def get_distorted(image, params, orient = "horizont"):
shifts = []
np_image = array(image.convert("L"))
for el in params:
if el[0] == "sin":
shifts.append(lambda x: np_image.shape[0] / el[1] * \
np.sin(x * el[2] / np_image.shape[1]))
if el[0] == "cos":
shifts.append(lambda x: np_image.shape[0] / el[1] * \
np.cos(x * el[2] / np_image.shape[1]))
if el[0] == "triang":
lambda x: np_image.shape[0] / el[1] * \
(x / el[2] / np_image.shape[1] - math.floor(x / (el[2] / np_image.shape[1])))
if el[0] == "erosion":
np_image = erosion(np_image, square(el[1]))
if el[0] == "dilation":
np_image = dilation(np_image, square(el[1]))
if orient == "horizont":
for idx in xrange(np_image.shape[0]):
for shift in shifts:
np_image[idx,:] = np.roll(np_image[idx,:], int(shift(idx)))
if orient == "vert":
for idx in xrange(np_image.shape[1]):
for shift in shifts:
np_image[:, idx] = np.roll(np_image[:, idx], int(shift(idx)))
return Image.fromarray(np_image)
def get_symbols(image):
dil_eros = bin_search(dilatation_cross_numb, [image], (1, 16), 1.0, "dec")
block_size = 50
binary_adaptive_image = erosion(dilation(threshold_adaptive(
array(image.convert("L")), block_size, offset=10),
square(dil_eros)), square(dil_eros))
all_labels = label(binary_adaptive_image, background = True)
objects = find_objects(all_labels)
av_width = av_height = 0
symbols = []
for obj in objects:
symb = (binary_adaptive_image[obj], (obj[0].start, obj[1].start))
symbols.append(symb)
av_height += symb[0].shape[0]
av_width += symb[0].shape[1]
av_width /= float(len(objects))
av_height /= float(len(objects))
symbols = [symb for symb in symbols
if symb[0].shape[0] >= av_height and symb[0].shape[1] >= av_width]
return symbols
def morphoNoiseRemoval(img):
"Removes noise by succession of 5 opening/closing morphological operators"
for i in range(0,5):
img = opening2(img, square(3))
img = closing2(img, square(3))
return img
def removeChessboard(img):
# Get the major lines in the image
edges, dilatedEdges, (h, theta, d) = findLines(img)
# Create image with ones to fill inn lines
lines = np.ones(img.shape[:2])
# Add lines to image as zeroes
for _, angle, dist in zip(*hough_line_peaks(h, theta, d)):
y0 = (dist - 0 * np.cos(angle)) / np.sin(angle)
y1 = (dist - img.shape[1] * np.cos(angle)) / np.sin(angle)
x, y = line(int(y1), 0, int(y0), img.shape[1] - 1)
x = np.clip(x, 0, img.shape[0] - 1)
y = np.clip(y, 0, img.shape[1] - 1)
lines[x, y] = 0
# Remove border edges from image with all edges
w = 4
edges = np.pad(edges[w:img.shape[0] - w, w:img.shape[1] - w], w, mode='constant')
# Erode the lines bigger, such that they cover the original lines
lines = erosion(lines, square(13))
# Remove major lines and close shape paths
removedChessboard = closing(edges * lines, square(8))
return removedChessboard
def calculate_masked_stats():
plate_no = "59798"
parsed = get_plate_files(plate_no)
for w in ['w2']:
files = filter(lambda f: f.wave == w[1], parsed)
# accum = np.zeros((2160, 2160), dtype=np.uint32)
# files = filter(lambda x: 's1' not in x and 's7' not in x, all_files)
nof = len(files)
for i, frame in enumerate(files[0:5], 1):
LogHelper.logText(frame.fullpath)
img = imread(frame.fullpath)
t = filters.threshold_yen(img)
b1 = img > t
b2 = binary_erosion(b1, square(2))
b3 = binary_dilation(b2, square(10))
b4 = binary_closing(b3, square(3))
imm = np.ma.masked_where(b4, img)
mn, mx = np.percentile(imm, (1, 99))
LogHelper.logText(
'%3d of %d, %4d-%4d-%4d-%5d, %.0f-%.0f'
% (i, nof, imm.min(), mn, mx, imm.max(), imm.mean(), imm.std())
)
im2 = imm.filled(int(imm.mean()))
out_name = "{0}\\{5}-{1}{2}-{3}-{4}.tif".format(ROOT_DIR, frame.row, frame.column, frame.site, LogHelper.init_ts, frame.experiment)
imsave(out_name, im2)
def morph(img, tparams):
ops = [mor.grey.erosion, mor.grey.dilation]
t = ops[np.random.randint(2)]
if t == 0:
selem = mor.square(np.random.randint(1, tparams['selem_size'][0]))
else:
selem = mor.square(np.random.randint(1, tparams['selem_size'][1]))
return t(img, selem)
def seg_sect(self, img):
img_canny = canny(img, sigma=self.sigma,
low_threshold=self.low_threshold)
img_dilate = binary_dilation(img_canny, square(3))
img_erode = binary_erosion(img_dilate, square(3))
img_fill = binary_fill_holes(img_erode)
return img_fill
def process_cell(img):
# la binariza en caso de que sea escala de grises
if not img.dtype == 'bool':
img = img > 0 # Binarizar
# Calcular máscaras para limpiar lineas largas verticales
h_k = 0.8
sum0 = np.sum(img, 0) # Aplastar la matriz a una fila con las sumas de los valores de cada columna.
