = data >= thresh
else:
mask = data > thresh
labels = label(mask)
return (labels)
def test_otsu_edge_case():
# This is an edge case that causes OTSU to appear to misbehave
# Pixel [1, 1] may take a value of of 41 or 81. Both should be considered
# valid. The value will change depending on the particular implementation
# of OTSU.
# To better understand, see
# https://mybinder.org/v2/gist/hmaarrfk/4afae1cfded1d78e44c9e4f58285d552/master
selem = np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]], dtype=np.uint8)
img = np.array([[0, 41, 0], [30, 81, 106], [0, 147, 0]], dtype=np.uint8)
result = rank.otsu(img, selem)
assert result[1, 1] in [41, 81]
img = np.array([[0, 214, 0], [229, 104, 141], [0, 172, 0]], dtype=np.uint8)
result = rank.otsu(img, selem)
assert result[1, 1] in [141, 172]
def _binarize_and_apply_background(image):
"""Performs plain Otsu binarization to get threshold,
but only sets the background to 0, retains all the foreground
intensities."""
selem = numpy.ones((80, 80), dtype='uint8')
local_otsu = rank.otsu(image, selem)
# thr = threshold_otsu(image, nbins=256)
output = image * 1
output[output < local_otsu] = 0
return output
def robust_binarize(base_image,
_dilation=0,
heterogeity_size=10,
feature_size=50):
if np.percentile(base_image, 99) < 0.20:
if np.percentile(base_image, 99) > 0:
mult = 0.20 / np.percentile(
base_image, 99) # poissonean background assumptions
else:
mult = 1000. / np.sum(base_image)
base_image = base_image * mult
base_image[base_image > 1] = 1
clustering_markers = np.zeros(base_image.shape, dtype=np.uint8)
selem = disk(heterogeity_size)
smooth = gaussian_filter(base_image, heterogeity_size, mode='constant')
smooth_median = median(smooth, selem)
uniform_median = median(base_image, selem)
selem2 = disk(feature_size)
local_otsu = rank.otsu(smooth_median, selem2)
uniform_median_otsu = rank.otsu(uniform_median, selem2)
clustering_markers[smooth_median < local_otsu * 0.9] = 1
clustering_markers[smooth_median > local_otsu * 1.1] = 2
# dbg.random_walker_debug(smooth_median, clustering_markers)
# dbg.robust_binarize_debug(base_image, smooth_median, smooth_median, local_otsu, clustering_markers,
# 0, uniform_median, uniform_median_otsu)
binary_labels = random_walker(
smooth_median, clustering_markers, beta=10, mode='bf') - 1
if _dilation:
selem = disk(_dilation)
binary_labels = dilation(binary_labels, selem)
# dbg.robust_binarize_debug(binary_labels, base_image)
# dbg.voronoi_debug(binary_labels, local_maxi, dist, segmented_cells_labels)
# dbg.Kristen_robust_binarize(binary_labels, base_image)
return binary_labels
def test_otsu():
# test the local Otsu segmentation on a synthetic image
# (left to right ramp * sinus)
test = np.tile([128, 145, 103, 127, 165, 83, 127, 185, 63, 127, 205, 43, 127, 225, 23, 127], (16, 1))
test = test.astype(np.uint8)
res = np.tile([1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1], (16, 1))
selem = np.ones((6, 6), dtype=np.uint8)
th = 1 * (test >= rank.otsu(test, selem))
assert_equal(th, res)
def test_otsu_edge_case():
