def bright_lines(features):
im = features['im_no_fingers']
h, w = im.shape
if 'finger_period_row' in features:
rh = int(round(features['finger_period_row']))
cw = int(round(features['finger_period_col']))
else:
rh = int(round(features['finger_period']))
cw = int(round(features['finger_period']))
f_v = im - np.maximum(np.roll(im, shift=2 * cw, axis=1),
np.roll(im, shift=-2 * cw, axis=1))
pixel_ops.ApplyThresholdLT_F32(f_v, f_v, 0.0, 0.0)
# filter
mask = (f_v > 0.02).astype(np.uint8)
min_size = 0.0005 * h * w
ip.remove_small_ccs(mask, min_size)
f_v[mask == 0] = 0
# features['_f_v'] = f_v.copy()
f_h = im - np.maximum(np.roll(im, shift=2 * rh, axis=0),
np.roll(im, shift=-2 * rh, axis=0))
pixel_ops.ApplyThresholdLT_F32(f_h, f_h, 0.0, 0.0)
# filter
mask = (f_h > 0.02).astype(np.uint8)
min_size = 0.0005 * h * w
ip.remove_small_ccs(mask, min_size)
f_h[mask == 0] = 0
# features['_f_h'] = f_h.copy()
# normalize
f_h /= 0.3
f_v /= 0.3
pixel_ops.ClipImage(f_h, 0.0, 1.0)
pixel_ops.ClipImage(f_v, 0.0, 1.0)
features['ov_lines_horizontal_u8'] = (f_h * 255).astype(np.uint8)
features['ov_lines_vertical_u8'] = (f_v * 255).astype(np.uint8)
features['bright_lines_horizontal'] = f_h.mean() * 100
features['bright_lines_vertical'] = f_v.mean() * 100
if False:
view = ImageViewer(im)
ImageViewer(f_v)
ImageViewer(f_h)
view.show()
sys.exit()
def dark_spots(features):
im = features['im_no_fingers']
h, w = im.shape
im_mini = im[::6, ::6]
im_mini_med = cv2.medianBlur(im_mini, ksize=5)
im_mini_smooth = cv2.GaussianBlur(im_mini_med, ksize=(0, 0), sigmaX=1)
background = cv2.resize(im_mini_smooth, (w, h))
dark_areas = background - im
pixel_ops.ApplyThresholdLT_F32(dark_areas, dark_areas, 0.0, 0.0)
foreground_mask = ((features['bl_cropped_u8'] == 0) |
(features['bl_cropped_u8'] == 4))
structure = ndimage.generate_binary_structure(2, 1)
foreground_mask = ndimage.binary_erosion(foreground_mask,
structure=structure,
iterations=3)
dark_areas[~foreground_mask] = 0
DARK_SPOT_SENSITIVITY = 0.08
dark_spots = (dark_areas > DARK_SPOT_SENSITIVITY).astype(np.uint8)
min_size = int(h * w * 0.0001)
ip.remove_small_ccs(dark_spots, min_size)
dark_spots_outline = ndimage.binary_dilation(
dark_spots, structure=structure, iterations=2) - dark_spots
features['mk_dark_spots_filled_u8'] = dark_spots
features['mk_dark_spots_outline_u8'] = dark_spots_outline
if False:
view = ImageViewer(im)
ImageViewer(background)
ImageViewer(dark_spots)
ImageViewer(ip.overlay_mask(im, dark_spots_outline))
view.show()
def robust_dislocations(smooth, impure, features):
c = parameters.ROBUST_CROP
smooth = np.ascontiguousarray(smooth[c:-c, c:-c])
impure = np.ascontiguousarray(impure[c:-c, c:-c])
struct = ndimage.generate_binary_structure(2, 1)
# robust dislocation mask
dog1 = (cv2.dilate(
smooth,
cv2.getStructuringElement(
cv2.MORPH_ELLIPSE,
(parameters.DOG_STRUCT_SIZE, parameters.DOG_STRUCT_SIZE))) -
smooth)
dog2 = (ip.fast_smooth(smooth, sigma=parameters.DOG_SIGMA2) -
cv2.GaussianBlur(smooth, (0, 0),
parameters.DOG_SIGMA1,
borderType=cv2.BORDER_REPLICATE))
dog = dog1 + dog2
IMP_THRESH = 0.4
pixel_ops.ApplyThresholdLT_F32(impure, dog, IMP_THRESH, 0)
if False:
view = ImageViewer(dog1)
ImageViewer(dog2)
ImageViewer(dog1 + dog2)
ImageViewer(dog)
view.show()
defect_mask = np.zeros_like(dog, np.uint8)
DOG_THRESH = parameters.BLOCK_DISLOCATION_THRESH
pixel_ops.ApplyThresholdGT_F32_U8(dog, defect_mask, DOG_THRESH, 1)
num_pure_pixels = pixel_ops.CountThresholdGT_F32(impure, IMP_THRESH)
defect_robust = (pixel_ops.CountEqual_U8(defect_mask,
1)) / float(num_pure_pixels)
# compute surface area
eroded = defect_mask - cv2.erode(defect_mask, struct.astype(np.uint8))
defect_pixels = float(pixel_ops.CountEqual_U8(defect_mask, 1))
if defect_pixels > 0:
defect_surface = pixel_ops.CountEqual_U8(eroded, 1) / defect_pixels
else:
defect_surface = 0
if False:
print defect_robust, defect_surface
view = ImageViewer(smooth)
ImageViewer(defect_mask)
ImageViewer(eroded)
view.show()
sys.exit()
features['defect_robust_area_fraction'] = defect_robust
features['defect_surface'] = defect_surface
def dark_spots(features):
im = features['im_no_fingers']
# shrink to standard size
h, w = 300, 300
im_small = cv2.resize(im, (h, w))
dark_areas = np.zeros_like(im_small)
pixel_ops.DarkSpots(im_small, dark_areas, 8)
candidates = (dark_areas > parameters.DARK_SPOT_MIN_STRENGTH).astype(np.uint8)
ip.remove_small_ccs(candidates, parameters.DARK_SPOT_MIN_SIZE)
candidates = cv2.resize(candidates, (im.shape[1], im.shape[0]))
candidates[features['mask_busbar_filled']] = 0
dark_spots_outline = ndimage.binary_dilation(candidates, iterations=3).astype(np.uint8) - \
ndimage.binary_dilation(candidates, iterations=1).astype(np.uint8)
features['mk_dark_spots_outline_u8'] = dark_spots_outline
features['mk_dark_spots_filled_u8'] = candidates
features['dark_spots_area_fraction'] = candidates.mean()
dark_areas_no_noise = dark_areas - parameters.DARK_SPOT_MIN_STRENGTH
pixel_ops.ApplyThresholdLT_F32(dark_areas_no_noise, dark_areas_no_noise, 0.0, 0.0)
features['dark_spots_strength'] = dark_areas_no_noise.mean() * 10000
features['dark_spots_count'] = ip.connected_components(candidates)[1]
if False:
print features['dark_spots_area_fraction']
print features['dark_spots_strength']
print features['dark_spots_count']
rgb = ip.overlay_mask(im, dark_spots_outline)
view = ImageViewer(rgb)
ImageViewer(dark_areas)
ImageViewer(dark_areas_no_noise)
ImageViewer(candidates)
view.show()
def efficiency_analysis(features):
im = features['im_no_fingers']
im_peaks = features['im_norm'][features['_peak_row_nums'], :]
bbs = features['_busbar_cols']
# make sure no zero values
im_peaks = im_peaks.copy()
pixel_ops.ApplyThresholdLT_F32(im_peaks, im_peaks, 0.01, 0.01)
im = im.copy()
pixel_ops.ApplyThresholdLT_F32(im, im, 0.01, 0.01)