thr0 = sum0 < h_k * img.shape[0]
thr0 = thr0.reshape(len(thr0), 1) # Convertirlo a vector de una dimensión
# Calcular máscaras para limpiar lineas largas horizontales
w_k = 0.5
sum1 = np.sum(img, 1)
thr1 = sum1 < w_k * img.shape[1]
thr1 = thr1.reshape(len(thr1), 1)
mask = thr0.transpose() * thr1 # Generar máscara final para la celda
mask_lines = mask.copy()
elem = morphology.square(5)
mask = morphology.binary_erosion(mask, elem) # Eliminar ruido
img1 = np.bitwise_and(mask, img) # Imagen filtrada
# segmentación del bloque de números
kerw = 5 # Kernel width
thr_k = 0.8
# Calcular mascara para marcar inicio y fin de región con dígitos horizontalmente
sum0 = np.sum(img1, 0)
sum0 = signal.medfilt(sum0, kerw)
thr0 = sum0 > thr_k * np.median(sum0)
thr0 = np.bitwise_and(thr0.cumsum() > 0, np.flipud(np.flipud(thr0).cumsum() > 0))
thr0 = thr0.reshape(len(thr0), 1)
# Calcular mascara para marcar inicio y fin de región con dígitos verticalmente
sum1 = np.sum(img1, 1)
sum1 = signal.medfilt(sum1, kerw)
thr1 = sum1 > thr_k * np.median(sum1)
thr1 = np.bitwise_and(thr1.cumsum() > 0, np.flipud(np.flipud(thr1).cumsum() > 0))
thr1 = thr1.reshape(len(thr1), 1)
# Mascara final para inicio y fin de caracteres (bounding box of digit region)
mask = thr0.transpose() * thr1
mask = morphology.binary_dilation(mask, morphology.square(2))
img = np.bitwise_and(mask_lines.astype(img.dtype), img) # Aplicar máscara para quitar lineas
img = morphology.binary_dilation(img, morphology.disk(1)) # Dilatación para unir números quebrados por la máscara anterior
img = morphology.binary_erosion(img, morphology.disk(1)) # Volver a la fomorma 'original' con los bordes unidos
return np.bitwise_and(mask, img)
def _getPoseMask(peaks, height, width, radius=4, var=4, mode='Solid'):
## MSCOCO Pose part_str = [nose, neck, Rsho, Relb, Rwri, Lsho, Lelb, Lwri, Rhip, Rkne, Rank, Lhip, Lkne, Lank, Leye, Reye, Lear, Rear, pt19]
# find connection in the specified sequence, center 29 is in the position 15
# limbSeq = [[2,3], [2,6], [3,4], [4,5], [6,7], [7,8], [2,9], [9,10], \
# [10,11], [2,12], [12,13], [13,14], [2,1], [1,15], [15,17], \
# [1,16], [16,18], [3,17], [6,18]]
# limbSeq = [[2,3], [2,6], [3,4], [4,5], [6,7], [7,8], [2,9], [9,10], \
# [10,11], [2,12], [12,13], [13,14], [2,1], [1,15], [15,17], \
# [1,16], [16,18]] # , [9,12]
# limbSeq = [[3,4], [4,5], [6,7], [7,8], [9,10], \
# [10,11], [12,13], [13,14], [2,1], [1,15], [15,17], \
# [1,16], [16,18]] #
limbSeq = [[2,3], [2,6], [3,4], [4,5], [6,7], [7,8], [2,9], [9,10], \
[10,11], [2,12], [12,13], [13,14], [2,1], [1,15], [15,17], \
[1,16], [16,18], [2,17], [2,18], [9,12], [12,6], [9,3], [17,18]] #
indices = []
values = []
for limb in limbSeq:
p0 = peaks[limb[0] -1]
p1 = peaks[limb[1] -1]
if 0!=len(p0) and 0!=len(p1):
r0 = p0[0][1]
c0 = p0[0][0]
r1 = p1[0][1]
c1 = p1[0][0]
ind, val = _getSparseKeypoint(r0, c0, 0, height, width, radius, var, mode)
indices.extend(ind)
values.extend(val)
ind, val = _getSparseKeypoint(r1, c1, 0, height, width, radius, var, mode)
indices.extend(ind)
values.extend(val)
distance = np.sqrt((r0-r1)**2 + (c0-c1)**2)
sampleN = int(distance/radius)
# sampleN = 0
if sampleN>1:
for i in xrange(1,sampleN):
r = r0 + (r1-r0)*i/sampleN
c = c0 + (c1-c0)*i/sampleN
ind, val = _getSparseKeypoint(r, c, 0, height, width, radius, var, mode)
indices.extend(ind)
