def slice_pre(data_slice):
data_normalized = normalize(data_slice)
data_oryg = data_normalized.copy()
data_hist = exposure.equalize_adapthist(data_normalized,
clip_limit=0.1)
data_median = filters.median(data_hist, selem=disk(3))
data_median = exposure.adjust_gamma(data_median, gamma=10)
thresholds = filters.threshold_multiotsu(data_median)
regions = np.digitize(data_normalized, bins=thresholds)
data_normalized[regions != 2] = 0
data_pre = exposure.equalize_hist(data_normalized)
thresholds = filters.threshold_multiotsu(data_pre)
regions = np.digitize(data_pre, bins=thresholds)
data_mask = label2rgb(regions)
data_mask = rgb2gray(data_mask)
data_mask[data_mask != np.max(data_mask)] = 0
data_mask[data_mask == np.max(data_mask)] = 1
data_mask = closing(data_mask, selem=disk(3)).astype(int)
data_mask = remove_small_holes(data_mask, area_threshold=300)
data_eq = exposure.equalize_adapthist(data_oryg, clip_limit=0.15)
data_preprocessed = data_eq * data_mask
data_preprocessed = opening(data_preprocessed, selem=disk(3))
return data_preprocessed, data_mask
def detect_people(img, img_path):
# local_logger.info(img.shape)
# First, predict if image has people
prediction = model(img, training=False).numpy()
# local_logger.info(prediction)
# Second, if image has peple then do the localisization
if prediction[0][0] > prediction[0][1]:
flat_img = get_flat_img(img)
sum_mat = get_2d_sum_mat(model_weights, flat_img)
# replace all negative values with 0
no_neg_sum_mat = sum_mat.copy()
no_neg_sum_mat[no_neg_sum_mat < 0] = 0
# Using Otsu threshold to locate people
# sum_mat = sum_mat.astype('float32')
# max = np.max(sum_mat)
# min = np.min(sum_mat)
# raw_th = max - 0.4*(max - min)
# otsu_th, otsu_mat = cv2.threshold(sum_mat, raw_th, max, cv2.THRESH_TOZERO+cv2.THRESH_OTSU)
# local_logger.info(max, min, otsu_th)
# draw_img_plot(img_path, otsu_mat, otsu_th, PLOT_DIR)
# thresh = threshold_otsu(sum_mat)
thresh_arr = threshold_multiotsu(no_neg_sum_mat, classes=3)
thresh = thresh_arr[-1]
# local_logger.info('Otsu threshold value: ' + repr(thresh))
# Considering threshold_multiotsu for better localization?
draw_img_plot(img_path, sum_mat, thresh, plot_path)
return 1
else:
return 0
def extract_foreground(img):
"""
Extracts the single largest object from grayscale image img.
Returns a boolean mask and a skimage RegionProperty for that object.
"""
thresholds = threshold_multiotsu(img, classes=3)
true_fg = np.digitize(img, [thresholds[0]])
mask_edge = get_edge_mask(true_fg, 100, 20)
masked_img = extract_mask(img, mask_edge)
new_true_fg = new_edge_threshold(masked_img, mask_edge, true_fg)
new_mask_edge = get_edge_mask(new_true_fg, 50, 10)
new_masked_img = extract_mask(img, new_mask_edge)
last_true_fg = new_edge_threshold(
new_masked_img,
new_mask_edge,
new_true_fg,
)
labels = label(last_true_fg)
props = regionprops(labels, img)
areas = np.asarray([prop.area for prop in props])
ind = areas.argmax()
prop = props[ind]
mask = binary_fill_holes(labels == prop.label)
return mask, prop
def segment(self, img):
"""
Applies Otsu's Multi-Tresholding to a Image
Parameters
----------
img: np.ndarray
The image to perform segmentation.
Returns
-------
str
The path where the segmented image was saved.