# IDEA:
# two defect mask:
# 1. existing one (highlights anything dark)
# 2. do a dark line (local mins). mask out & interpolate.
# this one won't pick up grain boundaries
# - slider blends between them
#################
# DEFECT MASK 1 #
#################
# - very sensitive to all dark areas
# need to interpolate values along edges/busbars so defects in these regions can be found
xs = np.arange(im_peaks.shape[0])
cols = [features['cell_edge_left'], features['cell_edge_right']]
cols += list(np.where(features['mask_busbar_edges'][0, :])[0])
for c in cols:
ys = im_peaks[:, c].copy()
ys[ys >
features['_bright_area_thresh']] = features['_bright_area_thresh']
params_op = optimize.fmin_powell(line_error, [0.0, ys.mean()],
disp=0,
args=(xs, ys),
xtol=0.05,
ftol=0.05)
vals = xs * params_op[0] + params_op[1]
im_peaks[:, c] = vals
if False:
print features['_bright_area_thresh']
mask = np.zeros_like(im, np.uint8)
mask[:, c] = 1
ImageViewer(ip.overlay_mask(im, mask))
plt.figure()
plt.plot(ys)
plt.plot(vals)
plt.show()
# max of actual val and: interpolate vertical line at:
# - left & right edge
# - left & right of each BB
# make monotonic (don't care about local mins)
bb_mono = between_bb_mono(im_peaks, bbs)
background1 = bb_mono
background1 = cv2.GaussianBlur(background1,
ksize=(0, 0),
sigmaX=3,
borderType=cv2.BORDER_REPLICATE)
# relative difference
foreground1 = background1 / im_peaks
foreground1 -= 1
pixel_ops.ClipImage(foreground1, 0, 3.0)
foreground1[:, features['mask_busbar_filled'][0, :]] = 0
# expand to full size
full_size = np.zeros(im.shape, np.float32)
pixel_ops.ExpandFingers(full_size, foreground1, features['_peak_row_nums'])
foreground1 = full_size
background_full = np.zeros(im.shape, np.float32)
pixel_ops.ExpandFingers(background_full, background1,
features['_peak_row_nums'])
if False:
view = ImageViewer(im)
ImageViewer(foreground1)
ImageViewer(background1)
view.show()
#################
# DEFECT MASK 2 #
#################
# - less likely to include dark grains
# - mask out local mins and areas of high gradient, and the interpolate background
flatten_cols = np.r_[im.mean(axis=0)]
im_flattened = im - flatten_cols
flatten_rows = np.c_[im_flattened.mean(axis=1)]
im_flattened -= flatten_rows
im_flattened[features['mask_busbar_filled']] = 0
im_smoothed = cv2.GaussianBlur(im_flattened, ksize=(0, 0), sigmaX=2)
# local mins
dark_lines = np.zeros_like(im_flattened, np.uint8)
pixel_ops.LocalMins(im_smoothed, dark_lines)
s = ndimage.generate_binary_structure(2, 1)
dark_lines = ndimage.binary_dilation(dark_lines, structure=s)
# high gradient
edgesH = cv2.Sobel(im_smoothed, cv2.CV_32F, 1, 0)
edgesV = cv2.Sobel(im_smoothed, cv2.CV_32F, 0, 1)
edges = cv2.magnitude(edgesH, edgesV)
# combine
defect_candidates = ((edges > 0.2) | dark_lines)
if False:
view = ImageViewer(im_flattened)
ImageViewer(ip.overlay_mask(im_flattened, dark_lines))
ImageViewer(ip.overlay_mask(im_flattened, edges > 0.2))
ImageViewer(ip.overlay_mask(im_flattened, defect_candidates))
view.show()
sys.exit()
background2 = interpolate_background(im_flattened,
defect_candidates.astype(np.uint8))
background2 += flatten_rows
background2 += flatten_cols
# relative difference
foreground2 = background2 / im
foreground2 -= 1
pixel_ops.ClipImage(foreground2, 0, 3.0)
foreground2[features['mask_busbar_filled']] = 0
if False:
view = ImageViewer(im)
ImageViewer(background2)
ImageViewer(foreground2)
view.show()
sys.exit()
if False:
features['_defect1'] = foreground1
features['_defect2'] = foreground2
# discrimination function
x1, y1 = 0.0, 0.5
x2, y2 = 0.4, 0.0
foreground = (-1 * ((y2 - y1) * foreground2 -
(x2 - x1) * foreground1 + x2 * y1 - y2 * x1) /
np.sqrt((y2 - y1)**2 + (x2 - x1)**2))
foreground += 0.1 + parameters.CELL_DISLOCATION_SENSITIVITY
foreground *= 0.25
pixel_ops.ClipImage(foreground, 0, 1)
features['ov_dislocations_u8'] = (foreground * 255).astype(np.uint8)
if False:
view = ImageViewer(im)
ImageViewer(foreground1)
ImageViewer(foreground2)
ImageViewer(foreground)
#ImageViewer(background_full)
# ImageViewer(foreground > 0.2)
view.show()
sys.exit()
################
# IMPURE AREAS #
################
def FindImpure(imp_profile, imp_profile_r, defects, debug=False):
if False:
ImageViewer(im)
plt.figure()
plt.plot(imp_profile)
plt.plot(defects)
plt.show()
imp_ratio = (imp_profile / imp_profile_r).astype(np.float32)
imp_ratio[imp_ratio > 0.9] = 0.9
imp_ratio /= 0.9
global_min = np.argmin(imp_ratio)
local_mins = np.where((imp_ratio < np.roll(imp_ratio, 1))
& (imp_ratio < np.roll(imp_ratio, -1)))[0]
# make monotonic from global minimum
imp_mono = imp_ratio.copy()
flip = False
if global_min > len(imp_mono) // 2:
flip = True
imp_mono = imp_mono[::-1]
global_min = np.argmin(imp_mono)
rest = np.ascontiguousarray(imp_mono[global_min:])
rest_mono = np.empty_like(rest)
pixel_ops.MakeMonotonic(rest, rest_mono)
imp_mono[global_min:] = rest_mono
# if edge_dist < 0.075:
# imp_mono[:global_min] = imp_ratio[global_min]
if flip:
imp_mono = imp_mono[::-1]
global_min = np.argmin(imp_mono)
# for a real impure area, the global minimum should be close to an edge
edge_dist = min(global_min,
len(imp_ratio) - global_min) / float(len(imp_ratio))
edge_spot = int(0.03 * len(imp_mono))
imp_at_edge = min(imp_mono[edge_spot], imp_mono[-edge_spot])
imp_1d = np.ones_like(imp_mono)
# check the defect content in the "impure" area
if (imp_mono < 1.0).sum() == 0:
defect_strength = 0
else:
# defect_strength = defects[imp_mono < 1.0].mean()
defect_strength = np.median(defects[imp_mono < 1.0])
if (edge_dist < 0.075 and # lowest point close to edge
imp_at_edge < 0.8 and # edge is dark
defect_strength < 0.1 and # not too many defects
# (global_min == local_mins[0] or global_min == local_mins[-1]) and # no local mins closer to edge
(imp_mono - imp_ratio).mean() < 0.035): # no large non-impure dips
imp_1d = imp_mono.copy()
imp_1d -= 0.3
if global_min < len(imp_profile) // 2:
imp_1d[:global_min] = imp_1d[global_min]
else:
imp_1d[global_min:] = imp_1d[global_min]
if debug:
print edge_dist, edge_dist < 0.075
print imp_at_edge, imp_at_edge < 0.8
print defect_strength, defect_strength < 0.1
# print global_min, local_mins[0], (global_min == local_mins[0] or global_min == local_mins[-1])
print(imp_mono -
imp_ratio).mean(), (imp_mono - imp_ratio).mean() < 0.035
ImageViewer(im)
plt.figure()
plt.plot(imp_profile, 'r')
plt.plot(imp_mono, 'g')
plt.plot(imp_ratio, 'b')
# plt.plot((0, len(signal_var)), (0.1, 0.1))
plt.plot(defects, 'c')
plt.plot(imp_1d, 'c')
plt.show()
# find impure edge width
THRESH = 0.5
if imp_1d[0] < THRESH:
edge_width = np.where(imp_1d < THRESH)[0][-1] / float(
len(imp_profile))
left = True
elif imp_1d[-1] < THRESH:
edge_width = (len(imp_profile) -
np.where(imp_1d < THRESH)[0][0]) / float(
len(imp_profile))
left = False
else:
edge_width = 0
left = True
return imp_1d, edge_width, left
if False:
# ignore defect areas
defect_mask = foreground > 0.2
mx = ma.masked_array(im, mask=defect_mask)
if False:
view = ImageViewer(im)
ImageViewer(defect_mask)
view.show()
'''
# left/right edges
cols = np.apply_along_axis(stats.scoreatpercentile, 0, im, per=75)
cols[cols > 1.0] = 1.0
imp_profile = ndimage.gaussian_filter1d(cols, sigma=3, mode="nearest")
imp_profile_r = imp_profile[::-1]
if len(bbs) >= 2:
mid = (bbs[0] + bbs[-1]) // 2
else:
mid = im.shape[1] // 2
imp_profile_r = np.roll(imp_profile_r, mid - (len(imp_profile) // 2))
col_defect = foreground.mean(axis=0)
imp_h, ew_h, e_left = FindImpure(imp_profile, imp_profile_r, col_defect, debug=False)
'''
# top/bottom edges
rows = np.apply_along_axis(stats.scoreatpercentile, 1, im, per=75)
rows[rows > 1.0] = 1.0
imp_profile = ndimage.gaussian_filter1d(rows, sigma=3, mode="nearest")
imp_profile_r = imp_profile[::-1]
row_defect = foreground.mean(axis=1)
imp_v, ew_v, e_top = FindImpure(imp_profile,
imp_profile_r,
row_defect,
debug=False)
features['impure_edge_width'] = ew_v
if e_top:
features['impure_edge_side'] = 0
else:
features['impure_edge_side'] = 2
impure = np.ones_like(im)
impure[:, :] = np.c_[imp_v]
if False:
print features['impure_edge_width'], features['impure_edge_side']
view = ImageViewer(impure)
view.show()
sys.exit()
imp_cutoff = 0.55
pixel_ops.ApplyThresholdGT_F32(impure, impure, imp_cutoff, imp_cutoff)
impure /= imp_cutoff
impure_overlay = np.log10(2 - impure)
if False:
plt.figure()
plt.plot(impure[:, 0], 'r')
plt.plot(np.log(impure[:, 0] + 1), 'g')
plt.plot(np.log10(impure[:, 0] + 1), 'b')
plt.show()
view = ImageViewer(impure)
view.show()
pixel_ops.ClipImage(impure_overlay, 0, 1)
features['ov_impure2_u8'] = (impure_overlay * 255).astype(np.uint8)
###########
# METRICS #
###########
num_pixels = im.shape[0] * im.shape[1]
# impure
impure_thresh = 0.9 # 0.8
dislocation_thresh = 0.1
num_impure_pixels = pixel_ops.CountThresholdLT_F32(impure, impure_thresh)
features['impure_area_fraction'] = (num_impure_pixels / float(num_pixels))
if features['impure_area_fraction'] > 0.001:
pure_mask = (impure > impure_thresh) & (foreground <
dislocation_thresh)
features['impure_strength'] = (im[pure_mask].mean() /
im[impure < impure_thresh].mean()) - 1
else:
features['impure_strength'] = 0
features['impure_area_fraction'] = 0
features['impure_strength2'] = features['impure_strength'] * features[
'impure_area_fraction'] * 100
# dislocations
num_dislocations = pixel_ops.CountThresholdGT_F32(foreground,
dislocation_thresh)
features['dislocation_area_fraction'] = (num_dislocations /
float(num_pixels))
features['_foreground'] = foreground
features['_dislocation_thresh'] = dislocation_thresh
features['_impure'] = impure
features['_impure_thresh'] = impure_thresh
# find the average distance between dislocation pixels
ys, xs = np.where(foreground > dislocation_thresh)
points = np.c_[ys, xs]
num_samples = 1500
if len(ys) > 0:
points = points[::max(1, points.shape[0] // num_samples), :]
pixel_dists = distance.pdist(points)
avg_dist = np.mean(pixel_dists)
avg_dist = (avg_dist - 0.3 * im.shape[0]) / (0.5 * im.shape[0])
else:
avg_dist = 0
features['dislocation_density'] = 1.0 - avg_dist
if len(ys) > 0:
dis_vals = foreground[ys, xs]
dislocation_strength = math.sqrt((dis_vals**2).mean())
