def compositeThreshold(gray, mode='com'):
if mode == 'otsu':
otsu = threshold_otsu(gray)
otsu_bin = gray > otsu
otsu_bin = otsu_bin.astype(np.uint8) * 255
return otsu_bin
elif mode == 'yen':
yen = threshold_yen(gray)
yen_bin = gray > yen
yen_bin = yen_bin.astype(np.uint8) * 255
return yen_bin
elif mode == 'li':
li = threshold_li(gray)
li_bin = gray > li
li_bin = li_bin.astype(np.uint8) * 255
return li_bin
elif mode == 'niblack':
niblack = threshold_niblack(gray, window_size=13, k=0.8)
niblack_bin = gray > niblack
niblack_bin = niblack_bin.astype(np.uint8) * 255
return niblack_bin
elif mode == 'sauvola':
sauvola = threshold_sauvola(gray, window_size=13)
sauvola_bin = gray > sauvola
sauvola_bin = sauvola_bin.astype(np.uint8) * 255
return sauvola_bin
elif mode == 'com':
li = threshold_li(gray)
li_bin = gray > li
li_bin = li_bin.astype(np.uint8) * 255
otsu = threshold_otsu(gray)
otsu_bin = gray > otsu
otsu_bin = otsu_bin.astype(np.uint8) * 255
yen = threshold_yen(gray)
yen_bin = gray > yen
yen_bin = yen_bin.astype(np.uint8) * 255
return cv2.min(cv2.min(otsu_bin, li_bin), yen_bin)
elif mode == "niblack-multi":
thr = np.zeros((gray.shape), dtype=np.uint8)
thr[thr >= 0] = 255
for k in np.linspace(-0.8, 0.2, 5): #(-1.8,0.2,5)
thresh_niblack = threshold_niblack(gray, window_size=25, k=k)
binary_niblack = gray > thresh_niblack
binary_niblack = binary_niblack.astype(np.uint8) * 255
showResult("binary_niblack", binary_niblack)
thr = cv2.min(thr, binary_niblack)
return thr
else:
sauvola = threshold_sauvola(gray, window_size=25, k=0.25)
sauvola_bin = gray > sauvola
sauvola_bin = sauvola_bin.astype(np.uint8) * 255
niblack = threshold_niblack(gray, window_size=25, k=0.25)
niblack_bin = gray > niblack
niblack_bin = niblack_bin.astype(np.uint8) * 255
return cv2.max(sauvola, niblack)
def cell_detect(frame):
try:
thresh = threshold_yen(frame)
except:
thresh = threshold_yen(frame)
binary = frame >= thresh
closed = binary_closing(binary)
# dilated = dilation(binary, square(5))
label_img = label(closed)
cellLocs = regionprops(label_img)
cellLocs = [p for p in cellLocs if p.area > 100]
return cellLocs
def hysteresis(image):
high = filters.threshold_yen(image)
low = high * 0.9
hight = (image > high).astype(int)
lowt = (image > low).astype(int)
binary = filters.apply_hysteresis_threshold(image, low, high)
return binary
def threshold(image, algorithm='otsu', nbins=256):
"""Computes thresholding value according to specified algorithm.
Args:
image (array-like): Input image. Is converted to grayscale if RGB.
algorithm (str, {'otsu', 'li', 'yen'}): Thresholding algorithm to
determine threshold value. Defaults to 'otsu'.
nbins (int): The number of bins used to calculate histogram as input to
thresholding algorithms. Defaults to 256 bins.
Returns:
thresh (float): Thresholding value.
"""
_image = _check_image(image)
if algorithm == 'otsu':
thresh = filters.threshold_otsu(_image, nbins=nbins)
elif algorithm == 'li':
thresh = filters.threshold_li(_image)
elif algorithm == 'yen':
thresh = filters.threshold_yen(_image, nbins=nbins)
else:
raise ValueError('Algorithm {} not available'.format(algorithm))
return thresh
def calculate_masked_stats():
plate_no = "59798"
parsed = get_plate_files(plate_no)
for w in ['w2']:
files = filter(lambda f: f.wave == w[1], parsed)
# accum = np.zeros((2160, 2160), dtype=np.uint32)
# files = filter(lambda x: 's1' not in x and 's7' not in x, all_files)
nof = len(files)
for i, frame in enumerate(files[0:5], 1):
LogHelper.logText(frame.fullpath)
img = imread(frame.fullpath)
t = filters.threshold_yen(img)
b1 = img > t
b2 = binary_erosion(b1, square(2))
b3 = binary_dilation(b2, square(10))
b4 = binary_closing(b3, square(3))
imm = np.ma.masked_where(b4, img)
mn, mx = np.percentile(imm, (1, 99))
LogHelper.logText(
'%3d of %d, %4d-%4d-%4d-%5d, %.0f-%.0f'
% (i, nof, imm.min(), mn, mx, imm.max(), imm.mean(), imm.std())
)
im2 = imm.filled(int(imm.mean()))
out_name = "{0}\\{5}-{1}{2}-{3}-{4}.tif".format(ROOT_DIR, frame.row, frame.column, frame.site, LogHelper.init_ts, frame.experiment)
imsave(out_name, im2)
def get_img_thr(img, ratio=10):
thr = threshold_yen(img)
background = img[img<thr]
if thr < ratio*np.mean(background):
print("thr:{0:.5f}, ratio*mean:{1:.5f}".format(thr,ratio*img.mean()))
return 0
return thr
def autothreshold(data, threshold_type='otsu', z=2.3264, set_max_ceiling=True):
if threshold_type.endswith('_p'):
data = data[data > 0]
else:
data = data[data != 0]
if (threshold_type == 'otsu') or (threshold_type == 'otsu_p'):
lthres = filters.threshold_otsu(data)
uthres = data[data > lthres].mean() + (z * data[data > lthres].std())
# Otsu N (1979) A threshold selection method from gray-level histograms. IEEE Trans. Sys., Man., Cyber. 9: 62-66.
elif (threshold_type == 'li') or (threshold_type == 'li_p'):
lthres = filters.threshold_li(data)
uthres = data[data > lthres].mean() + (z * data[data > lthres].std())
# Li C.H. and Lee C.K. (1993) Minimum Cross Entropy Thresholding Pattern Recognition, 26(4): 617-625
elif (threshold_type == 'yen') or (threshold_type == 'yen_p'):
lthres = filters.threshold_yen(data)
uthres = data[data > lthres].mean() + (z * data[data > lthres].std())
# Yen J.C., Chang F.J., and Chang S. (1995) A New Criterion for Automatic Multilevel Thresholding IEEE Trans. on Image Processing, 4(3): 370-378.