"""
# Apply Gaussian Blur to smooth the image (5x5 kernel)
img = filters.gaussian(img)
# Apply otsu's global thresholding method
thresholds = filters.threshold_multiotsu(img,
classes=self.n_thresholds)
# Use the found thresholds to segment image
img = np.digitize(img, bins=thresholds)
# Scale the image
img = scale_img(img)
return img
def extract_foreground_biofilms(img, area_threshold=9000):
thresholds = threshold_multiotsu(img, classes=3)
true_fg = np.digitize(img, [thresholds[0]])
mask_edge = get_edge_mask(true_fg, 100, 20)
masked_img = extract_mask(img, mask_edge)
new_true_fg = new_edge_threshold(masked_img, mask_edge, true_fg)
new_mask_edge = get_edge_mask(new_true_fg, 50, 10)
new_masked_img = extract_mask(img, new_mask_edge)
last_true_fg = new_edge_threshold(
new_masked_img,
new_mask_edge,
new_true_fg,
)
labels = label(last_true_fg)
props = regionprops(labels, img)
areas = np.asarray([prop.area for prop in props])
mask = np.zeros_like(labels)
inds = np.arange(len(areas))[areas > area_threshold]
for i, ind in enumerate(inds):
prop = props[ind]
mask[binary_fill_holes(labels == prop.label)] = i + 1
return mask
def transform_image(original, classes=3, cmap_result='gray', filename=None):
thresholds = threshold_multiotsu(original, classes=classes)
regions = np.digitize(original, bins=thresholds)
fig, ax = plt.subplots(nrows=1, ncols=3, figsize=(10, 3.5))
# Plotting the original image.
ax[0].imshow(original, cmap='gray')
ax[0].set_title('Grayscale')
ax[0].axis('off')
# Plotting the histogram and the two thresholds obtained from
# multi-Otsu.
ax[1].hist(original.ravel(), bins=255)
ax[1].set_title('Histogram')
for thresh in thresholds:
ax[1].axvline(thresh, color='r')
# Plotting the Multi Otsu result.
ax[2].imshow(regions, cmap=cmap_result)
ax[2].set_title(str(classes) + ' gray levels')
ax[2].axis('off')
plt.subplots_adjust()
plt.savefig('./img/preprocess_image_' + filename + '_' + str(classes) + 'classes.png', transparent=True)
plt.show()
def extract_foreground_biofilms(img, area_threshold=9000):
"""
Extracts the single largest object from grayscale image img.
Returns a boolean mask and a skimage RegionProperty for that object.
"""
thresholds = threshold_multiotsu(img, classes=3)
true_fg = np.digitize(img, [thresholds[0]])
mask_edge = get_edge_mask(true_fg, 100, 20)
masked_img = extract_mask(img, mask_edge)
new_true_fg = new_edge_threshold(masked_img, mask_edge, true_fg)
new_mask_edge = get_edge_mask(new_true_fg, 50, 10)
new_masked_img = extract_mask(img, new_mask_edge)
last_true_fg = new_edge_threshold(
new_masked_img,
new_mask_edge,
new_true_fg,
)
labels = label(last_true_fg)
props = regionprops(labels, img)
areas = np.asarray([prop.area for prop in props])
mask = np.zeros_like(labels)
inds = np.arange(len(areas))[areas > area_threshold]
for i, ind in enumerate(inds):
prop = props[ind]
mask[binary_fill_holes(labels == prop.label)] = i + 1
return mask
def _binarise(self, arr):
threshes = filters.threshold_multiotsu(arr, classes=2)
# if type(threshes) is np.ndarray: # Some thresholds return multiple levels - reduce to 2
# threshes = threshes[0]
binarised = arr > threshes
return binarised
def cloud_mask_otsu(image):
image = np.array(image)
thresh = threshold_multiotsu(image, 4)
max_thresh = max(thresh)
mask = closing(image > max_thresh, square(10))
del max_thresh, thresh
return np.array(mask)
def segmentation(image, arrow_bb):
"""
returns a binary image
- Input : RGB image
- Output : binary image
"""
# crop robot from image
minr_a, minc_a, maxr_a, maxc_a = arrow_bb
test_im = image.copy()
test_im[minr_a-30:maxr_a+50, minc_a-30:maxc_a+50] = 255
# Change exposure to get a brighter image
bright_im = skimage.exposure.adjust_gamma(test_im, gamma=3/5, gain=1)
gray = skimage.color.rgb2gray(test_im)
# Contrast stretching
a, b = np.percentile(gray, (1, 70))
img_rescale = exposure.rescale_intensity(gray, in_range=(a, b))
# Multi thresholds to get digits and operators at once
thresholds = threshold_multiotsu(img_rescale)
