def generate_bg(img_name):
# img_name = '../data/data_sep2019/EXP1/09192019 Graphene/6 graphene-1.tiff'
image = Image.open(img_name)
im_rgb = np.array(image).astype('float')
im_gray = np.array(image.convert(
'L', (0.2989, 0.5870, 0.1140, 0))).astype('float')
imH, imW = im_gray.shape
# im_hsv = color.rgb2hsv(im_rgb)
# im_hsv[:,:,2] = im_hsv[:,:,2]/255.0
bg_rgb = []
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
for c in range(3):
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_rgb[:, :, c], [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_rgb.append(pred_map)
bg_rgb = np.stack(bg_rgb, axis=2).astype(np.uint8)
bg_hsv = color.rgb2hsv(bg_rgb)
# bg_hsv[:,:,2] = bg_hsv[:,:,2]/255.0
# bg_rgb: [0, 255]. bg_hs [0, 1.0], v [0, 255]
return bg_rgb, bg_hsv
def perform_robustfit_multichannel(im_hsv, im_gray, im_thre=10, size_thre=10):
# im_hsv = im_hsv.astype('float')
# im_gray = im_gray.astype('float')
im_ghs = np.concatenate([np.expand_dims(im_gray, 2), im_hsv[:, :, :2]],
axis=2)
imH, imW, _ = im_ghs.shape
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
res_map = np.zeros([imH, imW])
for c in range(3):
im_c = im_ghs[:, :, c]
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_c, [-1]))
if c == 0:
w = 1
ref_s = brob_rlm_model.sigma
else:
w = ref_s / brob_rlm_model.sigma
res_map = res_map + w * np.abs(
np.reshape(brob_rlm_model.resid, [imH, imW]))
outlier_map = res_map > im_thre
outlier_map = outlier_map.astype(np.uint8)
# connected component detection
nCC, image_labelmap, _, flake_centroids = cv2.connectedComponentsWithStats(
outlier_map)
# flake_centroid: [m, 2] array, indicates row, column of the centroid
flake_centroids = np.flip(flake_centroids, 1)
flake_centroids = flake_centroids[1:].astype('int')
_, flake_sizes = np.unique(image_labelmap, return_counts=True)
# remove the background size
flake_sizes = flake_sizes[1:]
if size_thre > 0:
# remove small connect component
large_flakes = flake_sizes > size_thre
large_flake_idxs = np.nonzero(large_flakes)[0]
new_image_labels = np.zeros([imH, imW])
cnt = 0
for idx in large_flake_idxs:
cnt += 1
new_image_labels[image_labelmap == idx + 1] = cnt
image_labelmap = new_image_labels
num_flakes = large_flakes.sum()
flake_centroids = flake_centroids[large_flake_idxs]
flake_sizes = flake_sizes[large_flake_idxs]
else:
num_flakes = nCC - 1
return res_map, image_labelmap, flake_centroids, flake_sizes, num_flakes
def perform_robustfit(im_gray, im_thre=3, size_thre=0):
# im_gray = im_gray.astype('float')
imH, imW = im_gray.shape
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
# res_map = np.zeros([imH, imW])
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_gray, [-1]))
print(brob_rlm_model.sigma)
res_map = np.abs(np.reshape(brob_rlm_model.resid, [imH, imW]))
outlier_map = res_map > im_thre * brob_rlm_model.sigma
outlier_map = outlier_map.astype(np.uint8)
# connected component detection
nCC, image_labelmap, _, flake_centroids = cv2.connectedComponentsWithStats(
outlier_map)
# flake_centroid: [m, 2] array, indicates row, column of the centroid
flake_centroids = np.flip(flake_centroids, 1)
flake_centroids = flake_centroids[1:].astype('int')
_, flake_sizes = np.unique(image_labelmap, return_counts=True)
# remove the background size
flake_sizes = flake_sizes[1:]
if size_thre > 0:
# remove small connect component
large_flakes = flake_sizes > size_thre
large_flake_idxs = np.nonzero(large_flakes)[0]
new_image_labels = np.zeros([imH, imW])
cnt = 0
for idx in large_flake_idxs:
cnt += 1
new_image_labels[image_labelmap == idx + 1] = cnt
image_labelmap = new_image_labels
num_flakes = large_flakes.sum()
flake_centroids = flake_centroids[large_flake_idxs + 1]
flake_sizes = flake_sizes[large_flake_idxs + 1]
else:
num_flakes = nCC - 1
return res_map, image_labelmap, flake_centroids, flake_sizes, num_flakes
def process_one_image(img_name, save_name, fig_save_name, bg_name=None):
print('process %s' % (img_name))
image = Image.open(img_name)
im_rgb = np.array(image).astype('float')
im_gray = np.array(image.convert(
'L', (0.2989, 0.5870, 0.1140, 0))).astype('float')
imH, imW = im_gray.shape
# to have same result as matlab
im_hsv = color.rgb2hsv(im_rgb)
im_hsv[:, :, 2] = im_hsv[:, :, 2] / 255.0
if bg_name is not None:
bg_image = Image.open(bg_name)
bg_rgb = np.array(bg_image).astype('float')
bg_gray = np.array(bg_image.convert(