features['dislocation_severity_A'] = dislocation_strength
# create a second defect strength.
ratio2 = background_full / im
ratio2 = np.clip(ratio2, 1, 5)
ratio2[:, features['mask_busbar_filled'][0, :]] = 1
features['dislocation_severity_B'] = ratio2[ys, xs].mean()
if False:
view = ImageViewer(background_full)
ImageViewer(im)
ImageViewer(ratio2)
view.show()
else:
features['dislocation_severity_A'] = 0
features['dislocation_severity_B'] = 0
if False:
view = ImageViewer(im)
foreground[foreground < 0] = 0
ImageViewer(foreground)
ImageViewer(background_full)
view.show()
sys.exit()
# dislocation histogram features
foreground_bins = np.zeros((5), np.float32)
pixel_ops.BackgrounHistogram(foreground, foreground_bins)
foreground_bins = (foreground_bins / num_pixels) * 100
features['dislocation_hist_01'] = foreground_bins[0]
features['dislocation_hist_02'] = foreground_bins[1]
features['dislocation_hist_03'] = foreground_bins[2]
features['dislocation_hist_04'] = foreground_bins[3]
features['dislocation_hist_05'] = foreground_bins[4]
features['dislocation_strength'] = features[
'dislocation_area_fraction'] * features['dislocation_severity_A']
if False:
# print features['foreground_hist_01'], features['foreground_hist_02'], features['foreground_hist_03'],
# print features['foreground_hist_04'], features['foreground_hist_05']
view = ImageViewer(im)
ImageViewer(foreground)
ImageViewer(impure)
ImageViewer(create_overlay(features))
view.show()
def plir(im_sp, im_lp, im_pl, features, spline_plir, spline_plc):
t_start = timeit.default_timer()
pixel_ops.ApplyThresholdLT_F32(im_sp, im_sp, 1.0, 1.0)
pixel_ops.ApplyThresholdLT_F32(im_lp, im_lp, 1.0, 1.0)
pixel_ops.ApplyThresholdLT_F32(im_pl, im_pl, 1.0, 1.0)
if im_sp.shape != im_lp.shape:
print im_sp.shape, im_lp.shape
assert False
im_sp = im_sp.astype(np.float64)
im_lp = im_lp.astype(np.float64)
im_pl = im_pl.astype(np.float64)
if False:
view = ImageViewer(im_sp)
ImageViewer(im_lp)
ImageViewer(im_pl)
view.show()
sys.exit()
# vertical registration
c = np.argmax(im_sp.mean(axis=0))
profile_sp = im_sp[:, c - 10:c + 11].mean(axis=1)
profile_lp = im_lp[:, c - 10:c + 11].mean(axis=1)
shift_v = register(profile_sp, profile_lp, debug=False)
if False:
print c, shift_v
view = ImageViewer(im_lp)
ImageViewer(im_sp)
ImageViewer(np.roll(im_sp, shift=shift_v, axis=0))
view.show()
sys.exit()
im_sp = np.roll(im_sp, shift=shift_v, axis=0)
# compute plir (ratio of LP to SP)
plir = im_lp / im_sp
if False:
t = stats.scoreatpercentile(plir, per=90)
print plir.min(), t, plir.max()
plir[plir > t] = t
view = ImageViewer(im_lp)
ImageViewer(im_sp)
ImageViewer(plir)
view.show()
sys.exit()
# Get cropping and rotation parameters (based on short pass)
vals = im_sp[::2, ::2].flat
vals = np.sort(vals)
min_val = vals[int(0.025 * vals.shape[0])]
max_val = vals[int(0.975 * vals.shape[0])]
features['norm_range'] = max_val - min_val
features['norm_lower'] = min_val
im_normed_temp = (im_sp - min_val) / (max_val - min_val)
rotated_temp = block_rotate(im_normed_temp, features)
block_crop(rotated_temp, features)
rotation = features['crop_rotation']
x1, x2, y1, y2 = features['_crop_bounds']
if False:
cropped_temp = rotated_temp[y1:y2, x1:x2]
view = ImageViewer(im_sp)
ImageViewer(rotated_temp)
ImageViewer(cropped_temp)
view.show()
if 'input_param_skip_features' in features and int(
features['input_param_skip_features']) == 1:
return True
# rotate all images
if abs(rotation) > 0.01:
h, w = plir.shape
rot_mat = cv2.getRotationMatrix2D((w // 2, h // 2), rotation, 1.0)
plir_rotated = cv2.warpAffine(plir,
rot_mat, (w, h),
flags=cv2.INTER_LINEAR,
borderMode=cv2.BORDER_REPLICATE)
sp_rotated = cv2.warpAffine(im_sp,
rot_mat, (w, h),
flags=cv2.INTER_LINEAR,
borderMode=cv2.BORDER_REPLICATE)
lp_rotated = cv2.warpAffine(im_lp,
rot_mat, (w, h),
flags=cv2.INTER_LINEAR,
borderMode=cv2.BORDER_REPLICATE)
h, w = im_pl.shape
rot_mat = cv2.getRotationMatrix2D((w // 2, h // 2), rotation, 1.0)
nf_rotated = cv2.warpAffine(im_pl,
rot_mat, (w, h),
flags=cv2.INTER_LINEAR,
borderMode=cv2.BORDER_REPLICATE)
else:
plir_rotated = plir
sp_rotated = im_sp
lp_rotated = im_lp
nf_rotated = im_pl
# find marker location
features['marker_loc'] = find_marker(sp_rotated[y1:y2, x1:x2])
nf_to_sp_ratio = nf_rotated.shape[1] / float(sp_rotated.shape[1])
features['marker_loc'] *= nf_to_sp_ratio
# crop plir image
cropped_plir = plir_rotated[y1:y2, x1:x2]
cropped_plir = np.ascontiguousarray(cropped_plir)
cropped_sp = sp_rotated[y1:y2, x1:x2]
cropped_lp = lp_rotated[y1:y2, x1:x2]
if False:
_, upper = ip.get_percentile(cropped_plir, 0.005)
pixel_ops.ClipImageF64(cropped_plir, 0, upper)
print cropped_plir.min(), cropped_plir.dtype
view = ImageViewer(plir)
ImageViewer(cropped_plir)
ImageViewer(cropped_sp)
view.show()
sys.exit()
# convert plir image to bulk image
tau_bulk_plir = interpolate.splev(cropped_plir.flatten(),
spline_plir).reshape(cropped_plir.shape)
_, upper = ip.get_percentile(tau_bulk_plir, 0.0001)
pixel_ops.ClipImageF64(tau_bulk_plir, 0.1, upper)
if False:
ImageViewer(im_sp)
ImageViewer(im_lp)
plt.figure()
plt.imshow(cropped_plir)
plt.colorbar()
plt.figure()
plt.imshow(tau_bulk_plir)
plt.colorbar()
plt.show()
sys.exit()
# zoom bulk image to make the same size as NF
if im_pl.shape != im_sp.shape:
size_ratio_h = im_pl.shape[0] / float(im_sp.shape[0])
size_ratio_w = im_pl.shape[1] / float(im_sp.shape[1])
x1 = int(round(x1 * size_ratio_w))
x2 = int(round(x2 * size_ratio_w))
y1 = int(round(y1 * size_ratio_h))
y2 = int(round(y2 * size_ratio_h))
# correct and crop plir image (using params from short pass)
cropped_nf = nf_rotated[y1:y2, x1:x2]
# upsize low res bulk
tau_bulk_plir = ndimage.zoom(tau_bulk_plir, zoom=2.0, order=1)
# make sure same size
height = min(tau_bulk_plir.shape[0], cropped_nf.shape[0])
width = min(tau_bulk_plir.shape[1], cropped_nf.shape[1])
tau_bulk_plir = tau_bulk_plir[:height, :width]
cropped_nf = cropped_nf[:height, :width]
assert tau_bulk_plir.shape == cropped_nf.shape
else:
cropped_nf = nf_rotated[y1:y2, x1:x2]
if False:
view = ImageViewer(tau_bulk_plir)
ImageViewer(cropped_nf)
view.show()
sys.exit()
if parameters.PLIR_INTERPOLATE_MARKER_WIDTH > 0 and features[
'marker_loc'] > 0:
# interpolate marker
print features['marker_loc']
locs = np.array([int(round(features['marker_loc']))], np.int32)
cropped_nf = np.ascontiguousarray(cropped_nf, np.float32)
pixel_ops.InterpolateBBs(cropped_nf, locs,
parameters.PLIR_INTERPOLATE_MARKER_WIDTH)
tau_bulk_plir = np.ascontiguousarray(tau_bulk_plir, np.float32)
pixel_ops.InterpolateBBs(tau_bulk_plir, locs,
parameters.PLIR_INTERPOLATE_MARKER_WIDTH)
if False:
view = ImageViewer(cropped_nf)
ImageViewer(tau_bulk_plir)
view.show()
# correct for doping and transfer to bulk
c_vals = fit_c_vals(cropped_nf, tau_bulk_plir, spline_plc)
doping = ndimage.gaussian_filter1d(c_vals, sigma=2, mode="reflect")