# Using the threshold values, we generate the three regions.
regions = np.digitize(gray, bins=thresholds)
# Binarization, discriminate background from foreground
binarized = regions == 0
# Morphological operation
close = morphology.binary_dilation(binarized, skimage.morphology.selem.rectangle(1, 3))
return close
def _generate_otsu_tick_points(self) -> List[float]:
"""
Determine the Otsu threshold tick point.
"""
vals = filters.threshold_multiotsu(self.image,
classes=self.view.num_materials)
return self._normalise_tick_values(vals.tolist())
def area_extract(array, coordinates, otsu_bins=20, expand_distance=5):
h_upper, w_upper = array.shape
labeled_area = np.zeros_like(array)
# Extracting the available area from the given boxes
for lbl, (x, y, w, h, _) in enumerate(coordinates):
# Decide weather all the area inside the box is available
# Notice: the 'lbl' used here is different from the 'label' used in object annotating
# during the object recognition processing, but only for the pixel labeling.
xmin, xmax = np.clip(x - w / 2, 0,
None).astype(int), np.clip(x + w / 2, 0,
w_upper).astype(int)
ymin, ymax = np.clip(y - h / 2, 0,
None).astype(int), np.clip(y + h / 2, 0,
h_upper).astype(int)
# Extract available areas from boxes
strict_area = array[ymin:ymax, xmin:xmax]
otsu_thres = threshold_otsu(strict_area, nbins=otsu_bins)
# Labeling available areas
y_index, x_index = (strict_area >= otsu_thres).nonzero()
labeled_area[y_index + ymin, x_index + xmin] = lbl + 1
# Expanding the extracted areas
expanded_labels = expand_labels(labeled_area, distance=expand_distance)
# Re-thresholding of the expanded areas using Otsu-threshold
for lbl in range(1, np.max(expanded_labels).astype(int)):
lbl_area = (array - np.min(array)) * (expanded_labels == lbl)
regions = np.digitize(lbl_area, bins=threshold_multiotsu(lbl_area))
expanded_labels[regions == 1] = -lbl
expanded_labels[regions == 2] = lbl
return expanded_labels
def extractdisease(img):
#ekstrak bercak
lab = cv2.cvtColor(img, cv2.COLOR_BGR2LAB)
L, A, B = cv2.split(lab)
thresholds = threshold_multiotsu(A)
# Using the threshold values, we generate the three regions.
regions = np.digitize(A, bins=thresholds)
T = []
for thresh in thresholds:
T.append(thresh)
def th(array):
temp_img = np.copy(array)
for i in range(len(temp_img)):
for j in range(len(temp_img[0])):
if (temp_img[i][j] >= T[1] and temp_img[i][j] >= T[0]):
temp_img[i][j] = 255
else:
temp_img[i][j] = 0
return temp_img
th = th(A)
mask = th
result = cv2.bitwise_and(img, img, mask=mask)
return result
def otsu(image, n_classes):
try:
thresholds = threshold_multiotsu(image, classes=n_classes)
except ValueError:
# When output is constant can't apply otsu thresholding
thresholds = np.ones(1)
return np.digitize(image, bins=thresholds).astype('uint8')
def threshold_multiotsu(arr1d, classes):
"""
TypeError: ndarray() missing required argument 'shape' (pos 1)
:param arr1d:
:return:
"""
import skimage.filters as sf
thresh = sf.threshold_multiotsu(arr1d, classes, nbins=256)
return thresh
def extract_mesh(fname, vol, nmaterials=2, pitch=1.0):
"""
vol (torch.tensor)
"""
vol = (vol - vol.min()) / (vol.max() + -vol.min() + 1e-12)
if nmaterials == 2:
thresh = threshold_otsu(vol)
voln = skimage.restoration.denoise_tv_chambolle(voln, 0.0001)
verts, faces, normals, values = measure.marching_cubes_lewiner(
voln, level=thresh, allow_degenerate=False)
mesh = trimesh.Trimesh(verts, faces)
obj_ = trimesh.exchange.obj.export_obj(mesh)
with open(fname, "w") as f:
f.write(obj_)
else:
#from sklearn.cluster import KMeans
#kmeans = KMeans(n_clusters=3).fit(vol.reshape([-1,1]))
#c = sorted(kmeans.cluster_centers_[:,0])
#print("centroids of Kmeans:", c)
thresholds = threshold_multiotsu(image, nmaterials)
f = open(fname, 'w')
vert_start = 0
f.write(f"# attenations by kmeans: {str(c)}")
for i in range(nmaterials - 1):
f.write(f"o objecect{i} {i+1} {i}")
thresh = (c[i] + c[i + 1]) / 2.