'L', (0.2989, 0.5870, 0.1140, 0))).astype('float')
# to have same result as matlab
bg_hsv = color.rgb2hsv(bg_rgb)
bg_hsv[:, :, 2] = bg_hsv[:, :, 2] / 255.0
else:
# estimate bg image
bg_rgb = []
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
],
axis=1)
for c in range(3):
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_rgb[:, :, c], [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_rgb.append(pred_map)
bg_rgb = np.stack(bg_rgb, axis=2).astype('float')
bg_hsv = color.rgb2hsv(bg_rgb)
bg_hsv[:, :, 2] = bg_hsv[:, :, 2] / 255.0
bg_gray = color.rgb2gray(bg_rgb)
res_map, image_labelmap, flake_centroids, flake_sizes, num_flakes = utils.perform_robustfit_multichannel_v2(
im_hsv, im_gray, hyperparams['im_thre'], hyperparams['size_thre'])
if num_flakes != len(flake_sizes):
print(len(flake_sizes), num_flakes, img_name)
return
# get contrast color features
contrast_gray = im_gray - bg_gray
contrast_hsv = im_hsv - bg_hsv
contrast_rgb = im_rgb - bg_rgb
flakes = []
kernel = np.ones((5, 5), np.uint8)
im_tosave = im_rgb.astype(np.uint8)
# get features for each flake
for i in range(num_flakes):
f_mask_r, f_mask_c = np.nonzero(image_labelmap == i + 1)
f_mask_r_min = min(f_mask_r)
f_mask_r_max = max(f_mask_r)
f_mask_height = f_mask_r_max - f_mask_r_min
f_mask_c_min = min(f_mask_c)
f_mask_c_max = max(f_mask_c)
f_mask_width = f_mask_c_max - f_mask_c_min
flake_exact_bbox = [
f_mask_r_min, f_mask_r_max + 1, f_mask_c_min, f_mask_c_max + 1
]
flake_large_bbox = [
max(0, f_mask_r_min - int(0.1 * f_mask_height)),
min(imH, f_mask_r_max + int(0.1 * f_mask_height)),
max(0, f_mask_c_min - int(0.1 * f_mask_width)),
min(imW, f_mask_c_max + int(0.1 * f_mask_width))
]
bwmap = (image_labelmap == i + 1).astype(np.uint8)
_, flake_contours, _ = cv2.findContours(bwmap, cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_NONE)
im_tosave = cv2.drawContours(im_tosave, flake_contours[0], -1,
(255, 0, 0), 2)
flake_contours = np.squeeze(flake_contours[0], 1)
# row, column
flake_contours = np.flip(flake_contours, 1)
# compute convex hull of the contours
flake_convexhull = cv2.convexHull(flake_contours)
# shape fea
flake_shape_len_area_ratio = flake_contours.shape[0] / (bwmap.sum() +
0.0)
contours_center_dis = cdist(np.expand_dims(flake_centroids[i], 0),
flake_contours)
flake_shape_contour_hist = np.histogram(contours_center_dis,
bins=15)[0]
flake_shape_contour_hist = flake_shape_contour_hist / flake_shape_contour_hist.sum(
)
flake_shape_fracdim = utils.fractal_dimension(bwmap)
inner_bwmap = cv2.erode(bwmap, kernel, iterations=1)
# color fea
flake_color_fea = [im_gray[bwmap>0].mean(),
im_hsv[bwmap>0, 2].mean()] + \
[im_gray[bwmap>0].mean(), im_gray[bwmap>0].std()] + \
list(im_hsv[bwmap>0].mean(0)) + list(im_hsv[bwmap>0].std(0)) + \
list(im_rgb[bwmap>0].mean(0)) + list(im_rgb[bwmap>0].std(0))
# flake_color_entropy = entropy(im_gray[bwmap>0].astype('uint8'), disk(5))
flake_color_entropy = cv2.calcHist(
[im_gray[bwmap > 0].astype('uint8')], [0], None, [256], [0, 256])
flake_color_entropy = entropy(flake_color_entropy, base=2)
flake_inner_color_fea = [0] * 16
flake_inner_color_entropy = 0
flake_inner_contrast_color_fea = [0] * 16
if inner_bwmap.sum() > 0:
flake_inner_color_fea = [im_gray[inner_bwmap>0].mean(),
im_hsv[inner_bwmap>0, 2].mean()] + \
[im_gray[inner_bwmap>0].mean(), im_gray[inner_bwmap>0].std()] + \
list(im_hsv[inner_bwmap>0].mean(0)) + list(im_hsv[inner_bwmap>0].std(0)) + \
list(im_rgb[inner_bwmap>0].mean(0)) + list(im_rgb[inner_bwmap>0].std(0))
# flake_inner_color_entropy = entropy(im_gray[inner_bwmap>0].astype('uint8'), disk(5))
flake_inner_color_entropy = cv2.calcHist(
[im_gray[inner_bwmap > 0].astype('uint8')], [0], None, [256],
[0, 256])
flake_inner_color_entropy = entropy(flake_inner_color_entropy,
base=2)
flake_inner_contrast_color_entropy = cv2.calcHist(
[contrast_gray[inner_bwmap > 0].astype('uint8')], [0], None,
[256], [0, 256])
flake_inner_contrast_color_entropy = entropy(
flake_inner_contrast_color_entropy, base=2)
flake_inner_contrast_color_fea = [contrast_gray[inner_bwmap>0].mean(),
contrast_hsv[inner_bwmap>0, 2].mean()] + \
[contrast_gray[inner_bwmap>0].std()] + \
list(contrast_hsv[inner_bwmap>0].mean(0)) + list(contrast_hsv[inner_bwmap>0].std(0)) + \
list(contrast_rgb[inner_bwmap>0].mean(0)) + list(contrast_rgb[inner_bwmap>0].std(0)) + list(flake_inner_contrast_color_entropy)