# This is an edge case that causes OTSU to appear to misbehave
# Pixel [1, 1] may take a value of of 41 or 81. Both should be considered
# valid. The value will change depending on the particular implementation
# of OTSU. It also may depend on how the compiler chooses to optimize
# the order of the operations.
img = np.array([[0, 41, 0], [30, 81, 106], [0, 147, 0]], dtype=np.uint8)
selem = np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]], dtype=np.uint8)
otsu = rank.otsu(img, selem)
assert otsu[1, 1] in [41, 81]
def check_all():
selem = morphology.disk(1)
refs = np.load(
os.path.join(skimage.data_dir, "rank_filter_tests.npz"))
assert_equal(refs["autolevel"], rank.autolevel(self.image, selem))
assert_equal(refs["autolevel_percentile"],
rank.autolevel_percentile(self.image, selem))
assert_equal(refs["bottomhat"], rank.bottomhat(self.image, selem))
assert_equal(refs["equalize"], rank.equalize(self.image, selem))
assert_equal(refs["gradient"], rank.gradient(self.image, selem))
assert_equal(refs["gradient_percentile"],
rank.gradient_percentile(self.image, selem))
assert_equal(refs["maximum"], rank.maximum(self.image, selem))
assert_equal(refs["mean"], rank.mean(self.image, selem))
assert_equal(refs["geometric_mean"],
rank.geometric_mean(self.image, selem)),
assert_equal(refs["mean_percentile"],
rank.mean_percentile(self.image, selem))
assert_equal(refs["mean_bilateral"],
rank.mean_bilateral(self.image, selem))
assert_equal(refs["subtract_mean"],
rank.subtract_mean(self.image, selem))
assert_equal(refs["subtract_mean_percentile"],
rank.subtract_mean_percentile(self.image, selem))
assert_equal(refs["median"], rank.median(self.image, selem))
assert_equal(refs["minimum"], rank.minimum(self.image, selem))
assert_equal(refs["modal"], rank.modal(self.image, selem))
assert_equal(refs["enhance_contrast"],
rank.enhance_contrast(self.image, selem))
assert_equal(refs["enhance_contrast_percentile"],
rank.enhance_contrast_percentile(self.image, selem))
assert_equal(refs["pop"], rank.pop(self.image, selem))
assert_equal(refs["pop_percentile"],
rank.pop_percentile(self.image, selem))
assert_equal(refs["pop_bilateral"],
rank.pop_bilateral(self.image, selem))
assert_equal(refs["sum"], rank.sum(self.image, selem))
assert_equal(refs["sum_bilateral"],
rank.sum_bilateral(self.image, selem))
assert_equal(refs["sum_percentile"],
rank.sum_percentile(self.image, selem))
assert_equal(refs["threshold"], rank.threshold(self.image, selem))
assert_equal(refs["threshold_percentile"],
rank.threshold_percentile(self.image, selem))
assert_equal(refs["tophat"], rank.tophat(self.image, selem))
assert_equal(refs["noise_filter"],
rank.noise_filter(self.image, selem))
assert_equal(refs["entropy"], rank.entropy(self.image, selem))
assert_equal(refs["otsu"], rank.otsu(self.image, selem))
assert_equal(refs["percentile"],
rank.percentile(self.image, selem))
assert_equal(refs["windowed_histogram"],
rank.windowed_histogram(self.image, selem))
def test_otsu(self):
# test the local Otsu segmentation on a synthetic image
# (left to right ramp * sinus)
test = np.tile([128, 145, 103, 127, 165, 83, 127, 185, 63, 127, 205, 43,