# extract for each material
print(f"extract a material with a threshold {thresh}")
new_vol = vol.copy()
new_vol[new_vol < c[i]] = 0.
new_vol[new_vol >= c[i + 1]] = 1.
new_vol = (new_vol - c[i]) / (c[i + 1] - c[i] + 1e-8)
mesh = ops.matrix_to_marching_cubes(matrix=new_vol, pitch=pitch)
#mesh.export(fname[:-4]+str(i)+".obj")
for vert in mesh.vertices:
f.write('v %f %f %f\n' % tuple(vert + vert_start))
for face in mesh.faces:
f.write('f %d %d %d\n' % tuple(face + 1 + vert_start))
vert_start += mesh.vertices.shape[0]
print(vert_start)
f.close()
return
def get_forms(image):
"""
Function that highlight the regions of interest.
Input : - image --> image to labelize
Outputs : - shapes --> matrix with binarized image
- forms --> dictionnary with forms info with 'key' : [#pix, form_number, form region]
"""
# Dictionnary to stock information about the different shapes
forms = dict()
# Conversion to grayscale
gray = skimage.color.rgb2gray(image)
# Otsu to find the shapes
thresholds = threshold_multiotsu(gray, classes=2)
thresh_background = thresholds[0] * 1.38
##### Shapes detection (cutting the background) #####
shapes = np.zeros(gray.shape)
for i in range(gray.shape[0]):
for j in range(gray.shape[1]):
if gray[i][j] < thresh_background:
shapes[i][j] = 255
classes = np.zeros(shapes.shape)
k = 0
for i in range(shapes.shape[0]):
for j in range(shapes.shape[1]):
if shapes[i][j] == 255 and classes[i][
j] == 0: # When a new shape is encountered
k += 1
region = region_growing(shapes, [i, j], 10)
pix = 0
color = 0
for r in region: # Iterations into a shape
pix += 1 # Counter for the number of pixel inside a shape
color += gray[r[0]][r[1]]
classes[r[0]][r[
1]] = k # Separation of the different form by labelling
forms['Shape', k] = [pix, k, region]
# Cutting of the regions with more then 500 pixels
if forms['Shape', k][0] > 500 or forms['Shape', k][0] <= 3:
w = np.where(classes == forms['Shape', k][1])
shapes[w[0], w[1]] = 0
del forms['Shape', k]
return shapes, forms
def get_mask(channel: str = 'lab') -> List[np.ndarray]:
"""Calcule un masque de segmentation.
Si channel = 'lab', convertit au préalable l'image dans l'espace LAB.
Sinon, utilise le canal rouge, vert ou bleu pour calculer le ou les
seuils optimaux de séparation des différentes couches de l'image."""