# get contrast color features
flake_contrast_color_entropy = cv2.calcHist(
[contrast_gray[bwmap > 0].astype('uint8')], [0], None, [256],
[0, 256])
flake_contrast_color_entropy = entropy(flake_contrast_color_entropy,
base=2)
# gray, h, gray std, hsv mean, hsv std, rgb mean, rgb std, gray entropy
flake_contrast_color_fea = [contrast_gray[bwmap>0].mean(),
contrast_hsv[bwmap>0, 2].mean()] + \
[contrast_gray[bwmap>0].std()] + \
list(contrast_hsv[bwmap>0].mean(0)) + list(contrast_hsv[bwmap>0].std(0)) + \
list(contrast_rgb[bwmap>0].mean(0)) + list(contrast_rgb[bwmap>0].std(0)) + [flake_contrast_color_entropy]
flake_bg_color_fea = [bg_gray[bwmap>0].mean()] + \
[bg_gray[bwmap>0].std()] + \
list(bg_hsv[bwmap>0].mean(0)) + list(bg_hsv[bwmap>0].std(0)) + \
list(bg_rgb[bwmap>0].mean(0)) + list(bg_rgb[bwmap>0].std(0))
flake_i = dict()
flake_i['img_name'] = img_name
flake_i['flake_id'] = i + 1
flake_i['flake_size'] = flake_sizes[i]
flake_i['flake_exact_bbox'] = flake_exact_bbox
flake_i['flake_large_bbox'] = flake_large_bbox
flake_i['flake_contour_loc'] = flake_contours.astype('int16')
flake_i['flake_convexcontour_loc'] = flake_convexhull.astype('int16')
flake_i['flake_center'] = flake_centroids[i]
# flake_i['flake_img'] = im_rgb[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3], :].astype(np.uint8)
flake_i['flake_shape_fea'] = np.array([flake_shape_len_area_ratio] +
list(flake_shape_contour_hist) +
[flake_shape_fracdim])
flake_i['flake_color_fea'] = np.array(flake_color_fea +
[flake_color_entropy] +
flake_inner_color_fea +
[flake_inner_color_entropy])
flake_i['flake_contrast_color_fea'] = np.array(
flake_contrast_color_fea)
flake_i['flake_innercontrast_color_fea'] = np.array(
flake_inner_contrast_color_fea)
flake_i['flake_bg_color_fea'] = np.array(flake_bg_color_fea)
flake_i['flake_shape_fea_names'] = [
'len_area_ratio'
] + ['contour_hist'] * 15 + ['fracdim']
flake_i['flake_color_fea_names'] = [
'gray_avg', 'v_avg', 'gray_avg', 'gray_std', 'h_avg', 's_avg',
'v_avg', 'h_std', 's_std', 'v_std', 'r_avg', 'g_avg', 'b_avg',
'r_std', 'g_std', 'b_std', 'gray_entropy', 'inner_gray_avg',
'inner_v_avg', 'inner_gray_avg', 'inner_gray_std', 'inner_h_avg',
'inner_s_avg', 'inner_v_avg', 'inner_h_std', 'inner_s_std',
'inner_v_std', 'inner_r_avg', 'inner_g_avg', 'inner_b_avg',
'inner_r_std', 'inner_g_std', 'inner_b_std', 'inner_gray_entropy'
]
flake_i['flake_contrast_color_fea_names'] = [
'contrast_gray_avg',
'contrast_v_avg',
'contrast_gray_avg',
'contrast_gray_std',
'contrast_h_avg',
'contrast_s_avg',
'contrast_v_avg',
'contrast_h_std',
'contrast_s_std',
'contrast_v_std',
'contrast_r_avg',
'contrast_g_avg',
'contrast_b_avg',
'contrast_r_std',
'contrast_g_std',
'contrast_b_std',
'contrast_gray_entropy',
]
flake_i['flake_bg_color_fea_names'] = [
'bg_gray_avg', 'bg_gray_std', 'bg_h_avg', 'bg_s_avg', 'bg_v_avg',
'bg_h_std', 'bg_s_std', 'bg_v_std', 'bg_r_avg', 'bg_g_avg',
'bg_b_avg', 'bg_r_std', 'bg_g_std', 'bg_b_std'
]
# subsegment the flake
if flake_i['flake_size'] > 100:
n_clusters = hyperparams['n_clusters']
flake_rgb = im_rgb[bwmap > 0]
flake_gray = im_gray[bwmap > 0]
flake_hsv = im_hsv[bwmap > 0]
flake_contrast_rgb = im_rgb[bwmap > 0] - bg_rgb[bwmap > 0]
flake_contrast_gray = im_gray[bwmap > 0] - bg_gray[bwmap > 0]
flake_contrast_hsv = im_hsv[bwmap > 0] - bg_hsv[bwmap > 0]
pixel_features = np.concatenate(
[flake_rgb, flake_hsv,
np.expand_dims(flake_gray, 1)], 1)
pixel_features = StandardScaler().fit_transform(pixel_features)
cluster_rslt = KMeans(n_clusters=n_clusters,
random_state=0,
n_jobs=-1).fit(pixel_features)
assignment = cluster_rslt.labels_
# # get the overlayed image
# n_pixel = pixel_features.shape[0]
# overlay = np.zeros([n_pixel, 3], dtype=np.uint8)
# overlay[assignment==0] = (255,0,0)
# overlay[assignment==1] = (0,255,0)
# overlay[assignment==2] = (0,0,255)
# ori_bgr = im_bgr_tosave[bwmap>0]
# overlay_bgr = cv2.addWeighted(np.expand_dims(ori_bgr,0), 0.75, np.expand_dims(overlay,0), 0.25, 0)
# im_bgr_tosave[bwmap>0] = overlay_bgr[0,:,:]
all_subsegment_features = []
all_subsegment_keys = []
for ci in range(n_clusters):
subseg_gray = flake_gray[assignment == ci]
subseg_contrast_gray = flake_contrast_gray[assignment == ci]
# print(len(subseg_gray))
subseg_hsv = flake_hsv[assignment == ci]
subseg_rgb = flake_rgb[assignment == ci]