if False:
ImageViewer(cropped_nf)
plt.figure()
plt.plot(c_vals)
plt.plot(doping)
plt.show()
nf_dope = cropped_nf * np.r_[doping]
nf_dope[nf_dope > spline_plc[0][-1]] = spline_plc[0][-1]
tau_bulk_nf = interpolate.splev(nf_dope.flatten(), spline_plc).astype(
np.float32).reshape(cropped_nf.shape)
_, upper_p = ip.get_percentile(tau_bulk_nf, 0.0001)
pixel_ops.ClipImage(tau_bulk_nf, 0.1, upper_p)
features['_C_vals'] = doping.astype(np.float32)
features['im_tau_bulk_f32'] = tau_bulk_nf
features['im_tau_bulk_u8'] = (ip.scale_image(tau_bulk_nf) * 255).astype(
np.uint8)
features['im_cropped_nf_u8'] = (ip.scale_image(cropped_nf) * 255).astype(
np.uint8)
features['im_cropped_nf_u16'] = np.round(cropped_nf).astype(np.uint16)
features['im_cropped_sp_u16'] = np.round(cropped_sp).astype(np.uint16)
features['im_cropped_lp_u16'] = np.round(cropped_lp).astype(np.uint16)
if False:
print tau_bulk_nf.min(), tau_bulk_nf.max()
_, upper_p = ip.get_percentile(tau_bulk_nf, 0.001)
pixel_ops.ClipImage(tau_bulk_nf, 0.1, upper_p)
# print interpolate.splev([0.0, 0.0245], spline_plc)
#ImageViewer(cropped_nf * np.r_[doping])
#ImageViewer(tau_bulk_nf)
plt.figure()
plt.plot(tau_bulk_plir.mean(axis=0))
plt.plot(tau_bulk_nf.mean(axis=0))
# plt.figure()
# plt.hist(tau_bulk_full.flat, bins=100)
if False:
plt.figure()
plt.plot(doping)
plt.plot(c_vals)
plt.figure()
pl = np.mean(cropped_nf, axis=0)
plt.plot(pl, label="PL")
plt.legend()
plt.show()
# compute runtime
t_stop = timeit.default_timer()
features['runtime'] = t_stop - t_start
return True
def plir2(im_sp, im_lp, features, spline_plir, spline_sp):
pixel_ops.ApplyThresholdLT_F32(im_sp, im_sp, 1.0, 1.0)
pixel_ops.ApplyThresholdLT_F32(im_lp, im_lp, 1.0, 1.0)
if im_sp.shape != im_lp.shape:
print im_sp.shape, im_lp.shape
assert False
im_sp = im_sp.astype(np.float64)
im_lp = im_lp.astype(np.float64)
if False:
view = ImageViewer(im_sp)
ImageViewer(im_lp)
view.show()
sys.exit()
# register short and long pass images
def register(signal1, signal2, debug=False):
bandpass1 = ndimage.gaussian_filter1d(
signal1, sigma=10) - ndimage.gaussian_filter1d(signal1, sigma=3)
bandpass2 = ndimage.gaussian_filter1d(
signal2, sigma=10) - ndimage.gaussian_filter1d(signal2, sigma=3)
offsets = range(-10, 11)
fits = [(np.roll(bandpass1, shift=s) * bandpass2).mean()
for s in offsets]
optimal_shift = offsets[np.argmax(fits)]
if debug:
plt.figure()
plt.plot(signal1)
plt.plot(signal2)
plt.figure()
plt.plot(offsets, fits)
plt.figure()
plt.plot(np.roll(bandpass1, shift=optimal_shift))
plt.plot(bandpass2)
plt.show()
return optimal_shift
c = np.argmax(im_sp.mean(axis=0))
profile_sp = im_sp[:, c - 10:c + 11].mean(axis=1)
profile_lp = im_lp[:, c - 10:c + 11].mean(axis=1)
shift_v = register(profile_sp, profile_lp, debug=False)
if False:
print c, shift_v
view = ImageViewer(im_lp)
ImageViewer(im_sp)
ImageViewer(np.roll(im_sp, shift=shift_v, axis=0))
view.show()
sys.exit()
im_sp = np.roll(im_sp, shift=shift_v, axis=0)
# compute PL (ratio of LP to SP)
plir = im_lp / im_sp
if False:
t = stats.scoreatpercentile(plir, per=99)
print plir.min(), t, plir.max()
plir[plir > t] = t
view = ImageViewer(im_lp)
ImageViewer(im_sp)
ImageViewer(plir)
view.show()
sys.exit()
# Get cropping and rotation parameters (based on short pass)
# normalisation - find the 99th percentile
vals = im_sp[::4, ::4].flat
vals = np.sort(vals)
min_val = vals[int(0.025 * vals.shape[0])]
max_val = vals[int(0.975 * vals.shape[0])]
features['norm_range'] = max_val - min_val
features['norm_lower'] = min_val
im_normed_temp = (im_sp - min_val) / (max_val - min_val)
rotated_temp = block_rotate(im_normed_temp, features)
# get crop bounds crop
block_crop(rotated_temp, features)
rotation = features['crop_rotation']
x1, x2, y1, y2 = features['_crop_bounds']
if 'input_param_skip_features' in features and int(
features['input_param_skip_features']) == 1:
return True
if False:
cropped_temp = rotated_temp[y1:y2, x1:x2]
view = ImageViewer(im_sp)
ImageViewer(rotated_temp)
ImageViewer(cropped_temp)
view.show()
# correct and crop plir image (using params from short pass)
if abs(rotation) > 0.01:
h, w = plir.shape
rot_mat = cv2.getRotationMatrix2D((w // 2, h // 2), rotation, 1.0)
plir_rotated = cv2.warpAffine(plir,
rot_mat, (w, h),
flags=cv2.INTER_LINEAR,
borderMode=cv2.BORDER_REPLICATE)
sp_rotated = cv2.warpAffine(im_sp,
rot_mat, (w, h),
flags=cv2.INTER_LINEAR,
borderMode=cv2.BORDER_REPLICATE)
lp_rotated = cv2.warpAffine(im_lp,
rot_mat, (w, h),
flags=cv2.INTER_LINEAR,
borderMode=cv2.BORDER_REPLICATE)
else:
plir_rotated = plir
sp_rotated = im_sp
lp_rotated = im_lp
features['marker_loc'] = find_marker(sp_rotated[y1:y2, x1:x2])
plir_cropped = plir_rotated[y1:y2, x1:x2]
plir_cropped = np.ascontiguousarray(plir_cropped)
# continue with plir
_, upper = ip.get_percentile(plir_cropped, 0.005)
pixel_ops.ClipImageF64(plir_cropped, 0, upper)
if False:
_, upper = ip.get_percentile(plir, 0.005)
pixel_ops.ClipImageF64(plir, 0, upper)
print plir_cropped.min(), plir_cropped.dtype
view = ImageViewer(plir)
ImageViewer(plir_cropped)
view.show()
sys.exit()
tau_bulk_plir = interpolate.splev(plir_cropped.flatten(),
spline_plir).reshape(plir_cropped.shape)
_, upper = ip.get_percentile(tau_bulk_plir, 0.0001)
pixel_ops.ClipImageF64(tau_bulk_plir, 0.1, upper)
if False:
ImageViewer(im_sp)
ImageViewer(im_lp)
plt.figure()
plt.imshow(plir_cropped, cmap=cmaps.viridis)
plt.colorbar()
plt.figure()
plt.imshow(tau_bulk_plir, cmap=cmaps.viridis)
plt.colorbar()
plt.show()
sys.exit()
# dislocation and impure processing for PL image
cropped_sp = sp_rotated[y1:y2, x1:x2]
cropped_lp = lp_rotated[y1:y2, x1:x2]
# compute c-values
c_vals = fit_c_vals(cropped_sp, tau_bulk_plir, spline_sp)
doping = ndimage.gaussian_filter1d(c_vals, sigma=2, mode="reflect")
if False:
ImageViewer(cropped_sp)
plt.figure()
plt.plot(c_vals)
plt.plot(doping)
plt.show()
features['_C_vals'] = doping.astype(np.float32)
sp_dope = cropped_sp * np.r_[doping]
sp_dope[sp_dope > spline_sp[0][-1]] = spline_sp[0][-1]
tau_bulk_full = interpolate.splev(sp_dope.flatten(), spline_sp).astype(
np.float32).reshape(cropped_sp.shape)
# pixel_ops.ApplyThresholdLT_F32(tau_bulk_full, tau_bulk_full, 0.1, 0.1)
_, upper_p = ip.get_percentile(tau_bulk_full, 0.0001)
pixel_ops.ClipImage(tau_bulk_full, 0.1, upper_p)
features['im_tau_bulk_f32'] = tau_bulk_full
features['im_tau_bulk_u8'] = (ip.scale_image(tau_bulk_full) * 255).astype(
np.uint8)
features['im_cropped_sp_u8'] = (ip.scale_image(cropped_sp) * 255).astype(
np.uint8)
features['im_cropped_sp_u16'] = np.round(cropped_sp).astype(np.uint16)
features['im_cropped_lp_u16'] = np.round(cropped_lp).astype(np.uint16)
if False:
if True:
_, upper_p = ip.get_percentile(tau_bulk_full, 0.001)
pixel_ops.ClipImage(tau_bulk_full, 0.1, upper_p)
else:
tau_bulk_full = np.log(tau_bulk_full)