elif threshold_type == 'zscore_p':
lthres = data.mean() - (z * data.std())
uthres = data.mean() + (z * data.std())
if lthres < 0:
lthres = 0.001
else:
lthres = data.mean() - (z * data.std())
uthres = data.mean() + (z * data.std())
if set_max_ceiling: # for the rare case when uthres is larger than the max value
if uthres > data.max():
uthres = data.max()
return lthres, uthres
def psIImask(img, mode='thresh'):
'''
Input:
img = greyscale image
mode = type of thresholding to perform. Currently only 'thresh' is available
'''
# pcv.plot_image(img)
if mode is 'thresh':
# this entropy based technique seems to work well when algae is present
algaethresh = filters.threshold_yen(image=img)
threshy = pcv.threshold.binary(img, algaethresh, 255, 'light')
# mask = pcv.dilate(threshy, 2, 1)
mask = pcv.fill(threshy, 150)
mask = pcv.erode(mask, 2, 1)
mask = pcv.fill(mask, 45)
# mask = pcv.dilate(mask, 2,1)
final_mask = mask # pcv.fill(mask, 270)
else:
pcv.fatal_error(
'mode must be "thresh" (default) or an object of class pd.DataFrame'
)
return final_mask
def show_thresholds():
images = f['images']
filenames = f['filenames']
for i in range(21, 40):
image = images[i]
thresholds = {
"thresh_yen": skfilt.threshold_yen(image),
"thresh_otsu": skfilt.threshold_otsu(image),
"thresh_li": skfilt.threshold_li(image),
"thresh_iso": skfilt.threshold_isodata(image)
}
name = filenames[i]
fig = plt.figure(i)
arr = np.asarray(image)
ax = fig.add_subplot(3, 2, 1)
ax.imshow(arr, cmap='gray')
ax.set_title(name)
for i_plt, thresh_type in enumerate(thresholds.keys()):
thresh_val = thresholds[thresh_type]
ax1 = fig.add_subplot(3, 2, i_plt + 2)
ax1.imshow(image > thresh_val,
interpolation='nearest',
cmap='gray')
ax1.set_title(thresh_type +
": {}".format(np.round(thresholds[thresh_type])))
plt.show()
def threshold_yen_filter(
folder
): # iterate through folders, assembling feature, label, and classname data objects
class_id = 0
features = []
labels = np.array([])
classnames = []
for root, dirs, filenames in os.walk(folder):
for d in sorted(dirs):
#print("Reading data from", d)
classnames.append(
d) # use the folder name as the class name for this label
files = os.listdir(os.path.join(root, d))
for f in files:
imgFile = os.path.join(root, d, f) # Load the image file
img = plt.imread(imgFile)
img = cv2.resize(
img,
(128,
128)) # Resizing all the images to insure proper reading
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
threshold_yen_filt = threshold_yen(img)
features.append(threshold_yen_filt.ravel())
labels = np.append(
labels, class_id) # Add it to the numpy array of labels
class_id += 1
features = np.array(
features) # Convert the list of features into a numpy array
return features, labels, classnames
def binarize_imageset(image_set):
imgbin_otsu, imgbin_yen, imgbin_li, imgbin_iso, imgbin_tri, imgbin_mlss = [
[] for _ in range(6)
]
for idx, img in enumerate(image_set):
# Filtering
#img = ndimage.median_filter(img, size=(7, 7))
img = denoise_tv_chambolle(img, weight=0.05)
#img = rescale_intensity(img, in_range=(0, 0.5))
# Otsu
imgbin_otsu.append(binarize_imageset_aux(img < threshold_otsu(img)))
# Yen
imgbin_yen.append(binarize_imageset_aux(img < threshold_yen(img)))
# Li
imgbin_li.append(binarize_imageset_aux(img < threshold_li(img)))
# ISODATA
imgbin_iso.append(binarize_imageset_aux(img < threshold_isodata(img)))
# MLSS
aux = pd.read_csv('auto_count/mlss/imgbin_mlss' + str(idx + 1) +
'.csv')
imgbin_mlss.append(binarize_imageset_aux(np.asarray(aux,
dtype='bool')))
return imgbin_otsu, imgbin_yen, imgbin_li, imgbin_iso, imgbin_mlss
def apply(self, matrix):
binary = []
if self.func == 'global':
value = 0
if self.method == 'otsu':
value = threshold_otsu(matrix)
if self.method == 'isodata':
value = threshold_isodata(matrix)
if self.method == 'yen':
value = threshold_yen(matrix)
if self.method == 'median':
value = numpy.median(matrix)
if self.method == 'kmeans':
aa = numpy.array(matrix).reshape(-1)
aa.shape = (aa.shape[0], 1)
cc = k_means(aa, 5)
ccc = cc[0].reshape(-1)
ccc.sort()
value = ccc[len(ccc) - 2]
binary = matrix > value
if self.func == 'adaptive':
binary = threshold_adaptive(matrix, 127, self.method)
return binary.astype('float')
def get_background_and_foreground(channel):
# Binarizar imagen
tresh = threshold_yen(channel)
mask = channel > tresh
binarized_channel = channel.copy().astype('uint8')
binarized_channel[mask] = 255
binarized_channel[~mask] = 0
# Eliminar ruido
kernel = np.ones((3, 3), np.uint8)
opening = cv2.morphologyEx(
binarized_channel, cv2.MORPH_OPEN, kernel, iterations=3)
# Área que con seguridad no es una célula
sure_bg = cv2.dilate(opening, kernel, iterations=3)
# Area que con seguridad está dentro de la célula
# almost_sure_fg = cv2.erode(opening, kernel, iterations=1)
dist_transform = cv2.distanceTransform(
opening, cv2.DIST_L2, cv2.DIST_MASK_PRECISE)
_, sure_fg = cv2.threshold(
dist_transform, 0.1 * dist_transform.max(),
255, cv2.THRESH_BINARY)
# Área en la cual no tenemos certeza
sure_fg = np.uint8(sure_fg)
unknown = cv2.subtract(sure_bg, sure_fg)
return sure_bg, sure_fg, unknown
def to_binary_image(image):
"""
convert image to binary image using custom threshold algorithm
"""
threshold_value = threshold_yen(image)
binary_car_image = image < threshold_value
return binary_car_image
def gray_to_binary_with_thresh_method(image, is_gray, thresh_method):
### Set image to graycale if needed
if is_gray == 0:
### Convert to grayscale
grayscale = rgb2gray(image)
elif is_gray == 1:
### Does nothing to the image, already grayscale
grayscale = image
### Determine threshold method to use according to parameter thresh_method
if thresh_method == 'yen':
### Calculate treshold according to yen method
thresh = threshold_yen(grayscale)
elif thresh_method == 'isodata':
### Calculate treshold according to isodata method
thresh = threshold_isodata(grayscale)
else:
print('Invalid threshold method! Please choose isodata or yen. ')
### Generate binary image
binary = grayscale > thresh
### Show thresholded image
plt.imshow(binary, cmap='gray')
plt.show()
cv2.waitKey(0)
cv2.destroyAllWindows()
### Return binary image
return binary
def psIImask(img, mode='thresh'):
# pcv.plot_image(img)
if mode is 'thresh':
# this entropy based technique seems to work well when algae is present
algaethresh = filters.threshold_yen(image=img)
threshy = pcv.threshold.binary(img, algaethresh, 255, 'light')
# mask = pcv.dilate(threshy, 2, 1)
mask = pcv.fill(threshy, 250)
mask = pcv.erode(mask, 2, 1)
mask = pcv.fill(mask, 100)
final_mask = mask # pcv.fill(mask, 270)
elif isinstance(mode, pd.DataFrame):
mode = curvedf
rownum = mode.imageid.values.argmax()
imgdf = mode.iloc[[1, rownum]]
fm = cv2.imread(imgdf.filename[0])
fmp = cv2.imread(imgdf.filename[1])