subseg_contrast_hsv = flake_contrast_hsv[assignment == ci]
subseg_contrast_rgb = flake_contrast_rgb[assignment == ci]
sub_flake_color_entropy = cv2.calcHist(
[subseg_gray.astype('uint8')], [0], None, [256], [0, 256])
sub_flake_color_entropy = entropy(sub_flake_color_entropy,
base=2)[0]
sub_flake_contrast_color_entropy = cv2.calcHist(
[subseg_contrast_gray.astype('uint8')], [0], None, [256],
[0, 256])
sub_flake_contrast_color_entropy = entropy(
sub_flake_contrast_color_entropy, base=2)[0]
sub_flake_color_fea = [subseg_gray.mean(),
subseg_hsv[:, 2].mean()] + \
[subseg_hsv.std()] + \
list(subseg_hsv.mean(0)) + list(subseg_hsv.std(0)) + \
list(subseg_rgb.mean(0)) + list(subseg_rgb.std(0)) + [sub_flake_color_entropy] + \
[subseg_contrast_gray.mean(),
subseg_contrast_hsv[:, 2].mean()] + \
[subseg_contrast_gray.std()] + \
list(subseg_contrast_hsv.mean(0)) + list(subseg_contrast_hsv.std(0)) + \
list(subseg_contrast_rgb.mean(0)) + list(subseg_contrast_rgb.std(0)) + [sub_flake_contrast_color_entropy]
all_subsegment_features.append(sub_flake_color_fea)
all_subsegment_keys.append(sub_flake_color_fea[0])
# sort based on gray values
subsegment_features = []
key_ids = np.argsort(all_subsegment_keys)
for key_id in key_ids:
subsegment_features.extend(all_subsegment_features[key_id])
subsegment_features = np.array(subsegment_features)
subsegment_features[np.isnan(
subsegment_features
)] = 0 # some flake can only be clustered into one cluster.
if subsegment_features.shape[0] != 32 * n_clusters:
print('wrong', save_name, i, subsegment_features.shape)
assert subsegment_features.shape[0] == 32 * n_clusters
flake_i['subsegment_features_%d' %
(n_clusters)] = subsegment_features
flake_i['subsegment_assignment_%d' % (n_clusters)] = assignment
flakes.append(flake_i)
# save mat and images
to_save = dict()
to_save['bg_rgb'] = bg_rgb
to_save['res_map'] = res_map
to_save['image_labelmap'] = image_labelmap
to_save['flakes'] = flakes
pickle.dump(to_save, open(save_name + '.p', 'wb'))
cv2.imwrite(fig_save_name + '.png', np.flip(im_tosave, 2))
def load_one_image(args_color, flake_path, fname, data_path, size_thre):
tmp_flake = pickle.load(open(os.path.join(flake_path, fname), 'rb'))
image_labelmap = tmp_flake['image_labelmap']
tmp_flake = tmp_flake['flakes']
flakes = []
feats = []
if len(tmp_flake) > 0:
image = Image.open(os.path.join(data_path, fname[:-2] + 'tiff'))
im_rgb = np.array(image).astype('float')
im_hsv = color.rgb2hsv(im_rgb)
im_hsv[:, :, 2] = im_hsv[:, :, 2] / 255.0
im_gray = color.rgb2gray(im_rgb)
imH, imW, _ = im_rgb.shape
# background fitting
if args_color == 'contrast' or args_color == 'both' or 'bg' in args_color:
bg_rgb = []
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
],
axis=1)
for c in range(3):
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_rgb[:, :, c], [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_rgb.append(pred_map)
bg_rgb = np.stack(bg_rgb, axis=2).astype('float')
bg_hsv = color.rgb2hsv(bg_rgb)
bg_hsv[:, :, 2] = bg_hsv[:, :, 2] / 255.0
bg_gray = color.rgb2gray(bg_rgb)
for i in range(len(tmp_flake)):
if tmp_flake[i]['flake_size'] > size_thre:
# names.append(fname+'-'+str(tmp_flake[i]['flake_id']))
f_mask_r_min, f_mask_r_max, f_mask_c_min, f_mask_c_max = tmp_flake[
i]['flake_exact_bbox']
f_mask_height = f_mask_r_max - f_mask_r_min
f_mask_width = f_mask_c_max - f_mask_c_min
flake_large_bbox = [
max(0, f_mask_r_min - int(0.5 * f_mask_height)),
min(imH, f_mask_r_max + int(0.5 * f_mask_height)),
max(0, f_mask_c_min - int(0.5 * f_mask_width)),
min(imW, f_mask_c_max + int(0.5 * f_mask_width))
]
tmp_flake[i]['flake_large_bbox'] = flake_large_bbox
tmp_flake[i]['flake_img'] = im_rgb[
flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3], :].astype(
np.uint8)
flakes.append(tmp_flake[i])
tmp_fea_ori = tmp_flake[i]['flake_color_fea']
bwmap = (image_labelmap == i + 1).astype(np.uint8)
if 'ori' in args_color:
tmp_color_fea = list(tmp_fea_ori)
elif 'contrast' in args_color or 'both' in args_color:
# color fea
assert bwmap.sum() == tmp_flake[i]['flake_size']
contrast_gray = im_gray - bg_gray
contrast_hsv = im_hsv - bg_hsv
contrast_rgb = im_rgb - bg_rgb
flake_color_entropy = cv2.calcHist(
[contrast_gray[bwmap > 0].astype('uint8')], [0], None,
[256], [0, 256])
flake_color_entropy = entropy(flake_color_entropy, base=2)