# conversion du RGB au LAB
# plus de détails ici : https://en.wikipedia.org/wiki/CIELAB_color_space
# et ici pour la méthode de calcul:
# https://docs.opencv.org/3.4/de/d25/imgproc_color_conversions.html#color_convert_rgb_lab
new_img = img.copy()
mask = np.ones((img.shape[:2]))
# application de la méthode d'Otsu sur l'image dans l'espace de couleurs LAB
# ou sur les canaux Rouge, Vert ou Bleu de l'espace RGB.
if channel == 'A (LAB)':
lab = cv2.cvtColor(new_img, cv2.COLOR_BGR2LAB)[..., 1]
_t = threshold_multiotsu(lab, classes)[0]
elif channel == 'rouge (RGB)':
lab = new_img[..., 0]
_t = threshold_multiotsu(lab, classes)[1]
elif channel == 'vert (RGB)':
lab = new_img[..., 1]
_t = threshold_multiotsu(lab, classes)[1]
elif channel == 'bleu (RGB)':
lab = new_img[..., 2]
_t = threshold_multiotsu(lab, classes)[1]
# définition du masque de segmentation
if channel == 'A (LAB)':
mask = 1 - (lab < _t) * 1
else:
mask = (lab < _t) * 1
lab = 1 - lab
# les pixels du fond sont codés en RGB comme (255, 255, 255)
new_img[np.where(mask == 0)] = 255
if smooth:
mask = binary_closing(mask, iterations=15)
mask = binary_opening(mask, iterations=10)
if fill_holes:
mask = binary_fill_holes(mask)
new_img[np.where(mask == 0)] = 255
return lab, mask, new_img
def get_master_mask(self, sigma=1, kernel_size=5, mask_ext=5, nuclear_ext=2, multi_otsu_nucleus_mask=True):
""" Whole cell mask building by Ca dye channel data with Otsu thresholding.
Filters greater element of draft Otsu mask and return master mask array.
mask_ext - otsu mask extension value in px
"""
trun = lambda k, sd: (((k - 1)/2)-0.5)/sd # calculate truncate value for gaussian fliter according to sigma value and kernel size
self.detection_img = filters.gaussian(np.mean(self.ca_series, axis=0), sigma=sigma, truncate=trun(kernel_size, sigma))
# multi Otsu mask for nucleus detection
self.multi_otsu_nucleus_mask = multi_otsu_nucleus_mask
if self.multi_otsu_nucleus_mask:
multi_otsu = filters.threshold_multiotsu(self.detection_img, classes=3)
self.element_label = np.digitize(self.detection_img, bins=multi_otsu) # 1 - cell elements, 2 - intracellular and nuclear elements
# get larger multi Otsu cellular element
cell_element = (self.element_label == 1) | (self.element_label == 2)
cell_element_label = measure.label(cell_element)
cell_element_area = {element.area : element.label for element in measure.regionprops(cell_element_label)}
cell_border_mask = cell_element_label == cell_element_area[max(cell_element_area.keys())]
self.cell_distances, _ = distance_transform_edt(~cell_border_mask, return_indices=True)
self.cell_mask = self.cell_distances <= mask_ext
# get larger multi Otsu intracellular element
nuclear_element = self.element_label == 2
nuclear_element_label = measure.label(nuclear_element)
nuclear_element_area = {element.area : element.label for element in measure.regionprops(nuclear_element_label)}
nuclear_element_border = nuclear_element_label == nuclear_element_area[max(nuclear_element_area.keys())]
self.nuclear_distances, _ = distance_transform_edt(~nuclear_element_border, return_indices=True)
self.nuclear_mask = self.nuclear_distances <= nuclear_ext
self.master_mask = np.copy(self.cell_mask)
self.master_mask[self.nuclear_mask] = 0
else:
# please, DON'T use this option!
otsu = filters.threshold_otsu(self.detection_img)
draft_mask = self.detection_img > otsu
self.element_label, self.element_num = measure.label(draft_mask, return_num=True)
logging.info(f'{self.element_num} Otsu mask elements detected')
detection_label = np.copy(self.element_label)
element_area = {element.area : element.label for element in measure.regionprops(detection_label)}
self.master_mask = detection_label == element_area[max(element_area.keys())]
# mask expansion
self.cell_distances, _ = distance_transform_edt(~self.master_mask, return_indices=True)
self.master_mask = self.cell_distances <= mask_ext
self.total_byte_prot_img = filters.gaussian(util.img_as_ubyte(np.mean(self.prot_series, axis=0)/np.max(np.abs(np.mean(self.prot_series, axis=0)))), sigma=sigma, truncate=trun(kernel_size, sigma))
self.total_mask_ctrl_img = label2rgb(self.master_mask, image=self.total_byte_prot_img, colors=['blue'], alpha=0.2)
def get_mask(self):
"""
Gets the binary mask of detected nuclei, as well as the labeled image
"""
# compute threshold (to detect nuclei)
# threshold = filters.threshold_minimum(filt_img) #nuclei are among the darkest parts of the image
thresholds = filters.threshold_multiotsu(self.gray_img,
classes=self.numClasses)
threshold = thresholds[0]
# binarize
self.binary_img = self.gray_img < threshold
# label
self.labeled_img = measure.label(self.binary_img, background=0)
def _do_locate_reference_cell(
image: Image, reference_area: int, scale: float = 0.1,
) -> Polygon:
"""Perform localization of reference cell"""
# filter + binarize
image_f = transform.rescale(image.data, scale)
thresh = filters.threshold_multiotsu(image_f, classes=5)[0]
image_t = image_f > thresh
# find regions
labeled = morphology.label(image_t)
regions = measure.regionprops(labeled)
# drop areas that are not approximately square
regions = [
r
for r in regions
if np.abs(r.bbox[2] - r.bbox[0]) / np.abs(r.bbox[3] - r.bbox[1]) > 0.8
and np.abs(r.bbox[2] - r.bbox[0]) / np.abs(r.bbox[3] - r.bbox[1]) < 1.8
]
# convert to Polygon
tmp: List[Polygon] = []
for r in regions:
bbox = [int(r.bbox[i] * 1 / scale) for i in range(4)]
y0, x0 = max(0, bbox[0]), max(0, bbox[1])
y1, x1 = (
min(image.shape[0], bbox[2]),
min(image.shape[1], bbox[3]),
)
box = Polygon.from_bounds(x0, y0, x1, y1)
tmp.append(box)
# drop boxes that intersect with others
regions = [
r for r in tmp if not np.any([x.intersects(r) and x is not r for x in tmp])
]
if len(regions) == 0:
return None
# process regions
area_dev = [np.abs((r.area - reference_area) / reference_area) for r in regions]
min_dev_idx = np.argmin(area_dev)
if area_dev[min_dev_idx] < 2.0:
return affinity.scale(regions[min_dev_idx], xfact=0.5, yfact=0.5)
else:
return None
def SegmentByOtsu(Image):
from skimage.filters import threshold_multiotsu
IM = Image.copy()
if (len(IM.shape) == 3):
IM = cv2.cvtColor(IM, cv2.COLOR_RGB2GRAY)
thresh = threshold_multiotsu(IM)
Mask0 = (IM > thresh[0])
Mask1 = (IM > thresh[1])
Mask0 = Mask0.astype(int)
Mask1 = Mask1.astype(int)
return Mask0, Mask1, thresh
def otsu(self, image, num_classes=None):
'''
image: str or array
'''
if num_classes is None:
num_classes = self.classes
# Read image if it is a string
if type(image) == str:
image = imread(image)
thresholds = threshold_multiotsu(image, classes=num_classes)
segm = np.digitize(image, bins=thresholds)
return segm
def MultiThreshold(imageName, thresholdValues=None, classCount=3):
base_path = "./images"
# Setting the font size for all plots.
matplotlib.rcParams['font.size'] = 9
# The input image.
image = cv.imread(f"{base_path}/{imageName}", 0)
# Applying multi-Otsu threshold for the default value, generating
# three classes.
thresholds = threshold_multiotsu(image, classCount)
if thresholdValues:
if isinstance(thresholdValues, list):
thresholds = thresholdValues
else:
print("Threshold Values Must Be List!!!")
print("The Program Continues With Multi Otsu Method!!!")