values.extend(val)
shape = [height, width, 1]
## Fill body
dense = np.squeeze(_sparse2dense(indices, values, shape))
## TODO
# im = Image.fromarray((dense*255).astype(np.uint8))
# im.save('xxxxx.png')
# pdb.set_trace()
dense = dilation(dense, square(5))
dense = erosion(dense, square(5))
return dense
def getRegions():
"""Geocode address and retreive image centered
around lat/long"""
address = request.args.get('address')
results = Geocoder.geocode(address)
lat, lng = results[0].coordinates
zip_code = results[0].postal_code
map_url = 'https://maps.googleapis.com/maps/api/staticmap?center={0},{1}&size=640x640&zoom=19&sensor=false&maptype=roadmap&&style=visibility:simplified|gamma:0.1'
request_url = map_url.format(lat, lng)
req = urllib.urlopen(request_url)
img = io.imread(req.geturl(),flatten=True)
labels, numobjects = ndimage.label(img)
image = filter.canny(img, sigma=3)
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(3))
# remove artifacts connected to image border
cleared = bw.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(6, 6))
ax.imshow(image_label_overlay)
def estimate_rotation(img):
assert(img.dtype == 'bool')
# elimina bloques rellenos para acelerar la deteccion de lineas
elem = morphology.square(2)
aux = morphology.binary_dilation(img, elem) - morphology.binary_erosion(img, elem)
# Detección de lineas usando transformada de Hough probabilística
thres = 50
minlen = 0.1 * min(aux.shape)
maxgap = 0.01 * minlen
lines = transform.probabilistic_hough(aux, threshold=thres, line_length=minlen, line_gap=maxgap)
# me aseguro que el primer punto de cada línea sea el más próximo al origen
for lin in lines:
(x0,y0), (x1,y1) = lin
if x1*x1+y1*y1 < x0*x0+y0*y0:
(x0, x1) = (x1, x0)
(y0, y1) = (y1, y0)
# orientación dominante
angle_half_range = np.math.pi / 4
nbins = int(2 * angle_half_range * (180./np.math.pi) / 0.2)
orient = []
for lin in lines:
(x0,y0), (x1,y1) = lin
orient.append(np.math.atan2(y1-y0, x1-x0))
(h, binval) = np.histogram(orient, range=(-angle_half_range, angle_half_range), bins=nbins)
alpha = binval[h.argmax()] * (180./ np.math.pi)
return alpha + 0.5 * (binval[1] - binval[0]) * (180./ np.math.pi)
def process_image(image):
tic = time.clock()
# rescale intensity
p2, p98 = np.percentile(image, (1, 99.9))
image = rescale_intensity(1.0*image, in_range=(p2, p98))
# do simple filter based on color value
thresh = 0.5*threshold_func(image)
filtered_image = np.zeros_like(image,dtype=np.uint8) # set up all-zero image
filtered_image[image > thresh] = 1 # filtered values set to 1
# perform watershed transform to split clusters
distance = ndi.distance_transform_edt(filtered_image)
local_maxi = peak_local_max(distance, indices=False, footprint=morphology.square(7),
labels=filtered_image, exclude_border=False)
markers = ndi.label(local_maxi)[0]
# segment and label particles
labels = morphology.watershed(-distance, markers, mask=filtered_image)
backup_labels = labels.copy()
# remove boundaries and restore any small particles deleted in this process
labels[find_boundaries(labels)] = 0
for i in np.unique(backup_labels)[1:]:
if np.count_nonzero(labels[backup_labels == i]) == 0:
labels[backup_labels == i] = i
toc = time.clock()
procTime = toc - tic
return image, labels, procTime
def run4(self):
""" Cette fonction recadre les images grâce à SURF et RANSAC, fonctionne bien."""