# gray, h, gray std, hsv mean, hsv std, rgb mean, rgb std, gray entropy
tmp_fea_contrast = [contrast_gray[bwmap>0].mean(),
contrast_hsv[bwmap>0, 2].mean()] + \
[contrast_gray[bwmap>0].std()] + \
list(contrast_hsv[bwmap>0].mean(0)) + list(contrast_hsv[bwmap>0].std(0)) + \
list(contrast_rgb[bwmap>0].mean(0)) + list(contrast_rgb[bwmap>0].std(0)) + [flake_color_entropy]
if 'contrast' in args_color:
tmp_color_fea = list(tmp_fea_contrast)
elif 'both' in args_color:
tmp_color_fea = list(tmp_fea_ori) + list(
tmp_fea_contrast)
else:
raise NotImplementedError
if 'bg' in args_color:
tmp_bg_fea = [bg_gray[bwmap>0].mean()] + \
[bg_gray[bwmap>0].std()] + \
list(bg_hsv[bwmap>0].mean(0)) + list(bg_hsv[bwmap>0].std(0)) + \
list(bg_rgb[bwmap>0].mean(0)) + list(bg_rgb[bwmap>0].std(0))
tmp_color_fea = list(tmp_color_fea) + list(tmp_bg_fea)
if 'shape' in args_color:
tmp_shape_fea = tmp_flake[i]['flake_shape_fea']
len_area_ratio = tmp_shape_fea[0]
fracdim = tmp_shape_fea[-1]
tmp_color_fea = list(tmp_color_fea) + [
len_area_ratio, fracdim
]
feats.append(tmp_color_fea)
return flakes, feats
def process_one_image_step1(img_name, save_name, fig_save_name):
image = Image.open(img_name)
im_rgb = np.array(image).astype('float')
im_gray = np.array(image.convert(
'L', (0.2989, 0.5870, 0.1140, 0))).astype('float')
imH, imW = im_gray.shape
# im_hsv = np.array(image.convert('HSV')).astype('float')
# to have same result as matlab
im_hsv = color.rgb2hsv(im_rgb)
im_hsv[:, :, 2] = im_hsv[:, :, 2] / 255.0
im_ghs = np.concatenate([np.expand_dims(im_gray, 2), im_hsv[:, :, :2]],
axis=2)
if os.path.exists(save_name + '.p'):
rslt = pickle.load(open(save_name + '.p', 'rb'))
bg_ghs = rslt['bg_ghs']
bg_rgb = rslt['bg_rgb']
# return bg_ghs, bg_rgb
return bg_ghs, bg_rgb, im_ghs, im_rgb
print('process %s' % (img_name))
# res_map, image_labelmap, flake_centroids, flake_sizes, num_flakes = utils.perform_robustfit_multichannel(im_hsv, im_gray, hyperparams['im_thre'], hyperparams['size_thre'])
all_res_map, all_image_labelmap, all_flake_centroids, all_flake_sizes, all_num_flakes, bg_ghs = utils.perform_robustfit_multichannel_v4(
im_hsv, im_gray, hyperparams['ori_im_thre_pairs'],
hyperparams['size_thre'])
# if num_flakes != len(flake_sizes):
# print(len(flake_sizes), num_flakes, img_name)
# return
# get bg
bg_rgb = []
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
for c in range(3):
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_rgb[:, :, c], [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_rgb.append(pred_map)
bg_rgb = np.stack(bg_rgb, axis=2).astype('float')
bg_hsv = color.rgb2hsv(bg_rgb)
bg_hsv[:, :, 2] = bg_hsv[:, :, 2] / 255.0
bg_gray = color.rgb2gray(bg_rgb)
# # get contrast color features
# contrast_gray = im_gray - bg_gray
# contrast_hsv = im_hsv - bg_hsv
# contrast_rgb = im_rgb - bg_rgb
# flakes = []
# kernel = np.ones((5,5),np.uint8)
cv2.imwrite(fig_save_name + '_ori_bg.png',
np.flip(bg_rgb.astype(np.uint8), 2))
all_im_tosave = []
for pi, thre_pair in enumerate(hyperparams['ori_im_thre_pairs']):
im_tosave = im_rgb.astype(np.uint8)
# get features for each flake
for i in range(all_num_flakes[pi]):
bwmap = (all_image_labelmap[pi] == i + 1).astype(np.uint8)
_, flake_contours, _ = cv2.findContours(bwmap, cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_NONE)
im_tosave = cv2.drawContours(im_tosave, flake_contours[0], -1,
(255, 0, 0), 2)
all_im_tosave.append(im_tosave)
cv2.imwrite(
fig_save_name + '_ori_thre-' + str(thre_pair[0]) + '-' +
str(thre_pair[1]) + '.png', np.flip(im_tosave, 2))
# save mat and images
to_save = dict()
to_save['bg_rgb'] = bg_rgb
to_save['bg_ghs'] = bg_ghs
to_save['all_res_map'] = all_res_map
to_save['all_image_labelmap'] = all_image_labelmap
to_save['all_im_tosave'] = all_im_tosave
# to_save['flakes'] = flakes
pickle.dump(to_save, open(save_name + '.p', 'wb'))
return bg_ghs, bg_rgb, im_ghs, im_rgb
def perform_robustfit_multichannel_v4(im_hsv,
im_gray,
thre_pairs,
size_thre=10):
# im_hsv = im_hsv.astype('float')
# im_gray = im_gray.astype('float')
im_ghs = np.concatenate([np.expand_dims(im_gray, 2), im_hsv[:, :, :2]],
axis=2)
imH, imW, _ = im_ghs.shape
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
res_map = np.zeros([imH, imW])
bg_ghs = []
im_thres = []
for c in range(3):
im_c = im_ghs[:, :, c]
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_c, [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_ghs.append(pred_map)