npq = np.float32(np.divide(fm, fmp, where=fmp != 0) - 1)
npq = np.ma.array(fmp, mask=fmp < 200)
plt.imshow(npq)
# pcv.plot_image(npq)
final_mask = np.zeros_like(img)
else:
pcv.fatal_error(
'mode must be "thresh" (default) or an object of class pd.DataFrame'
)
return final_mask
def plot_bi(filename):
image = DatToMatrix(filename)
# dst =filters.threshold_local(data,11,'median')
thresh = filters.threshold_yen(image)
print "threshold:", thresh
dst = (image <= thresh) * 1.0
plt.figure('thresh', figsize=(11, 11))
plt.subplot(121)
plt.title('original image')
plt.imshow(image, plt.cm.gray)
plt.subplot(122)
plt.title('binary image')
plt.imshow(dst, plt.cm.gray)
dst1 = sm.erosion(image, sm.square(1))
dst2 = sm.erosion(image, sm.square(5))
dst3 = sm.erosion(image, sm.square(6))
dst4 = sm.erosion(image, sm.square(3))
plt.figure('morphology', figsize=(11, 11))
plt.subplot(141)
plt.title('morphological image_filter1*1')
plt.imshow(dst1, plt.cm.gray)
plt.subplot(142)
plt.title('morphological image_filter5*5')
plt.imshow(dst2, plt.cm.gray)
plt.subplot(143)
plt.title('morphological image_filter6*6')
plt.imshow(dst3, plt.cm.gray)
plt.subplot(144)
plt.title('morphological image_filter7*7')
plt.imshow(dst4, plt.cm.gray)
plt.show()
def __call__(self, img):
# img is a numpy rgb image
grey_img = rgb2grey(img)
t1 = filters.threshold_minimum(grey_img)
t2 = filters.threshold_yen(grey_img)
img1 = mark_boundaries(img, (grey_img > t1), color=(1, 0, 0))
img1 = mark_boundaries(img1, (grey_img > t2), color=(1, 0, 0))
img2 = mark_boundaries(img, grey_img < 0)
img = ((img1 + img2) / 2)
#img = mark_boundaries(img, quickshift(img_as_float(img), kernel_size =5, max_dist = 10, ratio = 1.0))
#img = mark_boundaries(img, slic(img_as_float(img), n_segments=10))
#fimg = rgb2grey(img)
#t = filters.threshold_otsu(fimg)
#img = mark_boundaries(img, (fimg > t).astype(np.uint8), color=(1,0,0))
#img = mark_boundaries(img, (fimg - filters.threshold_niblack(fimg)< 0).astype(np.uint8), color=(1,0,0))
#img_gray = rgb2grey(img)
#img_gray = img[:, :, 1]
# morphological opening (size tuned on training data)
#circle7 = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (7, 7))
#img_open = cv2.morphologyEx(img_gray, cv2.MORPH_OPEN, circle7)
# Otsu thresholding
#img_th = cv2.threshold(img_open, 0, 255, cv2.THRESH_OTSU)[1]
# Invert the image in case the objects of interest are in the dark side
#if (np.sum(img_th == 255) > np.sum(img_th == 0)):
# img_th = cv2.bitwise_not(img_th)
# second morphological opening (on binary image this time)
#bin_open = cv2.morphologyEx(img_th, cv2.MORPH_OPEN, circle7)
# connected components
#img = mark_boundaries(img,cv2.connectedComponents(bin_open)[1], color=(1,0,0))
return (img * 255).astype(np.uint8)
def thresholding(image, threshold):
if isinstance(threshold,int) or isinstance(threshold,float):
thresh = threshold
elif isinstance(threshold,str):
# Assume its Ok to use the same threshold for each layer.
parsestr = threshold.split(" ")
parsestr = [i.lower() for i in parsestr]
parsestr = set(parsestr)
if "otsu" in parsestr:
if "global" in parsestr:
ind = np.argmax([np.mean(i) for i in image])
thresh = filters.threshold_otsu(image[ind])
print thresh, ind
elif "local" in parsestr:
radius = int(parsestr[2])
mask = morphology.disk(radius)
thresh = filters.rank.otsu(image,mask)
if "li" in parsestr:
thresh = filters.threshold_li(image)
if "yen" in parsestr:
thresh = filters.threshold_yen(image)
threshinds = image<thresh
binimg = np.ones(image.shape)
binimg[threshinds] = 0
return binimg, thresh
def experiment_yen_threshold(image=None):
images = image_generator()
if image is not None:
img_path = os.path.join(BASE_DIR, "data/imgs/")
fn = os.path.join(img_path, image)
im = load_images([fn])[0].astype("int32")
images = itertools.chain([(fn, im)], images)
for fn, im in images:
imgs = [im]
titles = ["Original"]
print("computing yen threshold")
yen = threshold_yen(im)
channels = threshold_by_channel(im, yen)
titles.append("Yen Thresholded")
imgs.append(channels[0])
for cp in [175, 200, 225, 250]:
titles.append("Cutpoint %d" % cp)
print("cutting")
rtn = np.zeros(im.shape)
rtn[np.average(im, axis=2, weights=[0.7, 0.1, 0.2]) > cp, 0] = 255
for i in range(1, 3):
rtn[:, :, i] = rtn[:, :, 0]
imgs.append(rtn)
print("plotting")
plot_images(imgs, titles=titles, suptitle=fn.split("/")[-1])
def get_vert_lines(self, sz_filt):
img = self.CleanedImage
img -= np.min(img)
img /= np.max(img)
# Smooth image
if sz_filt > 0:
img = filters.median(img, morphology.disk(sz_filt))
# Use vertical Sobel filter (since we know the lines are always the same orientation)
sb = filters.sobel_v(img)
# Normalize data between 0 and 1
sb -= np.min(sb)
sb /= np.max(sb)
# Find Yen threshold
thr = filters.threshold_yen(sb)
thr_img = sb < thr
if np.sum(thr_img) > np.sum(~thr_img):
thr_img = ~thr_img
thr_img = morphology.binary_dilation(thr_img, morphology.square(4))
thr_img = morphology.binary_erosion(thr_img, morphology.square(4))
return thr_img
def count_ships(path, seg, date_mask):
struct = disk(2)
seg = binary_closing(seg, struct).astype(np.bool)
im = imread(path)
im = rgba2rgb(im)
grayscale = rgb2gray(im)
thresh = threshold_yen(grayscale)
yen = grayscale > thresh
eroded = binary_erosion(seg, struct).astype(np.bool)
grayscale = grayscale > 0.6
grayscale[(eroded == 0) | (date_mask == 1) | (yen == 0)] = 0
grayscale[date_mask == 1] = 0
grayscale = binary_fill_holes(grayscale)
grayscale = clear_border(grayscale)
l = label(grayscale)
for region in regionprops(l):
if region.area > 100 or region.extent < 0.2:
grayscale = flood_fill(grayscale, tuple(region.coords[0, :]), 0)
label_image, num = label(grayscale, return_num=True)
return num, grayscale
def skimage_cropping(filepath, target_height, target_width):
# First crop
img = imread(filepath)
image_crop = img[160:160 + 880, 580:580 + 820]
# Masking/closing pixel regions and labeling pixels
thresh = threshold_yen(image_crop)
img_closing = closing(image_crop > thresh, square(3))
img_label = sk_label(img_closing)
# Search for biggest area and extract centroid
max_area = 0
for region in regionprops(img_label):
if region.area > max_area:
max_area = region.area
biggest = region
center = biggest.centroid
# Draw square bounding box around centroid
square_side = 300
step = square_side / 2
min_row, max_row, min_col, max_col = max([0, int(center[0]-step)]),\
int(center[0]+step), \
max([0, int(center[1]-step)]),\
int(center[1]+step)
# Crop and resize image to square bounding box
image_square = image_crop[min_row:max_row, min_col:max_col]
image_resize = resize(image_square, [target_height, target_width],
preserve_range=True).astype(np.uint8)
return image_resize
def clean_region(region_bw, I_sub):
vals = I_sub.ravel()