ImageViewer(cropped_sp)
ImageViewer(sp_dope)
ImageViewer(tau_bulk_plir)
ImageViewer(tau_bulk_full)
plt.figure()
plt.plot(tau_bulk_plir.mean(axis=0))
plt.plot(tau_bulk_full.mean(axis=0))
if False:
plt.figure()
plt.plot(doping)
plt.plot(c_vals)
plt.show()
return True
def feature_extraction(im, features, crop=True, skip_features=False):
h, w = im.shape
if im.dtype != np.float32:
im = im.astype(np.float32)
if crop:
# cropping
rotation_corrected = block_rotate(im, features)
cropped_u16 = block_crop(rotation_corrected, features)
bounds = features['_crop_bounds']
else:
rotation_corrected = im
cropped_u16 = im
bounds = (0, w - 1, 0, h - 1)
features['_crop_bounds'] = bounds
features['crop_rotation'] = 0
# get original coordinates of the block corners
find_corners(im, features)
features['_rotation_corrected'] = rotation_corrected
if False:
view = ImageViewer(im)
ImageViewer(cropped_u16)
view.show()
sys.exit()
# normalisation
vals = cropped_u16[::2, ::2].flat
vals = np.sort(vals)
min_val = vals[int(0.01 * vals.shape[0])]
max_val = vals[int(0.99 * vals.shape[0])]
features['norm_range'] = max_val - min_val
features['norm_lower'] = min_val
im_normed = (cropped_u16 - min_val) / (max_val - min_val)
pixel_ops.ApplyThresholdLT_F32(im_normed, im_normed, 0.0, 0.0)
cropped = im_normed
croped_u8 = im_normed.copy()
pixel_ops.ApplyThresholdGT_F32(croped_u8, croped_u8, 1.0, 1.0)
features['im_cropped_u8'] = (croped_u8 * 255).astype(np.uint8)
features['im_cropped_u16'] = cropped_u16.astype(np.uint16)
if skip_features or ('input_param_skip_features' in features
and int(features['input_param_skip_features']) == 1):
return
if False:
view = ImageViewer(im)
ImageViewer(cropped, vmin=0, vmax=1)
view.show()
sys.exit()
# compute some row/column percentiles
col_sorted = np.sort(cropped[::4, :], axis=0)
features['_col_90'] = np.ascontiguousarray(
col_sorted[int(round(0.9 * 0.25 * cropped.shape[0])), :])
features['_col_60'] = np.ascontiguousarray(
col_sorted[int(round(0.6 * 0.25 * cropped.shape[0])), :])
row_sorted = np.sort(cropped[:, ::4], axis=1)
features['_row_90'] = np.ascontiguousarray(
row_sorted[:, int(round(0.9 * 0.25 * cropped.shape[1]))])
# background
background = block_background(cropped, features)
# foreground
foreground = block_foreground(cropped, features)
# normalise background
background /= background.max()
# calculate metrics
robust_dislocations(cropped, background, features)
# dislocation area
DIS_THRESH = 0.3
dislocation_area = (
pixel_ops.CountThresholdGT_F32(foreground, DIS_THRESH) /
float(foreground.shape[0] * foreground.shape[1]))
impure_area = 1 - (pixel_ops.CountThresholdGT_F32(background, 0.5) /
float(foreground.shape[0] * foreground.shape[1]))
# edge width
l4 = background.shape[1] // 4
profile = background[:, l4:-l4].mean(axis=1)
fg = np.where(profile > parameters.BRICK_EDGE_THRESH)[0]
if len(fg) > 0:
left_width, right = fg[[0, -1]]
right_width = len(profile) - right - 1
edge_width = max(left_width, right_width)
if edge_width < 0.05 * len(profile):
edge_width = 0
else:
edge_width = 100
features['edge_width'] = edge_width
if False:
print edge_width
ImageViewer(cropped)
plt.figure()
plt.plot(profile)
plt.show()
if False:
dislocations = np.zeros_like(foreground, dtype=np.uint8)
pixel_ops.ApplyThresholdGT_F32_U8(foreground, dislocations, DIS_THRESH,
1)
print features['defect_robust_area_fraction'], impure_area
view = ImageViewer(im)
ImageViewer(dislocations)
ImageViewer(foreground)
ImageViewer(background, vmin=0, vmax=1)
view.show()
# sys.exit()
imp_cutoff = 0.55
pixel_ops.ApplyThresholdGT_F32(background, background, imp_cutoff,
imp_cutoff)
background /= imp_cutoff
background = np.log10(2 - background)
dis_cutoff = 0.1
foreground -= dis_cutoff
foreground = np.clip(foreground, 0, 1)
foreground *= 0.5
features['ov_impure_u8'] = (background * 255).astype(np.uint8)
features['ov_defects_u8'] = (foreground * 255).astype(np.uint8)
features['_bounds'] = bounds
pixel_ops.ClipImage(im_normed, 0, 1)
features['dislocation_area_fraction'] = dislocation_area
features['impure_area_fraction'] = impure_area
return features
def block_foreground(im, features):
per_col = features['_col_60']
im_col = np.dot(np.ones((im.shape[0], 1), np.float32),
per_col.reshape(1, per_col.shape[0]))
per_row = features['_row_90']
im_row = np.dot(per_row.reshape(im.shape[0], 1),
np.ones((1, im.shape[1]), np.float32))
background = ip.fast_smooth(np.minimum(im_col, im_row), sigma=5)
foreground = background - im
pixel_ops.ApplyThresholdLT_F32(foreground, foreground, 0, 0)
pixel_ops.ApplyThresholdLT_F32(background, foreground, 0.3, 0)
if False:
view = ImageViewer(im, vmin=0, vmax=1)
ImageViewer(im_col, vmin=0, vmax=1)
ImageViewer(im_row, vmin=0, vmax=1)
ImageViewer(background, vmin=0, vmax=1)
ImageViewer(foreground, vmin=0, vmax=1)
view.show()
sys.exit()
# skeletonized version of defects
local_mins = np.zeros_like(foreground, np.uint8)
f = cv2.GaussianBlur(foreground * -1, ksize=(0, 0), sigmaX=2)
pixel_ops.LocalMins(f, local_mins)
dis = ((local_mins == 1) & (foreground > 0.1)).astype(np.uint8)
ys, xs = np.where(dis)
pixel_ops.FastThin(dis, ys.copy(), xs.copy(), ip.thinning_lut)
ip.remove_small_ccs(dis, 10)
if False:
crossing = np.zeros_like(dis)
pixel_ops.ComputeCrossings(dis, crossing)
junctions = crossing > 2
struct = ndimage.generate_binary_structure(2, 2)
junctions_d = ndimage.binary_dilation(junctions, struct)
branches = dis.copy()
branches[junctions_d] = 0
# find branches that touch an end point
ccs, num_ccs = ip.connected_components(branches)
spurs = np.zeros_like(dis)
for cc in set(ccs[crossing == 1]):
if cc == 0: continue
spurs[ccs == cc] = 1
# sys.exit()
remove = spurs.copy()
ip.remove_small_ccs(remove, 10)
removed = spurs - remove
pruned = dis - removed
crossing = np.zeros_like(dis)
pruned = pruned.astype(np.uint8)
pixel_ops.ComputeCrossings(pruned, crossing)
pruned[crossing == 1] = 0
dis = pruned
rgb = ip.overlay_mask(im, dis, colour='b')
ip.save_image("brick_lines_skeleton.png", dis)
ip.save_image("brick_lines_overlay.png", rgb)
view = ImageViewer(foreground, vmin=0, vmax=1)
ImageViewer(rgb)
view.show()
sys.exit()
# create a height-based profile of dislocation levels
# - crop impure areas at top and bottom,
imp = np.where(per_row < 0.5)[0]
mid = len(per_row) // 2
upper_half = imp[imp < mid]
if len(upper_half) > 0:
top = upper_half.max()
else:
top = 0
lower_half = imp[imp > mid]
if len(lower_half) > 0:
bottom = lower_half.min()
else:
bottom = len(per_row)
if False:
plt.figure()
plt.plot(per_row)
plt.vlines([top, bottom], ymin=0, ymax=1)
plt.show()
sys.exit()
foreground_pure = foreground[top:bottom, :]
dislocation_profile = foreground_pure.mean(axis=0)
dislocation_profile[per_col < 0.6] = 0
dislocation_profile = ndimage.gaussian_filter1d(dislocation_profile,
sigma=5)
features['_dis_avg_height'] = dislocation_profile