if c == 0:
w = 1
ref_s = brob_rlm_model.sigma
im_thre = brob_rlm_model.sigma
im_thres.append(im_thre)
else:
w = ref_s / brob_rlm_model.sigma
im_thre = w * brob_rlm_model.sigma
im_thres.append(im_thre)
res_map = res_map + w * np.abs(
np.reshape(brob_rlm_model.resid, [imH, imW]))
# print(im_thre, brob_rlm_model.sigma)
bg_ghs = np.stack(bg_ghs, axis=2).astype('float')
all_res_map = []
all_image_labelmap = []
all_flake_centroids = []
all_flake_sizes = []
all_num_flakes = []
for thre_pair in thre_pairs:
im_thre = np.sum(im_thres) * thre_pair[0]
# true_fg_map = res_map>im_thre
bg_map = res_map <= im_thre
# recompute threshold based on background regions
# bg_sigma = np.std(res_map[bg_map])
bg_sigma = get_sigma(res_map[bg_map])
outlier_map = res_map > bg_sigma * thre_pair[1]
outlier_map = outlier_map.astype(np.uint8)
# connected component detection
nCC, image_labelmap, _, flake_centroids = cv2.connectedComponentsWithStats(
outlier_map)
# flake_centroid: [m, 2] array, indicates row, column of the centroid
flake_centroids = np.flip(flake_centroids, 1)
flake_centroids = flake_centroids[1:].astype('int')
_, flake_sizes = np.unique(image_labelmap, return_counts=True)
# remove the background size
flake_sizes = flake_sizes[1:]
if size_thre > 0:
# remove small connect component
large_flakes = flake_sizes > size_thre
large_flake_idxs = np.nonzero(large_flakes)[0]
new_image_labels = np.zeros([imH, imW])
cnt = 0
for idx in large_flake_idxs:
cnt += 1
new_image_labels[image_labelmap == idx + 1] = cnt
image_labelmap = new_image_labels
num_flakes = large_flakes.sum()
flake_centroids = flake_centroids[large_flake_idxs]
flake_sizes = flake_sizes[large_flake_idxs]
else:
num_flakes = nCC - 1
all_res_map.append(res_map)
all_image_labelmap.append(image_labelmap)
all_flake_centroids.append(flake_centroids)
all_flake_sizes.append(flake_sizes)
all_num_flakes.append(num_flakes)
# print(num_flakes)
return all_res_map, all_image_labelmap, all_flake_centroids, all_flake_sizes, all_num_flakes, bg_ghs
def load_one_image_v2(data_path,
result_path,
fname,
exp_name,
subexp_name,
all_labeled_flake_name_ids,
output_img_size=256):
# fname = labeled_flake_name_ids.rsplit('-', 1)[0]
# flake_id = int(labeled_flake_name_ids.rsplit('-', 1)[1])
flake_info = pickle.load(
open(os.path.join(result_path, exp_name, subexp_name, fname), 'rb'))
img_name = fname.split('.')[0] + '.tiff'
image = Image.open(os.path.join(data_path, exp_name, subexp_name,
img_name))
im_rgb = np.array(image).astype('float')
im_hsv = color.rgb2hsv(im_rgb)
im_hsv[:, :, 2] = im_hsv[:, :, 2] / 255.0
im_gray = color.rgb2gray(im_rgb)
imH, imW = im_gray.shape
# get bg image
bg_rgb = []
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
for c in range(3):
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_rgb[:, :, c], [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_rgb.append(pred_map)
bg_rgb = np.stack(bg_rgb, axis=2).astype('float')
bg_hsv = color.rgb2hsv(bg_rgb)
bg_hsv[:, :, 2] = bg_hsv[:, :, 2] / 255.0
bg_gray = color.rgb2gray(bg_rgb)
# build a list of flakes
image_labelmap = flake_info['image_labelmap']
flakes = flake_info['flakes']
# print(labeled_flake_name_ids, flake_id, len(flakes))
flake = flakes[flake_id]
flake_centroids = flake['flake_center'].astype('int')
flake_large_bbox = [
max(0, flake_centroids[0] - output_img_size // 2),
min(imH, flake_centroids[0] + output_img_size // 2),
max(0, flake_centroids[1] - output_img_size // 2),
min(imW, flake_centroids[1] + output_img_size // 2)
]
f_img = np.zeros([output_img_size, output_img_size, 3], dtype=np.uint8)
r_min = output_img_size // 2 - (flake_centroids[0] - flake_large_bbox[0])
r_max = r_min + (flake_large_bbox[1] - flake_large_bbox[0])
c_min = output_img_size // 2 - (flake_centroids[1] - flake_large_bbox[2])
c_max = c_min + (flake_large_bbox[3] - flake_large_bbox[2])
# print(r_min, r_max, c_min, c_max)
f_img[r_min:r_max,
c_min:c_max, :] = im_rgb[flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3], :]
f_img = f_img.astype(np.uint8)
# get contour image
im_tosave_withcontour = im_rgb.astype(np.uint8)
contour_color = (255, 255, 255)
contours = flakes[flake_id]['flake_contour_loc']
contours = np.expand_dims(np.flip(contours), 1).astype(np.int32)
im_tosave_withcontour = cv2.drawContours(im_tosave_withcontour, contours,