bw_idx = region_bw.ravel().astype('bool')
vals = vals[bw_idx]
T = filters.threshold_yen(vals)
new_bw = (I_sub < T) * region_bw
# try find contours
return (new_bw)
def attempt2(img):
pimg = img
pimg = exposure.adjust_sigmoid(pimg, gain=100)
thr = filters.thresholding.threshold_otsu(pimg)
pimg = pimg > thr
num_white = np.sum(pimg)
num_black = np.prod(pimg.shape) - num_white
if num_white > num_black:
pimg = 1 - pimg
pimg = morphology.skeletonize(pimg)
lines = transform.probabilistic_hough_line(pimg)
directions = np.array([angle(point1, point2) for point1, point2 in lines])
directions = np.where(directions < 0, directions + 180, directions)
hist = np.histogram(directions, range=[0, 180], bins=180)
sort_indexes = np.argsort(hist[0])
hist = hist[0][sort_indexes], hist[1][sort_indexes]
a1, a2 = hist[1][-2:]
rot_pimg1 = transform.rotate(pimg, a1 - 90, resize=True)
rot_pimg2 = transform.rotate(pimg, a2 - 90, resize=True)
width = 3
kernel1 = np.pad(np.ones([rot_pimg1.shape[0], width]),
1,
mode='constant',
constant_values=-1)
kernel2 = np.pad(np.ones([rot_pimg2.shape[0], width]),
1,
mode='constant',
constant_values=-1)
corr1 = ndimage.correlate(rot_pimg1, kernel1, mode='constant')
corr2 = ndimage.correlate(rot_pimg2, kernel2, mode='constant')
corr_rot1 = cut(transform.rotate(corr1, 90 - a1, resize=True), pimg.shape)
corr_rot2 = cut(transform.rotate(corr2, 90 - a2, resize=True), pimg.shape)
binary1 = np.where(corr_rot1 > filters.threshold_yen(corr1), 1, 0)
binary2 = np.where(corr_rot2 > filters.threshold_yen(corr2), 1, 0)
selem = np.ones((10, 10))
binary_dilated1 = morphology.dilation(binary1, selem=selem)
binary_dilated2 = morphology.dilation(binary2, selem=selem)
mask = np.logical_or(binary_dilated1, binary_dilated2)
return (1 - mask) * pimg
def restaurar(img):
yen_threshold = threshold_yen(img) + 15
bright = rescale_intensity(img, (0, yen_threshold), (0, 255))
# cv.imshow('bright', bright)
bright = filtro_non_local_mean(bright)
bright = filtro_mediana(bright, 3)
return bright
def EnhanceContrast(img):
img = cv.cvtColor(img, cv.COLOR_RGB2GRAY)
yen_threshold = threshold_yen(img)
bright = rescale_intensity(img, (0, yen_threshold), (0, 255))
# increase line width
kernel = np.ones((3, 3), np.uint8)
imgMorph = cv.erode(bright, kernel, iterations=1)
return imgMorph
def make_tr_mask(tr_cropped):
tr_threshold = threshold_yen(tr_cropped)
tr_mask = tr_cropped > tr_threshold
if len(np.unique(tr_mask)) != 1:
tr_clean = remove_small_objects(tr_mask, min_size=5)
else:
tr_clean = np.zeros(tr_mask.shape, dtype=bool)
return tr_clean
def extract_roi(subjects, data_folder, out_folder, th_method='otsu'):
print(f'Building model ...')
stable_model = np.zeros(shape=(256, 256, 256))
conversion_model = np.zeros_like(stable_model)
n_stables = n_converters = 0 # Reset counters
affine = np.eye(4) # Default affine
for subject in tqdm(subjects, ncols=150, desc='Subjects', unit='subj'):
# Load subject volume
mag, angle, affine, label = load_subject_volume(subject_id=subject,
data_folder=data_folder,
space='edge')
if mag is None:
continue # Ignore subject
# Add up to model
if label == 'MCInc':
stable_model += mag
n_stables += 1
elif label == 'MCIc':
conversion_model += mag
n_converters += 1
# Compute average models
stable_model /= n_stables
conversion_model /= n_converters
difference_map = np.abs(stable_model - conversion_model)
# Thresholding
if th_method == 'otsu':
threshold = filters.threshold_otsu(difference_map[np.where(difference_map > 0)])
else:
threshold = filters.threshold_yen(difference_map)
# Raw ROI and eroded
roi_mask = (difference_map >= threshold).astype(np.int8)
roi_mask_closed = ndi.binary_erosion(roi_mask).astype(np.int8)
models_dict = {
'MCInc': stable_model,
'MCIc': conversion_model,
'diff': difference_map,
f'{th_method}_mask': roi_mask,
'eroded_mask': roi_mask_closed
}
# Create output folder
os.makedirs(out_folder, exist_ok=True)
# Create and save models as NIFTI images
print(f'Saving models ...')
for label, vol in models_dict.items():
nii_model = nb.Nifti1Image(vol, affine)
nb.save(nii_model, join(out_folder, f'{label.lower()}_model.nii.gz'))
print(f'\t- Stable subjects: {n_stables}')
print(f'\t- Converter subjects: {n_converters}')
print(f'\t- Threshold: {threshold:.2f} ({th_method})')
print(f'\t- Stats: {describe(stable_model.ravel())}')
return roi_mask, difference_map
def transform(self, images):
binary_images = []
for i in range(len(images)):
images[i] = np.array(images[i]).reshape(self.shape)
thresh_yen = threshold_yen(images[i])
binary_images.append((images[i] > thresh_yen).ravel())
return binary_images
def gt_transform(im):
im = rgb2gray(im)
if (GT_TRANSFORM == 'img_as_bool'):
return img_as_bool(im)
elif (GT_TRANSFORM == 'threshold_yen'):
return im > threshold_yen(im)
else:
raise NotImplementedError(
'`{}` tranform for GT not implemented.'.format(GT_TRANSFORM))
def auto_brightness_and_contrast(image: np.ndarray,
percent_factor=300) -> np.ndarray:
"""
See:
https://stackoverflow.com/questions/56905592/automatic-contrast-and-brightness-adjustment-of-a-color-photo-of-a-sheet-of-pape
"""
yen_threshold = threshold_yen(image) * percent_factor / 100
return rescale_intensity(image, (0, yen_threshold), (0, image.max()))
def run(self, image):
if not self.high:
self.high = filters.threshold_yen(image)
else:
self.high = self.high * image.max()
low = self.high * (1 - self.expansion)
self.mask = filters.apply_hysteresis_threshold(image, low, self.high)
self.image = self.apply_mask(image, self.mask)
return self.image
def experiement_yen_regions_bounding_rectangle(file=None, dilation_iterations=40, num_regions=5, radius=2):
from skimage.transform import warp
from skimage.transform import SimilarityTransform
images = image_generator()
images = add_image_to_image_generator(images, file)
n_points = 8 * radius
for fn, im in images:
image_arrays = []
histograms = []
image_titles = []
hist_titles = []
image_arrays.append(im)
image_titles.append("original image")
yen = threshold_yen(im)
yen_channels = threshold_by_channel(im, yen)
image_titles.append("Yen Thresholded Channel 1")
image_arrays.append(yen_channels[0])
binary_image = yen_channels[0][:, :, 0] > 0
structure = calculate_binary_opening_structure(binary_image)
binary_image = binary_opening(binary_image, structure=structure)
binary_image = binary_dilation(binary_image, iterations=dilation_iterations)
regions, labels = extract_largest_regions(binary_image, num_regions=num_regions)
for label in labels:
print("Cropping region %d" % label)
region = np.zeros(yen_channels[0].shape[:-1])
region[regions == label] = yen_channels[0][regions == label, 0]
# convex hull
verts = convex_hull_mask(region > 0, mask=False)
corners, rot, angle = minimum_bounding_rectangle(verts)