if False:
view = ImageViewer(im, vmin=0, vmax=1)
# ImageViewer(im_col, scale=0.5, vmin=0, vmax=1)
# ImageViewer(im_row, scale=0.5, vmin=0, vmax=1)
ImageViewer(background, vmin=0, vmax=1)
ImageViewer(foreground, vmin=0, vmax=1)
ImageViewer(foreground_pure, vmin=0, vmax=1)
plt.figure()
plt.plot(dislocation_profile)
view.show()
sys.exit()
return foreground
def firing_defects(features):
im = features['im_norm']
finger_rows = features['_finger_row_nums']
# im_fingers = features['_finger_im']
im_smooth = cv2.GaussianBlur(im, ksize=(0, 0), sigmaX=1)
im_fingers = im_smooth[finger_rows, :]
if False:
view = ImageViewer(im)
# view = ImageViewer(im_smooth)
ImageViewer(im_fingers)
view.show()
sys.exit()
# find depth of local minimums
S = 5
dips = np.minimum(np.roll(im_fingers, S, axis=1), np.roll(im_fingers, -S, axis=1)) - im_fingers
pixel_ops.ApplyThresholdLT_F32(dips, dips, 0, 0)
dips[:, features['mask_busbar_filled'][0, :]] = 0
dips[:, :features['cell_edge_left']] = 0
dips[:, features['cell_edge_right']:] = 0
# TODO: add upper bound as well
locs = ((im_fingers < np.roll(im_fingers, 1, axis=1)) &
(im_fingers < np.roll(im_fingers, -1, axis=1)) &
(dips > 0.02) & (dips < 0.05)).astype(np.float32)
# count num dips in a region. ignore areas with only 1
w = im.shape[1] // 10
weights = np.ones(w, np.int32)
local_count = ndimage.convolve1d(locs, weights, axis=1, mode="constant")
dips_filtered = dips.copy()
dips_filtered[local_count <= 1] = 0
if False:
view = ImageViewer(im)
ImageViewer(dips)
# ImageViewer(locs)
# ImageViewer(local_count)
# ImageViewer(dips_filtered)
view.show()
im_dots = cv2.GaussianBlur(dips_filtered, ksize=(0, 0), sigmaX=10, sigmaY=2)
# im_dots -= 0.001
if False:
view = ImageViewer(dips_filtered)
view = ImageViewer(im_dots)
view.show()
splotch = np.empty_like(im)
pixel_ops.ExpandFingers(splotch, im_dots, finger_rows)
splotch = ip.fast_smooth(splotch, sigma=10)
features["_firing"] = splotch.copy()
splotch *= 100.0 * (1.0 + parameters.FIRING_SENSITIVITY)
pixel_ops.ClipImage(splotch, 0.0, 1.0)
pixel_ops.ApplyThresholdGT_F32(features['im_center_dist_im'],
splotch, features['wafer_radius'], 0)
features["ov_splotches_u8"] = (splotch * 255).astype(np.uint8)
# metrics
if splotch.max() >= 0.2:
features['firing_area_strength'] = splotch.mean() * 100
mask_firing = (splotch > 0.2).astype(np.uint8)
im_pl = features['_cropped_f32']
firingPL = pixel_ops.MaskMean_F32(im_pl, mask_firing, 1)
goodPL = pixel_ops.MaskMean_F32(im_pl, mask_firing, 0)
features['firing_area_mean_PL'] = firingPL
features['firing_area_fraction'] = mask_firing.mean()
features['firing_area_PL_intensity_ratio'] = firingPL / max(1, goodPL)
else:
features['firing_area_strength'] = 0.0
features['firing_area_mean_PL'] = 0.0
features['firing_area_fraction'] = 0.0
features['firing_area_PL_intensity_ratio'] = 0.0
if False:
print features['firing_area_strength']
view = ImageViewer(im)
ImageViewer(splotch, vmin=0, vmax=1)
ImageViewer(mask_firing)
f2 = {'im_cropped_u8': features['im_cropped_u8'],
'ov_splotches_u8': features['ov_splotches_u8']}
ImageViewer(create_overlay(f2))
view.show()
sys.exit()
def dark_areas(features):
# dark areas (not dark spots)
im = features['im_norm']
h, w = im.shape
row_nums = features['_peak_row_nums']
cell_mask = features['bl_cropped_u8'][row_nums, :]
bb_locs = features['_busbar_cols']
# fill edges & corners
foreground = im[row_nums].copy()
edge = features['cell_edge_tb']
rr, cc = draw.circle_perimeter(features['wafer_middle_y'], features['wafer_middle_x'],
int(round(features['wafer_radius'])) - edge)
mask = (cc >= 0) & (cc < w) & np.in1d(rr, row_nums)
lut = np.zeros(h, np.int32)
lut[row_nums] = np.arange(len(row_nums))
rr = rr[mask]
cc = cc[mask]
rr = np.take(lut, rr)
pixel_ops.FillCorners(foreground, rr.astype(np.int32), cc.astype(np.int32))
foreground[:, :edge] = np.c_[foreground[:, edge]]
foreground[:, -edge:] = np.c_[foreground[:, -edge]]
# create background
# 1. make monotonic between edges & BBs
mono_lr = np.empty_like(foreground)
mono_rl = np.empty_like(foreground)
pixel_ops.MakeMonotonicBBs(foreground, mono_lr, bb_locs)
pixel_ops.MakeMonotonicBBs(np.ascontiguousarray(foreground[:, ::-1]), mono_rl,
np.ascontiguousarray(w - bb_locs[::-1]))
mono_rl = mono_rl[:, ::-1]
mono = np.minimum(mono_lr, mono_rl)
background = mono
da1 = background - foreground
# fill BBs and flatten
background2 = background.copy()
pixel_ops.InterpolateBBs(background2, features['_busbar_cols'], features['busbar_width'])
cols = background2.mean(axis=0)
background2 -= np.r_[cols]
rows = background2.mean(axis=1)
background2 -= np.c_[rows]
da2 = -1 * background2
pixel_ops.ApplyThresholdLT_F32(da2, da2, 0.0, 0.0)
if False:
view = ImageViewer(foreground)
ImageViewer(background)
ImageViewer(background2)
ImageViewer(da1)
ImageViewer(da2)
ImageViewer(da1 + da2)
# plt.figure()
# for x in range(0, background.shape[1], 50):
# plt.plot(background[:, x], label="Col %d"%(x))
# plt.legend()
view.show()
sys.exit()
dark_areas = da1 + da2
dark_areas -= (0.1 - parameters.DARK_AREA_SENSITIVITY)
dark_areas[(cell_mask == 1) | (cell_mask == 8)] = 0 # corners
pixel_ops.ClipImage(dark_areas, 0.0, 1.0)
dark_areas_full = np.empty_like(im)
pixel_ops.ExpandFingers(dark_areas_full, dark_areas, features['_peak_row_nums'])
if False:
pixel_ops.ApplyThresholdGT_F32(features['im_center_dist_im'], dark_areas_full,
features['wafer_radius'], 0)
print features['wafer_radius']
view = ImageViewer(dark_areas)
ImageViewer(dark_areas_full)
ImageViewer(features['im_center_dist_im'])
view.show()
dark_areas_full = cv2.GaussianBlur(dark_areas_full, ksize=(0, 0), sigmaX=1)
# metrics
mask_dark = (dark_areas_full > 0.2).astype(np.uint8)
features['dark_area_strength'] = dark_areas_full.mean() * 100
im_pl = features['_cropped_f32']
darkPL = pixel_ops.MaskMean_F32(im_pl, mask_dark, 1)
brightPL = pixel_ops.MaskMean_F32(im_pl, mask_dark, 0)
features['dark_area_mean_PL'] = darkPL
features['dark_area_fraction'] = mask_dark.mean()
features['dark_area_PL_intensity_ratio'] = brightPL / max(1, darkPL)
features['ov_dark_areas_u8'] = (dark_areas_full * 255).astype(np.uint8)
if False:
print features['dark_area_fraction'], features['dark_area_strength']
# plt.figure()
# plt.plot(cols)
# plt.plot(cols_mono)
view = ImageViewer(im)
ImageViewer(foreground)
ImageViewer(dark_areas)
ImageViewer(mask_dark)
ImageViewer(dark_areas_full)
view.show()
def finger_defects(features):
im = features['im_norm']
h, w = im.shape
row_nums = features['_finger_row_nums']
finger_im = im[row_nums, :] # .copy()
mask = features['bl_cropped_u8'][row_nums, :]
bb_locs = features['_busbar_cols']
# make a little more robust by averaging 3 locations:
# - finger, and a little above/below
offset = 1 # int(features['finger_period'] / 2.0)
off_up = im[row_nums - offset, :]
off_down = im[row_nums + offset, :]