-1, contour_color, 2)
f_img_withcontour = np.zeros([output_img_size, output_img_size, 3],
dtype=np.uint8)
f_img_withcontour[r_min:r_max, c_min:c_max, :] = im_tosave_withcontour[
flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3], :]
# stick withcontour and without contour together
black_strip = np.zeros(
[output_img_size, int(output_img_size * 0.03), 3], dtype=np.int)
f_img_withcontour = np.concatenate([f_img_withcontour, black_strip, f_img],
1)
# get bg image
f_bg_img = np.zeros([output_img_size, output_img_size, 3], dtype=np.uint8)
f_bg_img[r_min:r_max, c_min:c_max, :] = bg_rgb[
flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3], :]
f_bg_img = f_bg_img.astype(np.uint8)
# get mask
mask = (image_labelmap == flake['flake_id']).astype(np.uint8)
mask[mask == 1] = 255
f_mask = np.zeros([output_img_size, output_img_size], dtype=np.uint8)
f_mask[r_min:r_max,
c_min:c_max] = mask[flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3]]
f_contrast = np.zeros([output_img_size, output_img_size, 3],
dtype=np.uint8)
f_contrast[r_min:r_max, c_min:c_max, 0] = np.abs(im_gray[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3]] - \
bg_gray[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3]])
f_contrast[r_min:r_max, c_min:c_max, 1] = np.abs(im_hsv[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3], 0] - \
bg_hsv[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3], 0])
f_contrast = f_contrast.astype(np.uint8)
flake['flake_img'] = f_img
flake['flake_mask'] = f_mask
flake['flake_contrast'] = f_contrast
flake['flake_img_withcontour'] = f_img_withcontour
flake['bg_img'] = f_bg_img
return flake
def process_one_img(ins_name,
img_dir,
rslt_dir,
ae_img_path,
ae_mask_path,
ae_contrast_path,
ae_bg_path,
output_img_size=256):
ins_name = ins_name.split('.')[0]
# load the detected flake and get features for the flake
if not os.path.exists(os.path.join(rslt_dir, ins_name + '..p')):
return
flake_info = pickle.load(
open(os.path.join(rslt_dir, ins_name + '..p'), 'rb'))
image = Image.open(os.path.join(img_dir, ins_name + '.tiff'))
# im_gray = np.array(image.convert('L', (0.2989, 0.5870, 0.1140, 0))).astype('float')
# imH, imW = im_gray.shape
# im_hsv = np.array(image.convert('HSV')).astype('float')
# im_rgb = np.array(image).astype(np.uint8)
im_rgb = np.array(image).astype('float')
im_hsv = color.rgb2hsv(im_rgb)
im_hsv[:, :, 2] = im_hsv[:, :, 2] / 255.0
im_gray = color.rgb2gray(im_rgb)
imH, imW = im_gray.shape
# build a list of flakes
num_flakes = len(flake_info['flakes'])
image_labelmap = flake_info['image_labelmap']
assert num_flakes == image_labelmap.max()
flakes = flake_info['flakes']
large_flake_idxs = []
cnt = 0
# get bg image
bg_rgb = []
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
for c in range(3):
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_rgb[:, :, c], [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_rgb.append(pred_map)
bg_rgb = np.stack(bg_rgb, axis=2).astype('float')
bg_hsv = color.rgb2hsv(bg_rgb)
bg_hsv[:, :, 2] = bg_hsv[:, :, 2] / 255.0
bg_gray = color.rgb2gray(bg_rgb)
for i in range(num_flakes):
flake_size = flakes[i]['flake_size']
flake_centroids = flakes[i]['flake_center'].astype('int')
if flake_size > hyperparams['size_thre']:
# if flake_size > hyperparams['size_thre'] and flake_centroids[0] - output_img_size/2 >=0 and flake_centroids[0] + output_img_size/2 < imH and flake_centroids[1] - output_img_size/2 >=0 and flake_centroids[1] + output_img_size/2 < imW:
large_flake_idxs.append(i)
flake_large_bbox = [
max(0, flake_centroids[0] - output_img_size // 2),
min(imH, flake_centroids[0] + output_img_size // 2),
max(0, flake_centroids[1] - output_img_size // 2),
min(imW, flake_centroids[1] + output_img_size // 2)
]
f_img = np.zeros([output_img_size, output_img_size, 3],
dtype=np.uint8)
r_min = output_img_size // 2 - (flake_centroids[0] -
flake_large_bbox[0])
r_max = r_min + (flake_large_bbox[1] - flake_large_bbox[0])
c_min = output_img_size // 2 - (flake_centroids[1] -
flake_large_bbox[2])
c_max = c_min + (flake_large_bbox[3] - flake_large_bbox[2])
# print(r_min, r_max, c_min, c_max)
f_img[r_min:r_max, c_min:c_max, :] = im_rgb[
flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3], :]
f_img = f_img.astype(np.uint8)
f_bg_img = np.zeros([output_img_size, output_img_size, 3],
dtype=np.uint8)