yen_crop = rotate_crop_gray_image_from_mbr(region, corners, rot, angle)
image_titles.append("Yen Region %d Crop" % label)
image_arrays.append(yen_crop)
rgb_crop = rotate_crop_rgb_image_from_mbr(im, corners, rot, angle)
image_titles.append("RGB Crop %d" % label)
image_arrays.append(rgb_crop)
plot_images_and_histograms(
image_arrays=image_arrays, image_titles=image_titles, image_suptitle=fn.split("/")[-1]
)
def experiment_yen_mask_rescale(file=None):
images = image_generator()
if file is not None:
images = add_image_to_image_generator(images, file)
claheizer = cv2.createCLAHE()
for fn, im in images:
image_arrays = []
titles = []
# plot original image
titles.append("Original")
image_arrays.append(im)
# thresholded
yen = threshold_yen(im)
thresholded = threshold_by_channel(im, yen)[0]
titles.append("Yen Thresholded")
image_arrays.append(thresholded)
# masked and equalized
masked = im.copy()
masked[thresholded <= 0] = 0
titles.append("Masked")
image_arrays.append(masked)
# equalize
from skimage.util import img_as_ubyte
equalized = masked.copy()
for chan in range(1, 3):
img = masked[:, :, chan].astype("uint8")
rng = (0, 175) if chan == 1 else (175, 255)
rescaled = exposure.rescale_intensity(img, in_range=rng)
equalized[:, :, chan] = rescaled
break
titles.append("Equalied")
image_arrays.append(equalized)
# plot
subplot_images(image_arrays, titles=titles, show_plot=True, suptitle=fn.split("/")[-1])
def temp_filter_method_adaptive_thresholding(imageFile):
img = data.imread(imageFile, as_grey=True)
global_thresh = threshold_yen(img)
# True False binary matrix represent color value of the img using global thresholding
binary_global = img > global_thresh
block_size = 40
# True False binary matrix represent color value of the img using adaptive thresholding
binary_adaptive = threshold_adaptive(img, block_size, offset=0)
# 0 1 binary matrix
img_bin_global = clear_border(img_as_uint(binary_global))
# 0 1 binary matrix
img_bin_adaptive = clear_border(img_as_uint(binary_adaptive))
bin_pos_mat = ocr.binary_matrix_to_position(binary_adaptive)
np.savetxt("test.txt",bin_pos_mat) # %.5f specifies 5 decimal round
def CANNY(rgbImage):
image = color.rgb2gray(rgbImage)
image = image[100:-100, 100:-100]
image = transform.resize(image, (1000, 1000))
edges_mask = canny(image)
image[edges_mask] = 0.0
val = filters.threshold_yen(image)
mask = image <= val
regions = list(regionprops(label(mask)))
if len(regions) == 0:
return image
biggest_region = max(regions, key=lambda x: x.area)
minr, minc, maxr, maxc = biggest_region.bbox
image = image[minr:maxr, minc:maxc]
image = transform.resize(image, (100, 100))
return image
def experiment_thresholding(votes_min=3):
from skimage.filters import threshold_otsu
from skimage.filters import threshold_li
from skimage.filters import threshold_yen
from skimage.filters import threshold_adaptive
from scipy.ndimage import median_filter
images = image_generator()
for fn, im in images:
print("inspecting image: ", fn)
print("computing otsu threshold")
otsu = threshold_otsu(im)
otsu_ch1 = np.zeros(im.shape)
otsu_ch2 = np.zeros(im.shape)
otsu_ch3 = np.zeros(im.shape)
otsu_ch1[im[:, :, 0] > otsu, 0] = 255
otsu_ch2[im[:, :, 1] > otsu, 1] = 255
otsu_ch3[im[:, :, 2] > otsu, 2] = 255
otsu_ch1 = smallest_partition(otsu_ch1, 0)
otsu_ch2 = smallest_partition(otsu_ch2, 1)
otsu_ch3 = smallest_partition(otsu_ch3, 2)
print("computing yen threshold")
yen = threshold_yen(im)
yen_ch1 = np.zeros(im.shape)
yen_ch2 = np.zeros(im.shape)
yen_ch3 = np.zeros(im.shape)
yen_ch1[im[:, :, 0] > yen, 0] = 255
yen_ch2[im[:, :, 1] > yen, 1] = 255
yen_ch3[im[:, :, 2] > yen, 2] = 255
yen_ch1 = smallest_partition(yen_ch1, 0)
yen_ch2 = smallest_partition(yen_ch2, 1)
yen_ch3 = smallest_partition(yen_ch3, 2)
print("computing li threshold")
li = threshold_li(im)
li_ch1 = np.zeros(im.shape)
li_ch2 = np.zeros(im.shape)
li_ch3 = np.zeros(im.shape)
li_ch1[im[:, :, 0] > li, 0] = 255
li_ch2[im[:, :, 1] > li, 1] = 255
li_ch3[im[:, :, 2] > li, 2] = 255
li_ch1 = smallest_partition(li_ch1, 0)
li_ch2 = smallest_partition(li_ch2, 1)
li_ch3 = smallest_partition(li_ch3, 2)
print("computing average threshold")
av_ch1 = np.zeros(im.shape)
av_ch2 = np.zeros(im.shape)
av_ch3 = np.zeros(im.shape)
votes1 = otsu_ch1 + yen_ch1 + li_ch1
votes1 = otsu_ch1 + yen_ch1 + li_ch1
votes2 = otsu_ch2 + yen_ch2 + li_ch2
votes3 = otsu_ch3 + yen_ch3 + li_ch3
av_ch1[votes1[:, :, 0] >= (255 * votes_min), 0] = 255
av_ch2[votes2[:, :, 1] >= (255 * votes_min), 1] = 255
av_ch3[votes3[:, :, 2] >= (255 * votes_min), 2] = 255
thresholded_images = [
otsu_ch1,
otsu_ch2,
otsu_ch3,
yen_ch1,
yen_ch2,
yen_ch3,
li_ch1,
li_ch2,
li_ch3,
av_ch1,
av_ch2,
av_ch3,
]
print("filtering out specks")
for idx, im in enumerate(thresholded_images):
thresholded_images[idx] = median_filter(im, size=3)
titles = [
"Channel 1 Otsu",
"Channel 2 Otsu",
"Channel 3 Otsu",
"Channel 1 Yen",
"Channel 2 Yen",
"Channel 3 Yen",
"Channel 1 Li",
"Channel 2 Li",
"Channel 3 Li",
"Channel 1 Avg",
"Channel 2 Avg",
"Channel 3 Avg",
]
print("plotting")
plot_images(thresholded_images, titles=titles, suptitle=fn.split("/")[-1])
def get_threshold(self, image):
return Threshold.color_in_range(image, threshold_yen(image))
def create_slicemap_config(self):
filter = self.filter_name
slicemaps_paths = []
for i in range(0, self.slicemaps_number):
slicemaps_paths.append(
os.path.join(
self.relative_path_to_slicemaps_dir,
self.slicemap_name_format.format(
i,
self.row_col[0],
self.row_col[1],
int(self.slicemap_size[0]),
int(self.slicemap_size[1]),
self.filter_name,
),
)
)
rows_cols = self.row_col
slicemap_size = self.slicemap_size
slices_range = self.slices_range
original_slice_size = self.original_slice_size
volume_size = [
self.area_of_slice[1][0] - self.area_of_slice[0][0],
self.area_of_slice[1][1] - self.area_of_slice[0][1],
self.slices_range[1] - self.slices_range[0],
]
area_of_slice = [self.area_of_slice[0], self.area_of_slice[1]]
slice_path_to_middle_slice = self.slices_path_list[int((self.slices_range[0] + self.slices_range[1]) / 2)]
middle_slice = Image.open(slice_path_to_middle_slice)
middle_slice_numpy_array = numpy.array(middle_slice)
threshold_otsu_index = threshold_otsu(middle_slice_numpy_array) / 255.0
threshold_isodata_index = threshold_isodata(middle_slice_numpy_array) / 255.0
threshold_yen_index = threshold_yen(middle_slice_numpy_array) / 255.0
threshold_li_index = threshold_li(middle_slice_numpy_array) / 255.0
print("******************************************************************")
print("Slicemap size: {0},{1} px".format(self.slicemap_size[0], self.slicemap_size[1]))
print("Number of slicemaps: {0}".format(self.slicemaps_number))
print("Rows and cols: {0},{1}".format(rows_cols[0], rows_cols[1]))
print("Number of slices: {0}".format(self.number_of_slices))