127, 225, 23, 127],
(16, 1))
test = test.astype(np.uint8)
res = np.tile([1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1], (16, 1))
selem = np.ones((6, 6), dtype=np.uint8)
th = 1 * (test >= rank.otsu(test, selem))
assert_equal(th, res)
def img_tesseract_detect(c_rect, im):
# 由于使用minAreaRect获得的图像有-90~0的角度，所以给出的坐标顺序也不一定是
# 转换时候给的，这里需要判断出图像的左上、左下、右上、右下的坐标，便于后面的变换
pts = c_rect.reshape(4, 2)
rect = np.zeros((4, 2), dtype = "float32")
# the top-left point has the smallest sum whereas the
# bottom-right has the largest sum
s = pts.sum(axis = 1)
rect[0] = pts[np.argmin(s)]
rect[3] = pts[np.argmax(s)]
# compute the difference between the points -- the top-right
# will have the minumum difference and the bottom-left will
# have the maximum difference
diff = np.diff(pts, axis = 1)
rect[2] = pts[np.argmin(diff)]
rect[1] = pts[np.argmax(diff)]
width = rect[3][0] - rect[0][0]
height = rect[3][1] - rect[0][1]
width = (int)((50.0 / height) * width)
height = 50
dst = np.float32([[0,0],[0,height],[width,0],[width,height]])
M = cv2.getPerspectiveTransform(rect, dst)
warp = cv2.warpPerspective(im, M, (width, height))
img_show_hook("剪裁识别图像", warp)
warp = np.array(warp, dtype=np.uint8)
radius = 13
selem = disk(radius)
# 使用局部自适应OTSU阈值处理
local_otsu = rank.otsu(warp, selem)
l_otsu = np.uint8(warp >= local_otsu)
l_otsu *= 255
kernel = cv2.getStructuringElement(cv2.MORPH_RECT,(2,2))
l_otsu = cv2.morphologyEx(l_otsu, cv2.MORPH_CLOSE, kernel)
img_show_hook("局部自适应OTSU图像", l_otsu)
print("识别结果：")
print(pytesseract.image_to_string(Image.fromarray(l_otsu), lang="chi-sim"))
cv2.waitKey(0)
return
def img_tesseract_detect(c_rect, im):
# 由于使用minAreaRect获得的图像有-90~0的角度，所以给出的坐标顺序也不一定是
# 转换时候给的，这里需要判断出图像的左上、左下、右上、右下的坐标，便于后面的变换
pts = c_rect.reshape(4, 2)
rect = np.zeros((4, 2), dtype="float32")
# the top-left point has the smallest sum whereas the
# bottom-right has the largest sum
s = pts.sum(axis=1)
rect[0] = pts[np.argmin(s)]
rect[3] = pts[np.argmax(s)]
# compute the difference between the points -- the top-right
# will have the minumum difference and the bottom-left will
# have the maximum difference
diff = np.diff(pts, axis=1)
rect[2] = pts[np.argmin(diff)]
rect[1] = pts[np.argmax(diff)]
width = rect[3][0] - rect[0][0]
height = rect[3][1] - rect[0][1]
width = (int)((50.0 / height) * width)
height = 50
dst = np.float32([[0, 0], [0, height], [width, 0], [width, height]])
M = cv2.getPerspectiveTransform(rect, dst)
warp = cv2.warpPerspective(im, M, (width, height))
img_show_hook("剪裁识别图像", warp)
warp = np.array(warp, dtype=np.uint8)
radius = 13
selem = disk(radius)
# 使用局部自适应OTSU阈值处理
local_otsu = rank.otsu(warp, selem)
l_otsu = np.uint8(warp >= local_otsu)
l_otsu *= 255
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (2, 2))
l_otsu = cv2.morphologyEx(l_otsu, cv2.MORPH_CLOSE, kernel)
img_show_hook("局部自适应OTSU图像", l_otsu)
print("识别结果：")
print(pytesseract.image_to_string(Image.fromarray(l_otsu), lang="chi-sim"))
cv2.waitKey(0)
return
def test_otsu_edge_case():