finger_im = (finger_im + off_up + off_down) / 3.0
features['_finger_im'] = finger_im
if False:
view = ImageViewer(im)
ImageViewer(finger_im)
# ImageViewer(finger_im2)
view.show()
# make monotonic (don't care about local mins)
mono_lr = np.empty_like(finger_im)
mono_rl = np.empty_like(finger_im)
pixel_ops.MakeMonotonicBBs(finger_im, mono_lr, bb_locs)
pixel_ops.MakeMonotonicBBs(np.ascontiguousarray(finger_im[:, ::-1]), mono_rl,
np.ascontiguousarray(w - bb_locs[::-1]))
mono_rl = mono_rl[:, ::-1]
mono = np.minimum(mono_lr, mono_rl)
if False:
view = ImageViewer(im)
# ImageViewer(normed)
# ImageViewer(mono_lr)
# ImageViewer(mono_rl)
ImageViewer(mono)
view.show()
####################
# BROKEN FINGERS 1 #
####################
# Detect intensity changes along a finger
# - works best away from edges, and can handle breaks aligned in a column
# 1. at a break, the min on bright side should be greater than max on dark side
# 2. sharp local gradient, not a region with a steady (but high) gradient
finger_filled = mono.copy()
# 1 - brighter areas
s = 25
offset = s // 2 + 3
maxs = ndimage.maximum_filter(finger_filled, size=(1, s), mode="nearest")
pixel_ops.ApplyThresholdLT_F32(maxs, maxs, 0.1, 0.1)
mins = ndimage.minimum_filter(finger_filled, size=(1, s), mode="nearest")
d1 = np.roll(mins, offset, axis=1) / np.roll(maxs, -offset, axis=1)
d2 = np.roll(mins, -offset, axis=1) / np.roll(maxs, offset, axis=1)
break_strength = np.maximum(d1, d2)
# 2 - sharp local drop
f = np.array([[-1, -1, -1, -1, -1, 0, 1, 1, 1, 1, 1]], dtype=np.float32)
edges_abs = np.abs(ndimage.correlate(mono, weights=f, mode="nearest"))
edges_local = edges_abs - np.maximum(np.roll(edges_abs, 6, axis=1), np.roll(edges_abs, -6, axis=1))
break_strength += edges_local
features['_edges_abs'] = edges_abs
if False:
print parameters.BROKEN_FINGER_THRESHOLD1
print parameters.BROKEN_FINGER_EDGE_THRESHOLD
view = ImageViewer(finger_filled)
# ImageViewer(maxs)
# ImageViewer(mins)
# ImageViewer(d1)
# ImageViewer(d2)
# ImageViewer(edges_local)
ImageViewer(break_strength)
view.show()
sys.exit()
# find local maxes
breaks1 = ((break_strength >= np.roll(break_strength, 1, axis=1)) &
(break_strength >= np.roll(break_strength, -1, axis=1)) &
(break_strength > parameters.BROKEN_FINGER_THRESHOLD1)).astype(np.uint8)
# For this detector, ignore breaks near edges, corners & busbars
mask_background = mask == 8 # edges
mask2 = ndimage.binary_dilation(mask_background, np.ones((1, s + 4), np.uint8))
mask3 = ndimage.binary_dilation(mask2, np.ones((3, 1), np.uint8))
corners = mask2.sum(axis=0) > 2
mask2[:, corners] = mask3[:, corners]
bb_mask = features['mask_busbar_filled'][row_nums, :]
bb_mask = ndimage.binary_dilation(bb_mask, np.ones((1, 11), np.uint8))
mask2 = (mask2 | bb_mask)
breaks1[mask2] = 0
if False:
view = ImageViewer(im)
ImageViewer(break_strength)
ImageViewer(breaks1)
view.show()
sys.exit()
####################
# BROKEN FINGERS 2 #
####################
# - find breaks by comparing with fingers above/below (using bright lines image)
# - the advantage of this approach is that it can find breaks near edges
# and busbars
# - doesn't need to be very sensitive -- just find breaks near borders, which should be strong
# - note that there also needs to be a gradient at that spot, otherwise we get
# some phantom breaks
rows_filtered = np.zeros_like(mono)
pixel_ops.FilterV(mono, rows_filtered)
rows_filtered[:2, :] = finger_im[:2, :]
rows_filtered[-2:, :] = finger_im[-2:, :]
bright_lines = mono - rows_filtered
mask_background = ((mask == 1) | (mask == 8))
bright_lines[mask_background] = False
pixel_ops.ClipImage(bright_lines, 0.0, 1.0)
pixel_ops.ApplyThresholdLT_F32(mono, bright_lines, 0.4, 0.0)
if False:
view = ImageViewer(mono)
ImageViewer(mask)
ImageViewer(bright_lines)
view.show()
sys.exit()
# filter bright lines
min_length = w // 20
cc_sums = np.zeros_like(bright_lines)
breaks2 = np.zeros_like(bright_lines, np.uint8)
pixel_ops.BrightLineBreaks(bright_lines, cc_sums, breaks2, 0.04,
parameters.BROKEN_FINGER_THRESHOLD2, min_length)
if False:
for r in range(cc_sums.shape[0]):
if cc_sums[r, :].sum() == 0:
continue
print r
plt.figure()
plt.plot(bright_lines[r, :])
plt.plot((cc_sums[r, :] > 0) * bright_lines[r, :].max())
plt.figure()
plt.plot(mono[r, :])
plt.plot((cc_sums[r, :] > 0) * mono[r, :].max())
plt.show()
if False:
view = ImageViewer(im)
ImageViewer(bright_lines)
ImageViewer(cc_sums)
ImageViewer(breaks2)
view.show()
###########
# COMBINE #
###########
# if there are 2+ close together, only keep one with strongest gradient
if False:
# check break source
# green == independent lines (breaks1)
# red == relative lines (breaks2)
breaks_full = np.zeros_like(im)
breaks_full[features["_finger_row_nums"], :] = breaks1
breaks_full = ndimage.binary_dilation(breaks_full, structure=ndimage.generate_binary_structure(2, 1),
iterations=3)
rgb = ip.overlay_mask(im, breaks_full, 'g')
breaks_full = np.zeros_like(im)
breaks_full[features["_finger_row_nums"], :] = breaks2
breaks_full = ndimage.binary_dilation(breaks_full, structure=ndimage.generate_binary_structure(2, 1),
iterations=3)
rgb = ip.overlay_mask(rgb, breaks_full, 'r')
view = ImageViewer(rgb)
view.show()
sys.exit()
breaks = (breaks1 | breaks2).astype(np.uint8)
break_count = ndimage.correlate(breaks, weights=np.ones((1, 15), np.uint8), mode='constant') # .astype(np.uinut8)
pixel_ops.CombineBreaks(breaks, break_count, edges_abs)
# ignore breaks in cell edge or background
cell_template = features['bl_cropped_u8'][features['_finger_row_nums']]
breaks[((cell_template == 1) | (cell_template == 8))] = 0
# create break mask
breaks_full = np.zeros_like(im, np.uint8)
breaks_full[features["_finger_row_nums"], :] = breaks
features['mk_finger_break_u8'] = breaks_full
if False:
print breaks_full.sum()
view = ImageViewer(im)
ImageViewer(finger_filled)
ImageViewer(break_count)
ImageViewer(breaks)
view.show()
sys.exit()
def feature_combination(features):
if "ov_bright_area_u8" in features:
# dilate to find defects near edges
bright = (features['ov_bright_area_u8'] / 255.).astype(np.float32)
kernel = np.ones((15, 15), np.uint8)
bright = cv2.dilate(bright, kernel=kernel)
else:
bright = None
if "ov_splotches_u8" in features:
firing = (features['ov_splotches_u8'] / 255.).astype(np.float32)
else:
firing = None
if "ov_dark_areas_u8" in features:
dark = (features['ov_dark_areas_u8'] / 255.).astype(np.float32)
else:
dark = None
# bright areas causing dark areas
if bright is not None and dark is not None:
weight = 5.0
cols = bright.mean(axis=0)
rows = bright.mean(axis=1)
dark -= np.r_[cols] * weight
dark -= np.c_[rows] * weight
pixel_ops.ApplyThresholdLT_F32(dark, dark, 0.0, 0.0)
if False:
plt.figure()
plt.plot(cols)
plt.plot(rows)
view = ImageViewer(bright)
ImageViewer(features['ov_dark_areas_u8'] / 255.)