print(
"Original slice size: {0},{1} px".format(
int(self.original_slice_size[0]), int(self.original_slice_size[1])
)
)
print(
"Slicemap slice size: {0},{1} px".format(
int(self.slicemap_slice_size[0]), int(self.slicemap_slice_size[1])
)
)
print(
"Proposional slicemap slice size: {0},{1} px".format(
self.proposional_slicemap_slice_size[0], self.proposional_slicemap_slice_size[1]
)
)
print("Volume proportions: {0},{1},{2}".format(volume_size[0], volume_size[1], volume_size[2]))
print("Interpolation filter name: {0}".format(self.filter_name))
print("Number of rows and cols: {0},{1}".format(self.row_col[0], self.row_col[1]))
print(
"Global path to slicemaps: {0}".format(
os.path.join(
self.global_path_to_slicemaps_dir,
self.slicemap_name_format.format(
"n",
self.row_col[0],
self.row_col[1],
int(self.slicemap_size[0]),
int(self.slicemap_size[1]),
self.filter_name,
),
)
)
)
print(
"Relative path to slicemaps: {0}".format(
os.path.join(
self.relative_path_to_slicemaps_dir,
self.slicemap_name_format.format(
"n",
self.row_col[0],
self.row_col[1],
int(self.slicemap_size[0]),
int(self.slicemap_size[1]),
self.filter_name,
),
)
)
)
print("Path to slices: {0}".format(self.path_to_slices))
print("Name of fisrt slice: {0}".format(self.files_list[0]))
print(
"Name of fisrt slicemaps: {0}".format(
self.slicemap_name_format.format(
0,
self.row_col[0],
self.row_col[1],
int(self.slicemap_size[0]),
int(self.slicemap_size[1]),
self.filter_name,
)
)
)
print("Area_of_slice: {0},{1} px".format(self.area_of_slice[0], self.area_of_slice[1]))
print("threshold_otsu_index: {0}".format(threshold_otsu_index))
print("threshold_isodata_index: {0}".format(threshold_isodata_index))
print("threshold_yen_index: {0}".format(threshold_yen_index))
print("threshold_li_index: {0}".format(threshold_li_index))
data = {}
data["filter"] = self.filter_name
data["slicemaps_paths"] = []
for i in range(0, self.slicemaps_number):
data["slicemaps_paths"].append(
os.path.join(
self.relative_path_to_slicemaps_dir,
self.slicemap_name_format.format(
i,
self.row_col[0],
self.row_col[1],
int(self.slicemap_size[0]),
int(self.slicemap_size[1]),
self.filter_name,
),
)
)
data["row_col"] = rows_cols
data["slicemap_size"] = slicemap_size
data["slices_range"] = slices_range
data["original_slice_size"] = original_slice_size
data["slicemap_slice_size"] = self.slicemap_slice_size
data["volume_size"] = volume_size
data["area_of_slice"] = area_of_slice
data["threshold_indexes"] = {
"otsu": threshold_otsu_index,
"isodata": threshold_isodata_index,
"yen": threshold_yen_index,
"li": threshold_li_index,
}
jsonString = json.dumps(data)
print("************ CONFIG BEGIN ************ ")
print(jsonString)
print("************ CONFIG END ************** ")
if not (os.path.exists(self.path_to_configs_dir)):
os.makedirs(self.path_to_configs_dir)
config_file = open(self.path_to_config, "w")
config_file.write(jsonString)
config_file.close()
def experiment_yen_distort_reds(file=None):
images = image_generator()
if file is not None:
images = add_image_to_image_generator(images, file)
for fn, im in images:
image_arrays = []
titles = []
# plot original image
titles.append("Original")
image_arrays.append(im)
yen = threshold_yen(im)
thresholded = threshold_by_channel(im, yen)[0]
titles.append("Yen Thresholded")
image_arrays.append(thresholded)
# equalize
equalized = np.zeros_like(im)
for chan in range(3):
equalized[:, :, chan] = (exposure.equalize_hist(im[:, :, chan]) * 255).astype("uint8")
titles.append("Equalized")
image_arrays.append(equalized)
# experiments point to a reasonable threshold of 10 or 20
thresh = 140 # TUNE: 160
reds_ycbcr = extract_brightest_reds(equalized, thresh=thresh, verbose=False)
titles.append("Reds Thresholded YCBCR %d" % thresh)
image_arrays.append(reds_ycbcr)
filled_ycbcr = reds_ycbcr.copy()
mask = ndimage.binary_fill_holes((reds_ycbcr[:, :, 0] > 0))
# mask = ndimage.binary_fill_holes((np.amax(reds_ycbcr, axis=2) > 0))
filled_ycbcr[mask, :] = np.array([255, 0, 0])
titles.append("Filled YCBCR Reds")
image_arrays.append(filled_ycbcr)
smoothed_ycbcr = reds_ycbcr.copy()
smoothed_ycbcr[:, :, 0] = binary_closing(smoothed_ycbcr[:, :, 0] > 0, iterations=3) * 255
mask = np.amax(smoothed_ycbcr, axis=2) > 0
structure = calculate_binary_opening_structure(mask, weight=1, hollow=False)
mask = binary_opening(mask, structure=structure, iterations=1)
smoothed_ycbcr[mask <= 0, :] = 0
titles.append("Smoothed YCBCR Reds")
image_arrays.append(smoothed_ycbcr)
# plot
subplot_images(image_arrays, titles=titles, show_plot=True, suptitle=fn.split("/")[-1])
continue
# segmented image
segmented = segment_image(smoothed_ycbcr, n_segments=3, compactness=100, sigma=2)
titles.append("Segmented")
image_arrays.append(segmented)
titles.append("Least Gray Bright Region")
image_arrays.append(bright)
d, m, b = extract_colors_grays(segmented, n_grays=6)
grays = select_colors(segmented, [d, m, b])
titles.append("Gray Regions of Varied Intensity")
image_arrays.append(grays)
quantized = quantize_colors(
segmented,
n_colors=3,
n_samples=1000,
max_iter=300,
n_init=10,
n_jobs=1,
random_state=SEED,
verbose=True,
split=False,
)
titles.append("Quantized Image %d Colors" % 3)
image_arrays.append(quantized)
quantized = quantize_colors(
segmented,
n_colors=4,
n_samples=1000,
max_iter=300,
n_init=10,
n_jobs=1,
random_state=SEED,
verbose=True,
split=False,
)
titles.append("Quantized Image %d Colors" % 4)
image_arrays.append(quantized)
quantized = quantize_colors(
segmented,
n_colors=5,
n_samples=1000,
max_iter=300,
n_init=10,
n_jobs=1,
random_state=SEED,
verbose=True,
split=False,
)
titles.append("Quantized Image %d Colors" % 5)
image_arrays.append(quantized)
subplot_images(image_arrays, titles=titles, show_plot=True, suptitle=fn.split("/")[-1])
print(im.shape, im.dtype) binThrAd = filters.threshold_adaptive(im,21, method='median', offset=0, mode='reflect', param=None) thrIso = filters.threshold_isodata(im, nbins=256, return_all=False) binIso = im > thrIso tiIso = "Iso %d" % thrIso print(thrIso) thrLi = filters.threshold_li(im) binLi = im > thrLi tiLi = "Li %d" % thrLi thrOtsu = filters.threshold_otsu(im, nbins=256) binOtsu = im > thrOtsu tiOtsu = "Otsu %d" % thrOtsu thrYen = filters.threshold_yen(im, nbins=256) binYen = im > thrYen tiYen = "Yen %d" % thrYen # cImg = displayImg(binYen, name='coins-binYen') # cImg.show() fPan = displayAll([im, binThrAd, binIso, binLi, binOtsu, binYen], ["Original", "Adaptive", tiIso, tiLi, tiOtsu, tiYen], fSize=12) fPan.show()
#image = data.imread("/Users/exequiel/projects/roots/python/processing/1.15.AVI/selected/frame-54.tiff")
block_size = 35
gray = rgb2gray(image)
global_thresh = threshold_otsu(gray)
print global_thresh
global_thresh = 0.65