# This is an edge case that causes OTSU to appear to misbehave
# Pixel [1, 1] may take a value of of 41 or 81. Both should be considered
# valid. The value will change depending on the particular implementation
# of OTSU.
# To better understand, see
# https://mybinder.org/v2/gist/hmaarrfk/4afae1cfded1d78e44c9e4f58285d552/master
selem = np.array([[0, 1, 0],
[1, 1, 1],
[0, 1, 0]], dtype=np.uint8)
img = np.array([[ 0, 41, 0],
[ 30, 81, 106],
[ 0, 147, 0]], dtype=np.uint8)
result = rank.otsu(img, selem)
assert result[1, 1] in [41, 81]
img = np.array([[ 0, 214, 0],
[229, 104, 141],
[ 0, 172, 0]], dtype=np.uint8)
result = rank.otsu(img, selem)
assert result[1, 1] in [141, 172]
def t2():
"""
uses local/global thresholding, local doesn't seem to work well because the image is already
pretty binary
"""
from skimage.morphology import disk
from skimage.filters import threshold_otsu, rank
from skimage.util import img_as_ubyte
img = misc.imread('zones/0.png')
radius = 15
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
threshold_global_otsu = threshold_otsu(img)
global_otsu = img >= threshold_global_otsu
fig, axes = plt.subplots(2,
2,
figsize=(8, 5),
sharex=True,
sharey=True,
subplot_kw={'adjustable': 'box-forced'})
ax = axes.ravel()
plt.tight_layout()
fig.colorbar(ax[0].imshow(img, cmap=plt.cm.gray),
ax=ax[0],
orientation='horizontal')
ax[0].set_title('Original')
ax[0].axis('off')
fig.colorbar(ax[1].imshow(local_otsu, cmap=plt.cm.gray),
ax=ax[1],
orientation='horizontal')
ax[1].set_title('Local Otsu (radius=%d)' % radius)
ax[1].axis('off')
ax[2].imshow(img >= local_otsu, cmap=plt.cm.gray)
ax[2].set_title('Original >= Local Otsu' % threshold_global_otsu)
ax[2].axis('off')
ax[3].imshow(global_otsu, cmap=plt.cm.gray)
ax[3].set_title('Global Otsu (threshold = %d)' % threshold_global_otsu)
ax[3].axis('off')
plt.show()
def thr_conn(img,fname,stfolder,sfn,thrtyp,bs,mp,kv,rv,inv,ext,prev):
ofs=-5
if thrtyp=='Gauss':
tmp=cv2.adaptiveThreshold(img, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY, bs, ofs)
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Mean':
tmp=cv2.adaptiveThreshold(img, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY, bs, ofs)
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Gauss Sk':
ad_thr = threshold_local(img, bs,method='gaussian', offset=ofs)
tmp = 255*(img > ad_thr).astype('uint8')
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Mean Sk':
ad_thr = threshold_local(img, bs,method='mean', offset=ofs)
tmp = 255*(img > ad_thr).astype('uint8')
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Median Sk':
ad_thr = threshold_local(img, bs,method='median', offset=ofs)
tmp = 255*(img > ad_thr).astype('uint8')
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Otsu':
ret,tmp=cv2.threshold(img, 0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Otsu Loc':
radius = bs
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
tmp = 255*(img >= local_otsu).astype('uint8')
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Niblack':
ad_thr = threshold_niblack(img, window_size=bs, k=kv)
tmp = 255*(img > ad_thr).astype('uint8')
thrconnimg=Image.fromarray(tmp,mode='L')