ImageViewer(dark)
view.show()
features['ov_dark_areas_u8'] = (dark * 255).astype(np.uint8)
# dark middles
# remove dark spots & broken fingers in high firing areas
if firing is not None:
FIRING_THRESH = 0.1
# if "mk_cracks_u8" in features:
# pixel_ops.ApplyThresholdGT_F32_U8(firing, features["mk_cracks_u8"], FIRING_THRESH, 0)
if "mk_dark_spots_outline_u8" in features:
pixel_ops.ApplyThresholdGT_F32_U8(firing, features["mk_dark_spots_outline_u8"], FIRING_THRESH, 0)
if "mk_finger_break_u8" in features:
# TODO: handle finger breaks differently: look at sum along finger, and remove all
pixel_ops.ApplyThresholdGT_F32_U8(firing, features["mk_finger_break_u8"], FIRING_THRESH, 0)
if False:
view = ImageViewer(firing)
view.show()
# remove cracks, dark spots & broken fingers in bright areas
if bright is not None:
# expand a bit to get artifacts on corner
BRIGHT_THRESH = 0.1
# if "mk_cracks_u8" in features:
# pixel_ops.ApplyThresholdGT_F32_U8(bright, features["mk_cracks_u8"], BRIGHT_THRESH, 0)
if "mk_finger_break_u8" in features:
pixel_ops.ApplyThresholdGT_F32_U8(bright, features["mk_finger_break_u8"], BRIGHT_THRESH, 0)
if "mk_dark_spots_outline_u8" in features:
pixel_ops.ApplyThresholdGT_F32_U8(bright, features["mk_dark_spots_outline_u8"], BRIGHT_THRESH, 0)
if False:
view = ImageViewer(bright)
view.show()
# bright areas causing middle dark
# overlapping cracks and dark spots
if "mk_dark_spots_outline_u8" in features and "mk_cracks_u8" in features and \
features['mk_dark_spots_outline_u8'].max() > 0 and \
features['mk_cracks_u8'].max() > 0:
ccs, num_ccs = ip.connected_components(features["mk_dark_spots_outline_u8"])
remove_list = set(ccs[(features['mk_dark_spots_outline_u8'] == 1) & (features['mk_cracks_u8'] == 1)])
lut = np.ones(num_ccs + 1, np.int32)
lut[0] = 0
lut[list(remove_list)] = 0
removed = np.take(lut, ccs)
if False:
view = ImageViewer(features["mk_cracks_u8"])
ImageViewer(ccs)
ImageViewer(removed)
view.show()
features['mk_dark_spots_outline_u8'] = removed.astype(np.uint8)
def finger_defects(features):
# TODO: bright lines for top and bottom rows
im = features['im_norm']
row_nums = features['_finger_row_nums']
################
# BRIGHT LINES #
################
# highlight bright lines based on difference between lines above/below
finger_im = im[row_nums, :].copy()
# based on differences above & below
rows_smooth = finger_im
rows_filtered = np.zeros_like(rows_smooth)
pixel_ops.FilterV(rows_smooth, rows_filtered)
rows_filtered[:2, :] = finger_im[:2, :]
rows_filtered[-2:, :] = finger_im[-2:, :]
bright_lines = rows_smooth - rows_filtered
bright_lines /= max(0.1, (0.5 - parameters.BRIGHT_LINES_MULTI_SENSITIVITY))
# make less sensitive for multi
bright_lines -= 0.25
bright_lines /= 0.75
bright_lines = ndimage.uniform_filter(bright_lines, size=(1, 5))
pixel_ops.ClipImage(bright_lines, 0.0, 1.0)
if False:
plt.figure()
plt.plot(finger_im[42, :])
view = ImageViewer(finger_im)
ImageViewer(im)
ImageViewer(rows_filtered)
ImageViewer(bright_lines)
view.show()
sys.exit()
# get strength of each line (sum)
# - need to insert lines between rows for computing CCs
bl_cc = np.zeros((bright_lines.shape[0] * 2, bright_lines.shape[1]), np.uint8)
bl_cc[::2, :] = bright_lines > 0
ccs, num_ccs = ip.connected_components(bl_cc)
ccs = ccs[::2, :]
sums = ndimage.sum(bright_lines, ccs, range(num_ccs + 1))
sums /= (float(bright_lines.shape[1]) / 100.0)
line_strengths = np.take(sums, ccs)
bright_lines[line_strengths < parameters.BRIGHT_LINES_MULTI_THRESHOLD] = 0
features['bright_lines_count'] = (sums > parameters.BRIGHT_LINES_MULTI_THRESHOLD).sum()
if False:
print features['bright_lines_count']
view = ImageViewer(bl_cc)
ImageViewer(ccs)
ImageViewer(line_strengths)
ImageViewer(bright_lines)
view.show()
# create a full size image of bright lines
bright_lines_full = np.zeros_like(im)
bright_lines_full[row_nums, :] = bright_lines
bright_lines_full = cv2.GaussianBlur(bright_lines_full, sigmaX=2, ksize=(0, 0))
features['ov_bright_lines_u8'] = (bright_lines_full * 255).astype(np.uint8)
features['bright_lines_strength'] = bright_lines.mean()
features['bright_lines_length'] = (bright_lines > 0.5).sum()
if False:
im[row_nums, :] = 0
view = ImageViewer(im)
ImageViewer(finger_im)
ImageViewer(bright_lines > 0.5)
ImageViewer(bright_lines_full)
view.show()
sys.exit()
if True:
# want a 1-1 correspondence with bright lines, so:
# - threshold based on sum of line
# - add break to end with highest gradient
f = np.array([[-1, -1, -1, -1, -1, 0, 1, 1, 1, 1, 1]], dtype=np.float32)
edges_abs = np.abs(ndimage.correlate(finger_im, weights=f, mode="nearest"))
cc_labels = np.where(sums > parameters.BRIGHT_LINES_MULTI_THRESHOLD)[0]
max_pos = ndimage.maximum_position(edges_abs, ccs, cc_labels)
breaks = np.zeros_like(finger_im, np.uint8)
if len(max_pos) > 0:
ys, xs = zip(*max_pos)
breaks[np.array(ys, np.int32), np.array(xs, np.int32)] = 1
else:
####################
# BROKEN FINGERS 1 #
####################
# - find breaks by comparing with fingers above/below (using bright lines image)
# - the advantage of this approach is that it can find breaks near edges
# and busbars
# - since there is a step 2, doesn't need to be very sensitive -- just find
# breaks near borders, which should be strong
# - note that there also needs to be a gradient at that spot, otherwise we get
# some phantom breaks
w = 11
g = 3
s = g + (w // 2)
maxs = ndimage.maximum_filter(bright_lines, size=(1, w))
mins = ndimage.minimum_filter(bright_lines, size=(1, w))
diffs = np.maximum(np.roll(mins, s, axis=1) - np.roll(maxs, -s, axis=1),
np.roll(mins, -s, axis=1) - np.roll(maxs, s, axis=1))
diffs = ndimage.gaussian_filter1d(diffs, sigma=3, axis=1)
pixel_ops.ApplyThresholdLT_F32(diffs, diffs, 0.0, 0.0)
local_maxes = np.logical_and((diffs > np.roll(diffs, 1, axis=1)),
(diffs > np.roll(diffs, -1, axis=1)))
diffs[~local_maxes] = 0
f = np.array([[-1, -1, -1, -1, -1, 0, 1, 1, 1, 1, 1]], dtype=np.float32)
edges_abs = np.abs(ndimage.correlate(finger_im, weights=f, mode="nearest"))
breaks1 = ((diffs > parameters.BROKEN_FINGER_MULTI_THRESHOLD1) &
(edges_abs > parameters.BROKEN_FINGER_MULTI_EDGE_THRESHOLD))
breaks1[:, :features['cell_edge_left']] = False
breaks1[:, features['cell_edge_right']:] = False
if False:
view = ImageViewer(bright_lines)
ImageViewer(diffs)
ImageViewer(edges_abs)
ImageViewer(breaks1)
# ImageViewer(np.roll(mins, shift=s, axis=1) - np.roll(maxs, shift=-s, axis=1))
view.show()
sys.exit()
# add to defect mask
breaks_full = np.zeros_like(im)
breaks_full[features["_finger_row_nums"], :] = breaks
breaks_full = ndimage.binary_dilation(breaks_full, structure=ndimage.generate_binary_structure(2, 1), iterations=3)
features['mk_finger_break_u8'] = breaks_full.astype(np.uint8)
features['finger_break_count'] = breaks.sum()
if False:
view = ImageViewer(im)
ImageViewer(bright_lines)
# ImageViewer(break_strength)
ImageViewer(breaks)
ImageViewer(create_overlay(features))
view.show()
sys.exit()
def bright_areas(features):
im = features['im_norm']
row_nums = features['_finger_row_nums']
im_fingers = features['im_norm'][row_nums, :]
vals = np.sort(im_fingers.flat)
count = vals.shape[0]
p01 = vals[int(round(0.01 * count))]
p95 = vals[int(round(0.95 * count))]
p99 = vals[int(round(0.999 * count))]
# find highest peak
counts, edges = np.histogram(vals, bins=50, density=True)
i_max = np.argmax(counts)
val_mode = (edges[i_max] + edges[i_max + 1]) / 2.0
if p99 - p95 > 0.2:
# thresh 1: assuming a symmetric distribution, mode+spread on low ed
thresh1 = val_mode + (val_mode - p01) * 2
# thresh 2: look for a distribution that drops very low
below_02 = np.where(counts[i_max:] < 0.025)[0]
if len(below_02) > 0:
i = i_max + below_02[0]
thresh2 = (edges[i] + edges[i + 1]) / 2.0
thresh = min(thresh1, thresh2)
else:
thresh = thresh1
else:
thresh = im_fingers.max()
thresh -= parameters.BRIGHT_AREA_MULTI_SENSITIVITY
bright_areas = im_fingers - thresh
bright_areas /= 0.5
pixel_ops.ApplyThresholdLT_F32(bright_areas, bright_areas, 0.0, 0.0)
pixel_ops.ApplyThresholdGT_F32(bright_areas, bright_areas, 1.0, 1.0)
# create a full size image of bright lines
bright_lines_full = np.zeros_like(im)
bright_lines_full[row_nums, :] = bright_areas
bright_lines_full = cv2.GaussianBlur(bright_lines_full, sigmaX=1, sigmaY=2, ksize=(0, 0))
if 'ov_bright_area_u8' in features:
features['ov_bright_area_u8'] = np.maximum((bright_lines_full * 255).astype(np.uint8),
features['ov_bright_area_u8'])
else:
features['ov_bright_area_u8'] = (bright_lines_full * 255).astype(np.uint8)
features['bright_area_strength'] = bright_areas.mean() * 100
features['bright_area_fraction'] = (pixel_ops.CountThresholdGT_F32(bright_areas, 0.1)) / float(
im.shape[0] * im.shape[1])
features['_bright_area_thresh'] = thresh
if False:
print features['bright_area_strength']
print pixel_ops.CountThresholdGT_F32(bright_areas, 0.1) * 100 / float(im.shape[0] * im.shape[1])
print features['bright_area_fraction']
view = ImageViewer(im)
ImageViewer(im_fingers)
ImageViewer(bright_areas)
plt.figure()
plt.hist(im_fingers.flatten(), bins=50, normed=True)
plt.plot((edges[:-1] + edges[1:]) / 2.0, counts)
plt.vlines(thresh, 0, counts.max())
view.show()