for t in np.linspace(global_thresh,1.0,20):
binary_global = gray > t
#binary_global = gray > 0.90
print "threshold_otsu",threshold_otsu(gray)
print "threshold_isodata",threshold_isodata(gray)
print "threshold_li",threshold_li(gray)
print "threshold_yen",threshold_yen(gray)
label_img = label(binary_global, connectivity=binary_global.ndim)
props = regionprops(label_img)
boxes = []
for pp in props:
minr, minc, maxr, maxc = pp.bbox
boxes += [(minc, minr, maxc - minc, maxr - minr)]
valid_boxes = filter_valid_boxes(boxes,6,40,14,24,300,900)
if len(valid_boxes) > 0:
fig, ax = plt.subplots()
def segmentation(image, method='otsu'):
if (method == 'region'):
sobel_image = filters.sobel(image)
makers = sobel_image < sobel_image.max()*0.1
makers = ndi.label(makers)[0]
labels = watershed(sobel_image,makers)
elif (method == 'edge'):
edges = canny(image,3)
fill = ndi.binary_fill_holes(edges)
labels = remove_small_objects(fill,10)
elif (method == 'self_design'):
width = 100;
scale = 0.72;
[m, n] = image.shape
thre = np.zeros((m,n))
for i in range(0,n):
ind_s = max(0,int(np.ceil(i-width/2)))
ind_e = min(n-1,ind_s+width)
current_image = image[0:m-1, ind_s:ind_e]
thre[0:m-1, i] = filters.threshold_otsu(current_image)*0.8
labels = (image - thre) >=0
elif (method == 'thre_cons'):
global_thre = image.max() * 0.3
labels = image > global_thre
elif (method == 'global_otsu'):
global_thre = filters.threshold_otsu(image)
labels = image > global_thre
elif (method == 'local_otsu'):
selem=disk(80)
local_otsu = filters.rank.otsu(image, selem)
labels = image > (np.true_divide(local_otsu,255))
elif (method == 'yen'):
global_thre = filters.threshold_yen(image)
labels = image > (global_thre*2.5)
elif (method == 'li'):
global_thre = filters.threshold_li(image)
labels = image > global_thre
elif (method == 'isodata'):
global_thre = filters.threshold_isodata(image)
labels = image > global_thre
elif (method == 'adaptive'):
block_size = 100
image = np.true_divide(image,image.max()+np.spacing(1)) * 255
labels = filters.threshold_adaptive(image, block_size, offset=10)
elif (method == 'R_Walker'):
data = image + 0.35 * np.random.randn(*image.shape)
markers = np.zeros(data.shape, dtype=np.uint)
markers[data < -0.3] = 1
markers[data > 1.3] = 2
labels = random_walker(data, markers, beta=10, mode='cg_mg')
return labels
def processImage(captchaPath, report=None, backgroundLayerPath=None, canny_sigma=0.1, corner_min_dist=2, debug = False):
"""
Processes the given image and returns a number of feature points.
These feature points are presumably corner points of the tetragon.
"""
image = io.imread(captchaPath, True);
image_without_bg = None
# remove background, if available
if not None == backgroundLayerPath:
bgl = io.imread(backgroundLayerPath, True)
image_without_bg = (image - bgl)
else:
image_without_bg = image
# applying threshold operators
thresh = threshold_otsu(image_without_bg)
thrs_image = image_without_bg > thresh
thresh_li = threshold_li(image_without_bg)
thrs_image_li = image_without_bg > thresh_li
thresh_yen = threshold_yen(image_without_bg)
thrs_image_yen = image_without_bg > thresh_yen
# thrs_image = thrs_image * thrs_image_li * thrs_image_yen
thrs_image = image_without_bg * thrs_image
thrs_image = thrs_image * thrs_image_li
thrs_image = thrs_image * thrs_image_yen
# thrs_image = ndi.gaussian_filter(thrs_image, 0.8)
# take the gray image
gray_result = rgb2gray(thrs_image)
# find edges
# canny_result = feature.canny(gray_result, sigma=0.5, low_threshold=1.8)
canny_result = gray_result
# store image
processedImageName = captchaPath[0:len(captchaPath)-4] + "_processed.png"
io.imsave(processedImageName, canny_result.clip(-1, 1))
if not None == report:
report.setProcessedImage(processedImageName)
coords = feature.corner_peaks(feature.corner_harris(canny_result), min_distance=corner_min_dist)
if debug:
fig, axes = plt.subplots(nrows=6, figsize=(8, 3))
ax0, ax1, ax2, ax3, ax4, ax5 = axes
ax0.imshow(image, cmap=plt.cm.gray)
ax0.set_title('Original image')
ax0.axis('off')
ax1.imshow(image_without_bg, cmap=plt.cm.gray)
ax1.set_title('Image without background')
ax1.axis('off')
ax2.imshow(thrs_image, cmap=plt.cm.gray)
ax2.set_title('Thresholded image')
ax2.axis('off')
ax3.imshow(gray_result, cmap=plt.cm.gray)
ax3.set_title('After RGB -> Gray')
ax3.axis('off')
ax4.imshow(canny_result, cmap=plt.cm.gray)
ax4.set_title('After Canny')
ax4.axis('off')
ax5.imshow(canny_result, cmap=plt.cm.gray)
ax5.plot(coords[:, 1], coords[:, 0], '+r', markersize=15)
ax5.set_title('Detected Features')
ax5.axis('off')
plt.show()
return coords
def init_centroids(first_image_path, master_flat, master_dark, target_centroid,
max_number_stars=10, min_flux=0.2, plots=False):
first_image = np.median([(fits.getdata(path) - master_dark)/master_flat
for path in first_image_path], axis=0)
tophat_kernel = Tophat2DKernel(5)
convolution = convolve_fft(first_image, tophat_kernel, fftn=fft2, ifftn=ifft2)
convolution -= np.median(convolution)
mad = mad_std(convolution)
convolution[convolution < -5*mad] = 0.0
from skimage.filters import threshold_yen
from skimage.measure import label, regionprops
thresh = threshold_yen(convolution)/4 # Use /4 for planet c, /2 for planet b
#thresh = threshold_otsu(convolution)/15
masked = np.ones_like(convolution)
masked[convolution <= thresh] = 0
label_image = label(masked)
plt.figure()
plt.imshow(label_image, origin='lower', cmap=plt.cm.viridis)
plt.show()
# regions = regionprops(label_image, convolution)
regions = regionprops(label_image, first_image)
# reject regions near to edge of detector
buffer_pixels = 50
regions = [region for region in regions
if ((region.weighted_centroid[0] > buffer_pixels and
region.weighted_centroid[0] < label_image.shape[0] - buffer_pixels)
and (region.weighted_centroid[1] > buffer_pixels and
region.weighted_centroid[1] < label_image.shape[1] - buffer_pixels))]
#centroids = [region.weighted_centroid for region in regions]
#intensities = [region.mean_intensity for region in regions]
target_intensity = regions[0].mean_intensity
target_diameter = regions[0].equivalent_diameter
# and region.equivalent_diameter > 0.8 * target_diameter
centroids = [region.weighted_centroid for region in regions
if min_flux * target_intensity < region.mean_intensity]
# intensities = [region.mean_intensity for region in regions
# if min_flux * target_intensity < region.mean_intensity]
# centroids = np.array(centroids)[np.argsort(intensities)[::-1]]
distances = [np.sqrt((target_centroid[0] - d[0])**2 +
(target_centroid[1] - d[1])**2) for d in centroids]
centroids = np.array(centroids)[np.argsort(distances)]
positions = np.vstack([[y for x, y in centroids], [x for x, y in centroids]])
if plots:
apertures = CircularAperture(positions, r=12.)