f_bg_img[r_min:r_max, c_min:c_max, :] = bg_rgb[
flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3], :]
f_bg_img = f_bg_img.astype(np.uint8)
# get mask
mask = (image_labelmap == i + 1).astype(np.uint8)
mask[mask == 1] = 255
f_mask = np.zeros([output_img_size, output_img_size],
dtype=np.uint8)
f_mask[r_min:r_max,
c_min:c_max] = mask[flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3]]
f_contrast = np.zeros([output_img_size, output_img_size, 3],
dtype=np.uint8)
f_contrast[r_min:r_max, c_min:c_max, 0] = np.abs(im_gray[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3]] - \
bg_gray[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3]] )
f_contrast[r_min:r_max, c_min:c_max, 1] = np.abs(im_hsv[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3], 0] - \
bg_hsv[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3], 0])
f_contrast = f_contrast.astype(np.uint8)
cv2.imwrite(
os.path.join(ae_img_path, '%s-%d.png' % (ins_name, cnt)),
np.flip(f_img, 2))
cv2.imwrite(
os.path.join(ae_mask_path, '%s-%d.png' % (ins_name, cnt)),
f_mask)
cv2.imwrite(
os.path.join(ae_contrast_path, '%s-%d.png' % (ins_name, cnt)),
f_contrast)
cv2.imwrite(
os.path.join(ae_bg_path, '%s-%d.png' % (ins_name, cnt)),
np.flip(f_bg_img, 2))
cnt += 1
def load_one_image(fname, flake_path, data_path, output_img_size=256):
flake_info = pickle.load(open(os.path.join(flake_path, fname), 'rb'))
img_name = fname.split('.')[0] + '.tiff'
image = Image.open(os.path.join(data_path, img_name))
im_rgb = np.array(image).astype('float')
im_hsv = color.rgb2hsv(im_rgb)
im_hsv[:, :, 2] = im_hsv[:, :, 2] / 255.0
im_gray = color.rgb2gray(im_rgb)
imH, imW = im_gray.shape
# get bg image
bg_rgb = []
[C, R] = np.meshgrid(np.arange(0, imW), np.arange(0, imH))
Y = np.reshape(R, [-1]) / (imH - 1) - 0.5
X = np.reshape(C, [-1]) / (imW - 1) - 0.5
A = np.stack([
np.ones([imH * imW]),
X * X,
Y * Y,
X * Y,
X,
Y,
], axis=1)
for c in range(3):
brob_rlm_model = robustfit.RLM()
brob_rlm_model.fit(A, np.reshape(im_rgb[:, :, c], [-1]))
pred_map = np.reshape(brob_rlm_model.predict(A), [imH, imW])
bg_rgb.append(pred_map)
bg_rgb = np.stack(bg_rgb, axis=2).astype('float')
bg_hsv = color.rgb2hsv(bg_rgb)
bg_hsv[:, :, 2] = bg_hsv[:, :, 2] / 255.0
bg_gray = color.rgb2gray(bg_rgb)
# build a list of flakes
num_flakes = len(flake_info['flakes'])
image_labelmap = flake_info['image_labelmap']
flakes = flake_info['flakes']
large_flake_idxs = []
for i in range(num_flakes):
flake_size = flakes[i]['flake_size']
if flake_size > hyperparams['size_thre']:
large_flake_idxs.append(i)
flake_centroids = flakes[i]['flake_center'].astype('int')
flake_large_bbox = [
max(0, flake_centroids[0] - output_img_size // 2),
min(imH, flake_centroids[0] + output_img_size // 2),
max(0, flake_centroids[1] - output_img_size // 2),
min(imW, flake_centroids[1] + output_img_size // 2)
]
f_img = np.zeros([output_img_size, output_img_size, 3],
dtype=np.uint8)
r_min = output_img_size // 2 - (flake_centroids[0] -
flake_large_bbox[0])
r_max = r_min + (flake_large_bbox[1] - flake_large_bbox[0])
c_min = output_img_size // 2 - (flake_centroids[1] -
flake_large_bbox[2])
c_max = c_min + (flake_large_bbox[3] - flake_large_bbox[2])
# print(r_min, r_max, c_min, c_max)
f_img[r_min:r_max, c_min:c_max, :] = im_rgb[
flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3], :]
f_img = f_img.astype(np.uint8)
# get mask
mask = (image_labelmap == flakes[i]['flake_id']).astype(np.uint8)
mask[mask == 1] = 255
f_mask = np.zeros([output_img_size, output_img_size],
dtype=np.uint8)
f_mask[r_min:r_max,
c_min:c_max] = mask[flake_large_bbox[0]:flake_large_bbox[1],
flake_large_bbox[2]:flake_large_bbox[3]]
f_contrast = np.zeros([output_img_size, output_img_size, 3],
dtype=np.uint8)
f_contrast[r_min:r_max, c_min:c_max, 0] = np.abs(im_gray[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3]] - \
bg_gray[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3]])
f_contrast[r_min:r_max, c_min:c_max, 1] = np.abs(im_hsv[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3], 0] - \
bg_hsv[flake_large_bbox[0]: flake_large_bbox[1], flake_large_bbox[2]:flake_large_bbox[3], 0])
f_contrast = f_contrast.astype(np.uint8)
flakes[i]['flake_img'] = f_img
flakes[i]['flake_mask'] = f_mask
flakes[i]['flake_contrast'] = f_contrast
flakes = [flakes[j] for j in large_flake_idxs]
return flakes