# Using the threshold values, we generate the three regions.
regions = np.digitize(image, bins=thresholds)
fig, ax = plt.subplots(nrows=1, ncols=3, figsize=(15, 5))
# Plotting the original image.
ax[0].imshow(image, cmap='gray')
ax[0].set_title('Original')
ax[0].axis('off')
# Plotting the histogram and the two thresholds obtained from
# multi-Otsu.
ax[1].hist(image.ravel(), bins=255)
ax[1].set_title('Histogram')
for thresh in thresholds:
ax[1].axvline(thresh, color='r')
# Plotting the Multi Otsu result.
ax[2].imshow(
regions,
cmap='jet',
)
ax[2].set_title('Multi-Otsu result')
ax[2].axis('off')
plt.subplots_adjust()
plt.show()
def threshold(index):
'''
Caluclates shoreline value threshold from water index image and plots histogram
Yarran Doherty & Kilian Vos 2020
'''
# Convert to 1d array and ermove nan values
vec_im = np.copy(index)
vec = vec_im.reshape(vec_im.shape[0] * vec_im.shape[1])
vec = vec[~np.isnan(vec)]
# Perform multi otsu thresholding
t_otsu = filters.threshold_multiotsu(vec)
# Plot histogram
plt.ioff()
# create figure
fig = plt.figure()
fig.tight_layout()
fig.set_size_inches([8, 8])
ax = fig.add_subplot(111)
# Set labels
ax.set_title('NDWI Pixel Value Histogram Thresholding', fontsize=10)
ax.set_xlabel('NDWI Pixel Value', fontsize=10)
#ax.set_ylabel("Pixel Count", fontsize= 10)
ax.set_ylabel("Pixel Class PDF", fontsize=10)
ax.axes.yaxis.set_ticks([])
# Plot threshold value(s)
ax.axvline(x=t_otsu[0], color='k', linestyle='--', label='Class Threshold')
ax.axvline(x=t_otsu[1],
color='k',
linestyle='--',
label='Shoreline Threshold')
# Add legend
ax.legend(bbox_to_anchor=(1, 1),
loc='lower right',
framealpha=1,
fontsize=8) #, fontsize = 'xx-small')
# Plot histogram
ax.hist(vec, 150, color='blue', alpha=0.8, density=True)
plt.show()
return t_otsu
def get_model_freqs(probas, n_classes=3):
freqs = []
pbar = tqdm.tqdm(total=len(probas))
for prob in probas:
thr = threshold_multiotsu(prob, classes=n_classes)[0]
freqs.append((prob >= thr).sum() / prob.size)
pbar.set_description('[obsrv]')
pbar.update(1)
pbar.close()
return freqs
def pick_Threshold(listClasses):
from skimage.filters import threshold_multiotsu
listImage = []
multi_threshold = []
[listImage.extend(classList) for classList in listClasses]
for image_path in listImage:
img = process_img(image_path)
image_gray = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
image_dilation = IncreaseDescreaseMask(image_gray, 3)
image_erosion = IncreaseDescreaseMask(image_gray, -3)
image_re_dilation = IncreaseDescreaseMask(image_erosion, 6)
image_compare = image_re_dilation - image_dilation
multi_threshold.append(threshold_multiotsu(image_compare))
return np.mean(np.array(multi_threshold), axis=0).tolist()
def GetFeature_Differential_GrayInfo_Mean(image_color, multi_thresholds):
from skimage.filters import threshold_multiotsu
image_gray = cv2.cvtColor(image_color, cv2.COLOR_RGB2GRAY)
image_dilation = IncreaseDescreaseMask(image_gray, 6)
image_erosion = IncreaseDescreaseMask(image_gray, -3)
image_re_dilation = IncreaseDescreaseMask(image_erosion, 9)
# image_compare_1 = image_dilation - image_re_dilation
image_compare = image_re_dilation - image_dilation
threshold_compare = threshold_multiotsu(image_compare)
image_differential = (image_compare > multi_thresholds[0]) * (
image_compare < multi_thresholds[1])
return [np.mean(image_differential), np.mean(threshold_compare)]
def thresholded(input_image: np.ndarray,