if thrtyp=='Sauvola':
ad_thr = threshold_sauvola(img, window_size=bs, k=kv, r=rv)
tmp = 255*(img > ad_thr).astype('uint8')
thrconnimg=Image.fromarray(tmp,mode='L')
kernel1 = cv2.getStructuringElement(cv2.MORPH_ELLIPSE,(4,4))
openimg = Image.fromarray(cv2.morphologyEx(tmp,cv2.MORPH_OPEN,kernel1),mode='L')
# openimg2 = Image.fromarray(remove_small_objects((tmp/255).astype('uint8'),mp),mode='L')
opimg=255*remove_small_objects((tmp/255).astype('uint8').astype('bool'),mp).astype('uint8')
openimg2 = Image.fromarray(opimg,mode='L')
# skel=255*skeletonize((opimg/255).astype('uint8'))
# skelimg=Image.fromarray(skel,mode='L')
if prev=='N':
save_tif(stfolder,sfn,fname,openimg2,thrtyp,ext)
return openimg2#thrconnimg
def getIntensityThresholdOtsu(s, params):
logging.info(
f"{s['filename']} - \tLightDarkModule.getIntensityThresholdOtsu")
name = "otsu"
local = strtobool(params.get("local", "False"))
radius = float(params.get("radius", 15))
selem = disk(radius)
img = s.getImgThumb(s["image_work_size"])
img = color.rgb2gray(img)
if local:
thresh = rank.otsu(img, selem)
name += "local"
else:
thresh = threshold_otsu(img)
map = img < thresh
s["img_mask_" + name] = map > 0
if strtobool(params.get("invert", "False")):
s["img_mask_" + name] = ~s["img_mask_" + name]
io.imsave(s["outdir"] + os.sep + s["filename"] + "_" + name + ".png",
img_as_ubyte(s["img_mask_" + name]))
prev_mask = s["img_mask_use"]
s["img_mask_use"] = s["img_mask_use"] & s["img_mask_" + name]
s.addToPrintList(
name,
printMaskHelper(params.get("mask_statistics", s["mask_statistics"]),
prev_mask, s["img_mask_use"]))
if len(s["img_mask_use"].nonzero()
[0]) == 0: # add warning in case the final tissue is empty
logging.warning(
f"{s['filename']} - After LightDarkModule.getIntensityThresholdOtsu:{name} NO tissue remains "
f"detectable! Downstream modules likely to be incorrect/fail")
s["warnings"].append(
f"After LightDarkModule.getIntensityThresholdOtsu:{name} NO tissue remains detectable! "
f"Downstream modules likely to be incorrect/fail")
return
def transform():
files = []
with open('list.txt', r) as f:
files = f.readlines()
f.close()
for file in files:
print("Processing " + file + "...")
# Import file
data = tifffile.imread(file)
# Convert 3-band RGB to 1-band grayscale
grayscale = rgb2gray(data)
# Calculate standard deviation
mult_1 = np.multiply(grayscale, grayscale)
blur_1 = gaussian(mult_1, sigma=(9, 9), truncate=3.5, multichannel=False)
blur_2 = gaussian(grayscale, sigma=(9, 9), truncate=3.5, multichannel=False)
mult_2 = np.multiply(blur_2, blur_2)
std_hat = np.sqrt(blur_1 - mult_2)
# Calculate entropy
sigma_hat = entropy(std_hat, square(9))
# Phase symmetry
psym = phasesym(sigma_hat)
# Threshold
selem = square(9)
local_otsu = rank.otsu(psym, selem)
threshold_global_otsu = threshold_otsu(psym)
global_otsu = (psym >= threshold_global_otsu)
# Skeletonize and invert colors
skeleton = skeletonize(global_otsu, method='lee')
skeleton[skeleton == 255] = 1
skeleton[skeleton == 0] = 255
skeleton[skeleton == 1] = 0
# Save intermediate files as png
plt.imsave(alignedname, skeleton, cmap=plt.cm.gray, dpi=300)
print("File " + file + " done!")