apertures.plot(color='r', lw=2, alpha=1)
plt.imshow(first_image, vmin=np.percentile(first_image, 0.01),
vmax=np.percentile(first_image, 99.9), cmap=plt.cm.viridis,
origin='lower')
plt.scatter(positions[0, 0], positions[1, 0], s=150, marker='x')
plt.show()
return positions
def experiment_yen_reds_fit_region(file=None):
images = image_generator()
if file is not None:
images = add_image_to_image_generator(images, file)
for fn, im in images:
print(fn)
image_arrays = []
titles = []
# plot original image
titles.append("Original")
image_arrays.append(im)
# threshold
yen = threshold_yen(im)
thresholded = threshold_by_channel(im, yen)[0]
titles.append("Yen Thresholded")
image_arrays.append(thresholded)
# reds
equalized = np.zeros_like(im, dtype="uint8")
for chan in range(3):
equalized[:, :, chan] = (exposure.equalize_hist(im[:, :, chan]) * 255).astype("uint8")
# reds
thresh = 160
reds = extract_brightest_reds(equalized, thresh=thresh, verbose=False)
titles.append("Reds Thresholded YCBCR %d" % thresh)
image_arrays.append(reds)
# encode
encoded = np.zeros_like(im[:, :, 0], dtype="uint8") * -1
encoded[thresholded[:, :, 0] > 0] = 2
encoded[np.amax(reds, axis=2) > 0] = 1
encoded = encoded.astype("uint8")
titles.append("Encoded")
image_arrays.append(encoded)
print("fitting reference frame")
best_loc, best_val = None, 0
for x in range(100, 1000, 100):
print("x = ", x)
for y in range(3 * x // 2, 1500, 100):
print("y = ", y)
for h in range(y // 3 - 1, y, y // 3):
for z in range(x // 3 - 1, x, x // 3):
for i in range(1, 4):
theta = i * np.pi / 3
reference = draw_reference_frame(x, y, z, h, theta)
res = cv2.matchTemplate(encoded, reference, cv2.TM_SQDIFF)
_, max_val, _, max_loc = cv2.minMaxLoc(res)
if max_val > best_val:
best_val = max_val
best_loc = max_loc
print(x, y, z, h, np.degrees(theta))
print(max_val, best_loc)
print("\n")
# plot
subplot_images(
image_arrays,
titles=titles,
# show_plot=True,
save_plot=True,
suptitle="crop-" + fn.split("/")[-1],
)
def experiment_yen_distort_reds_entropy_blues(file=None):
images = image_generator()
if file is not None:
images = add_image_to_image_generator(images, file)
for fn, im in images:
image_arrays = []
titles = []
# plot original image
titles.append("Original")
image_arrays.append(im)
# threshold
yen = threshold_yen(im)
thresholded = threshold_by_channel(im, yen)[0]
titles.append("Yen Thresholded")
image_arrays.append(thresholded)
# distort
equalized = np.zeros_like(im, dtype="uint8")
for chan in range(3):
equalized[:, :, chan] = (exposure.equalize_hist(im[:, :, chan]) * 255).astype("uint8")
# entropy
ent = skimage.filters.rank.entropy(equalized[:, :, 0], skimage.morphology.disk(3))
titles.append("Entropy")
image_arrays.append(ent)
# thresholded
thresh = 1.5
blues = np.zeros_like(im, dtype="uint8")
blues[ent > thresh, :] = 0
blues[ent <= thresh] = 255
titles.append("Entropy Blues Thresholded %d" % thresh)
image_arrays.append(blues)
# reds
thresh = 160
reds = extract_brightest_reds(equalized, thresh=thresh, verbose=False)
titles.append("Reds Thresholded YCBCR %d" % thresh)
image_arrays.append(reds)
# union
union = np.zeros_like(im)
union[thresholded > 0] = 255
union[reds > 0] = 255
union[blues > 0] = 255
titles.append("Union")
image_arrays.append(union)
for name, color_image in zip(["yen", "blues", "reds", "union"], [thresholded, blues, reds, union]):
binary_image = color_image[:, :, 0] > 0
structure = calculate_binary_opening_structure(binary_image)
binary_image = binary_opening(binary_image, structure=structure)
binary_image = binary_dilation(binary_image, iterations=3)
if name == "yen":
regions, labels = extract_largest_regions(binary_image, num_regions=2)
else:
regions, labels = extract_largest_regions(binary_image, num_regions=3)
mask = convex_hull_mask(regions > 0, mask=True)
print(mask.shape)
crop = np.zeros_like(im)
crop[mask > 0, :] = im[mask > 0, :]
titles.append(name.title() + "Region")
image_arrays.append(crop)
# plot
subplot_images(
image_arrays,
titles=titles,
# show_plot=True,
save_plot=True,
suptitle="crop-" + fn.split("/")[-1],
)
def yen_func(img_slice):
return filters.threshold_yen(img_slice)
img_orig = '/home/andrea/Desktop/20160713_NCP_GO_Talos_121.jpg'
img_lowpass = '******'
out_dir = '/home/andrea/Desktop/test'
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
os.chdir(out_dir)
# print('Processing original')
# image_orig = imread(img_orig, as_grey=True, flatten = True)
# thresh_orig = threshold_isodata(image_orig)
# binary_orig = image_orig > thresh_orig
print('Processing lowpass isodata')
image = imread(img_lowpass, as_grey=True, flatten = True)
thresh_isodata = threshold_isodata(image)
thresh_otsu = threshold_otsu(image)
thresh_li = threshold_li(image)
thresh_yen = threshold_yen(image)
thresh_adaptive = threshold_adaptive(image, 3)
binary_isodata = image > thresh_isodata
binary_otsu = image > thresh_otsu
binary_li = image > thresh_li
binary_adaptive = image > thresh_adaptive
binary_yen = image > thresh_yen
# edges = canny(image_orig/255.)
# fill_image = ndi.binary_fill_holes(edges)
imshow(binary_isodata)
imshow(binary_otsu)
imshow(binary_yen)
imshow(binary_li)
imshow(binary_adaptive)
from pylab import imread, imshow, figure, show, subplot from skimage import data, img_as_uint, img_as_float import ocr from pylab import imread, imshow, figure, show, subplot, plot, scatter from scipy.cluster.vq import kmeans, vq from skimage import data, img_as_uint, img_as_float from skimage.external.tifffile import imsave from skimage.filters import threshold_otsu, threshold_adaptive, threshold_yen from skimage.segmentation import clear_border imageFile = '../pics/14.png' image = imread(imageFile) img = data.imread(imageFile, as_grey=True) global_thresh = threshold_yen(img) # True False binary matrix represent color value of the img using global thresholding binary_global = img > global_thresh block_size = 40 # True False binary matrix represent color value of the img using adaptive thresholding binary_adaptive = threshold_adaptive(img, block_size, offset=10) # 0 1 binary matrix img_bin_global = clear_border(img_as_uint(binary_global)) # 0 1 binary matrix img_bin_adaptive = clear_border(img_as_uint(binary_adaptive))
def yen_mask(rgbImage):
gray_image = color.rgb2gray(rgbImage)
val = filters.threshold_yen(gray_image)
return gray_image <= val