method: str,
binarize: bool = False) -> np.ndarray:
# https://scikit-image.org/docs/dev/api/skimage.filters.html#skimage.filters.threshold_isodata
foreground_image_mask = input_image.copy().astype(np.float32)
if method == 'otsu':
input_image_threshold = skimagefilters.threshold_otsu(
foreground_image_mask)
elif method == 'multi':
input_image_threshold = skimagefilters.threshold_multiotsu(
foreground_image_mask, classes=4)
elif method == 'adaptive':
input_image_threshold = skimagefilters.threshold_local(
foreground_image_mask,
block_size=3,
method='mean' # 'gaussian', 'median'
)
elif method == 'li':
input_image_threshold = skimagefilters.threshold_li(
foreground_image_mask)
elif method == 'triangle':
input_image_threshold = skimagefilters.threshold_triangle(
foreground_image_mask)
elif method == 'mean':
input_image_threshold = skimagefilters.threshold_mean(
foreground_image_mask)
else:
raise RuntimeError(f"threshold method {method} is not supported.")
if method == 'multi':
input_image_threshold = input_image_threshold.tolist()
max_val = np.max(input_image)
input_image_threshold = [0] + input_image_threshold + [max_val]
num_segments = len(input_image_threshold)
for segment in range(1, num_segments):
prev_thresh = input_image_threshold[segment - 1]
curr_thresh = input_image_threshold[segment]
foreground_image_mask[(foreground_image_mask >= prev_thresh) & (
foreground_image_mask < curr_thresh)] = round(prev_thresh)
highest_thresh = input_image_threshold[-1]
foreground_image_mask[foreground_image_mask >= highest_thresh] = round(
highest_thresh)
else:
foreground_image_mask[
foreground_image_mask < input_image_threshold] = 0.0
if binarize:
foreground_image_mask[foreground_image_mask > 0.0] = 1.0
# foreground_image_mask = foreground_image_mask.astype(np.uint8)
return foreground_image_mask
def auto_thresh_obs(
adata,
obs_cols=["arcsinh_n_genes_by_counts"],
methods=["multiotsu"],
directions=["above"],
):
"""
automated thresholding on metrics in adata.obs
Parameters:
adata (anndata.AnnData): object containing unfiltered scRNA-seq data
obs_cols (list of str): name of column(s) to threshold from adata.obs
methods (list of str): one of 'otsu', 'multiotsu', 'li', or 'mean'
directions (list of str): 'below' or 'above', indicating which direction to keep
Returns:
thresholds (dict): keys are obs_cols and values are dictionaries with
"thresh" : threshold results & "direction" : direction to keep for training
"""
# convert to lists before looping
if isinstance(obs_cols, str):
obs_cols = [obs_cols]
if isinstance(methods, str):
methods = [methods]
if isinstance(directions, str):
methods = [directions]
# initiate output dictionary
thresholds = dict.fromkeys(obs_cols)
# add thresholds as subkey
for i in range(len(obs_cols)):
thresholds[obs_cols[i]] = {} # initiate empty dict
tmp = np.array(adata.obs[obs_cols[i]]) # grab values to threshold
if methods[i] == "multiotsu":
thresholds[obs_cols[i]]["thresh"] = threshold_multiotsu(tmp)
elif methods[i] == "otsu":
thresholds[obs_cols[i]]["thresh"] = threshold_otsu(tmp)
elif methods[i] == "li":
thresholds[obs_cols[i]]["thresh"] = threshold_li(tmp)
elif methods[i] == "mean":
thresholds[obs_cols[i]]["thresh"] = threshold_mean(tmp)
else:
raise ValueError(
"Please provide a valid threshold method ('otsu', 'multiotsu', 'li', 'mean')."
)
# add direction for thresholding as subkey
thresholds[obs_cols[i]]["direction"] = directions[i]
return thresholds