def nick_binarize(img_list):
'''Binarize linecut images using two differently sized local threshold kernels
Args:
img_list: list of grayscale linecut images
Returns:
results: binarized images in the same order as the input'''
results = []
for img in img_list:
try:
# img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
height = img.shape[0]
width = img.shape[1]
# Resize the images to 200 pixel height
scaling_factor = 100/img.shape[0]
new_w = int(scaling_factor*img.shape[1])
new_h = int(scaling_factor*img.shape[0])
# img = cv2.resize(img, (new_w, new_h))
img = np.array(Image.fromarray(img).resize((new_w, new_h), Image.ANTIALIAS))
# First pass thresholding
th1 = threshold_niblack(img, 13, 0.00)
# Second pass thresholding
radius = 101
structured_elem = disk(radius)
th2 = rank.otsu(img, structured_elem)
# Masking
img = (img > th1) | (img > th2)
img = img.astype('uint8')*255
img = np.array(Image.fromarray(img).resize((width, height), Image.ANTIALIAS))
results.append(img)
except Exception as e:
continue
return results
def local_otsu_denoising(img):
N = img.shape[0]
radius = np.arange(10, N/4, 10)
stds = []
out_images = []
for radii in radius:
selem = square(radii)
out = img.copy()
# Improve the contrast of the image
local_otsu = rank.otsu(img, selem)
stds.append(out[out <= local_otsu].std())
out[out >= local_otsu] = 255
out_images.append(out)
stds = np.array(stds)
arg = stds.argmin()
out = out_images[arg]
return out
def local_otsu_denoising(img):
N = img.shape[0]
radius = np.arange(10, N / 4, 10)
stds = []
out_images = []
for radii in radius:
selem = square(radii)
out = img.copy()
# Improve the contrast of the image
local_otsu = rank.otsu(img, selem)
stds.append(out[out <= local_otsu].std())
out[out >= local_otsu] = 255
out_images.append(out)
stds = np.array(stds)
arg = stds.argmin()
out = out_images[arg]
return out
def run_otsu(image_path):
# img = color.rgb2gray(io.imread(image_path))
img = io.imread(image_path, as_grey=True)
radius = 15
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
threshold_global_otsu = threshold_otsu(img)
global_otsu = img >= threshold_global_otsu
x = global_otsu.shape[1]
y = global_otsu.shape[0]
global_otsu = global_otsu.tolist()
for i in xrange(y):
for j in xrange(x):
if global_otsu[i][j] == False:
global_otsu[i][j] = 1
else:
global_otsu[i][j] = 0
global_otsu = np.array(global_otsu)
return global_otsu
def __calc_SNR(self,
img,
gaus_sd=1,
local_rad=15,
offset=70,
show_imgs=False):
'''
This function calculates the Signal to noise ration for a single image. Signal to noise is usually measured by: (i0 - ib) / sqrt(i0) where i0 is signal intensity, and ib is background intensity. To approximate this, we use otsu threshholding to separate background and signal peaks. We then use the mean value of the signal mask as i0 and the mean signal of the background mask as ib.
inputs
img <np.array> : image to prefore SNR analysis on
gaus_sd <int> : standard deviation in the gaussian filter applied before otsu threshold
local_rad <int> : otsu neighborhood
offset <int> : pixel intensity offset, higher value will decrease the area of the signal mask.
show_imgs <boolean> : if true, will plot the mask images, for use in diagnostics and parameter tuning
outputs
SNR <float> : Signal to noise ratio; (i0-ib) / sqrt(i0)
'''
img2 = gaussian_filter(img, gaus_sd)
selem = disk(local_rad)
local_otsu = rank.otsu(img2, selem)
if (show_imgs):
fig, axes = plt.subplots(2, 2)
axes = axes.flatten()
axes[0].imshow(img)
axes[1].imshow(img2)
axes[2].imshow(img2 >= local_otsu + offset)
plt.show()
i0 = np.average(img2[img2 >= (local_otsu + offset)])
ib = np.average(img2[img2 < (local_otsu + offset)])
SNR = (i0 - ib) / np.sqrt(i0)
return SNR
def local_otsu(img):
radius = 100
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
threshold_global_otsu = threshold_otsu(img)
global_otsu = img >= threshold_global_otsu
fig, ax = plt.subplots(2, 2, figsize=(8, 5), sharex=True, sharey=True, subplot_kw={'adjustable':'box-forced'})
ax1, ax2, ax3, ax4 = ax.ravel()
fig.colorbar(ax1.imshow(img, cmap=plt.cm.gray),
ax=ax1, orientation='horizontal')
ax1.set_title('Original')
ax1.axis('off')
fig.colorbar(ax2.imshow(local_otsu, cmap=plt.cm.gray),
ax=ax2, orientation='horizontal')
ax2.set_title('Local Otsu (radius=%d)' % radius)
ax2.axis('off')
ax3.imshow(img >= local_otsu, cmap=plt.cm.gray)
ax3.set_title('Original >= Local Otsu' % threshold_global_otsu)
ax3.axis('off')
ax4.imshow(global_otsu, cmap=plt.cm.gray)
ax4.set_title('Global Otsu (threshold = %d)' % threshold_global_otsu)
ax4.axis('off')
plt.show()
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))
from skimage import data
from skimage.morphology import disk
from skimage.filters import threshold_otsu, rank
from skimage.util import img_as_ubyte
matplotlib.rcParams['font.size'] = 9
img = img_as_ubyte(data.page())
radius = 15
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
threshold_global_otsu = threshold_otsu(img)
global_otsu = img >= threshold_global_otsu
fig, ax = plt.subplots(2, 2, figsize=(8, 5))
ax1, ax2, ax3, ax4 = ax.ravel()
fig.colorbar(ax1.imshow(img, cmap=plt.cm.gray),
ax=ax1, orientation='horizontal')
ax1.set_title('Original')
ax1.axis('off')
fig.colorbar(ax2.imshow(local_otsu, cmap=plt.cm.gray),
ax=ax2, orientation='horizontal')
ax2.set_title('Local Otsu (radius=%d)' % radius)
def pp_lotsu_eqhist(image, otsu_rad=5):
byte_img = img_as_ubyte(image)
selem = disk(otsu_rad)
local_otsu = rank.otsu(byte_img, selem)
eq_hist_img = equalize_hist(local_otsu)
return eq_hist_img
def otsuThresholdLocal(img, radius = 15):
selem = disk(radius)
local_otsu = rank.otsu(img, selem)
local_otsu = img >= local_otsu
return local_otsu.astype(int)
#
# Local is much slower than global thresholding. A function for global
# Otsu thresholding can be found in : `skimage.filters.threshold_otsu`.
#
# .. [4] http://en.wikipedia.org/wiki/Otsu's_method
from skimage.filters.rank import otsu
from skimage.filters import threshold_otsu
p8 = data.page()
radius = 10
selem = disk(radius)
# t_loc_otsu is an image
t_loc_otsu = otsu(p8, selem)
loc_otsu = p8 >= t_loc_otsu
# t_glob_otsu is a scalar
t_glob_otsu = threshold_otsu(p8)
glob_otsu = p8 >= t_glob_otsu
fig, ax = plt.subplots(2, 2, sharex=True, sharey=True)
ax1, ax2, ax3, ax4 = ax.ravel()
fig.colorbar(ax1.imshow(p8, cmap=plt.cm.gray), ax=ax1)
ax1.set_title('Original')
fig.colorbar(ax2.imshow(t_loc_otsu, cmap=plt.cm.gray), ax=ax2)
ax2.set_title('Local Otsu ($r=%d$)' % radius)
def local_otsu(image):
radius = 12
s_elem = disk(radius)
local = rank.otsu(image, s_elem)
return local
def lotsu(image, otsu_rad=5): byte_img = img_as_ubyte(image) selem = disk(otsu_rad) return rank.otsu(byte_img, selem)
rect[2] = pts[np.argmin(diff)]
rect[1] = pts[np.argmax(diff)]
dst = np.float32([[0,0],[0,100],[200,0],[200,100]])
M = cv2.getPerspectiveTransform(rect, dst)
warp = cv2.warpPerspective(img_org, M, (200, 100))
cv2.imshow("cropped image", warp)
cv2.waitKey(0)
warp = np.array(warp, dtype=np.uint8)
radius = 10
selem = disk(radius)
local_otsu = rank.otsu(warp, selem)
l_otsu = np.uint8(warp >= local_otsu)
l_otsu *= 255
kernel = cv2.getStructuringElement(cv2.MORPH_RECT,(6,6))
l_otsu = cv2.morphologyEx(l_otsu, cv2.MORPH_CLOSE, kernel)
cv2.imshow("binary image to be detected", l_otsu)
cv2.waitKey(0)
print("识别结果：")
print(pytesseract.image_to_string(Image.fromarray(l_otsu)))
cv2.waitKey(0)
# http://www.pyimagesearch.com/2014/03/10/building-pokedex-python-getting-started-step-1-6/