for x in xrange(len(self.stack)-1):
print('Traitement image ' + str(x+1))
im1,im2 = 255.*gaussian_filter(self.stack[x,...], sqrt(self.initial_sigma**2 - 0.25)), 255.*gaussian_filter(self.stack[x+1,...], sqrt(self.initial_sigma**2 - 0.25))
im1,im2 = enhance_contrast(normaliser(im1), square(5)), enhance_contrast(normaliser(im2), square(5))
im1, im2 = normaliser(im1), normaliser(im2)
b = cv2.SURF()
#b.create("Feature2D.BRISK")
k1,d1 = b.detectAndCompute(im1,None)
k2,d2 = b.detectAndCompute(im2,None)
bf = cv2.BFMatcher()
matches = bf.knnMatch(d1,d2, k=2)
# Apply ratio test
good = []
for m,n in matches:
if m.distance < 0.75*n.distance:
good.append(m)
g1,g2 = [],[]
for i in good:
g1.append(k1[i.queryIdx].pt)
g2.append(k2[i.trainIdx].pt)
model, inliers = ransac((np.array(g1), np.array(g2)), AffineTransform, min_samples=3, residual_threshold=self.min_epsilon, max_trials=self.max_trials, stop_residuals_sum=self.min_inlier_ratio)
self.stack[x+1,...] = warp(self.stack[x+1,...], AffineTransform(rotation=model.rotation, translation=model.translation), output_shape=self.stack[x+1].shape)
self.stack = self.stack.astype(np.uint8)
def dark_channel(image, structure=square(15)):
(h, w, c) = image.shape
dark_channels = np.zeros_like(image)
for i in range(c):
dark_channels[:, :, i] = minimum_filter(image[:, :, i], footprint=structure)
dark_channel = np.min(dark_channels, axis=2)
return dark_channel
def edge_confidence(epi, window=9, threshold=0.02):
"""
Calculates the edge confidence according to eq. 2.
This is a simple measurement which designates an edge if pixel intensities
of gray value changes. An edge is determined by the sum of difference in
pixel intensity of a central pixel to all pixels in a 1D window of size
window. It is assumed that there is an edge if the sum is greater than a
given threshold.
Parameters
----------
epi : numpy.array [v,u]
Set of all gray-value epis for scanline s_hat.
window_size : int, optional
The 1D window siz in pixels. As the window should be centered
symmetrically around the pixel to process the value shpuld be odd. For
even numbers the next higher odd number is chosen.
threshold : float, optional
The threshold giving the smallest difference in EPI luminescence which
must be overcome to designate an edge.
Returns
-------
Ce : numpy.array [v,u]
Edge confidence values for each EPI pixel.
Me : numpy.array [v,u] of boolean.
True means an edge was discovered for at that pixel.
"""
v_dim = epi.shape[0]
u_dim = epi.shape[1]
# Check dimensions of input data
assert epi.shape == (v_dim, u_dim,), 'Input EPI has wrong shape in function \'edge_confidence\'.'
# Make window size odd
if window % 2 == 0:
warnings.warn(
'window should be an odd number in function \'edge_confidence\'. Window size {g} was given but {u} is used instead.'.format(
g=window, u=window + 1))
window += 1
# We avoid the border problem by padding the epi.
padded_epi = np.pad(epi, ((0, 0), (int(window // 2), int(window // 2))), 'edge')
assert padded_epi.shape == (v_dim, u_dim + window - 1,), 'Padded epi has wrong shape in function \'edge_confidence\'.'
# Calculate confidence values
Ce = np.zeros(epi.shape, dtype=np.float32) # initiate array
for k in range(window):
Ce += (epi[...] - padded_epi[:, k:epi.shape[1] + k]) ** 2
Me = Ce > threshold # create confidence Mask
Me = binary_opening(Me, selem=square(2), out=Me) # work with square to avoid aliasing
# Let's see if our results have reasonable meaning'
assert np.all(
Ce >= 0), 'Negative edge confidence found in function \'edge_confidence\'.'
assert Ce.shape == (v_dim,
u_dim,), 'Ce output has incorrect shape in fucntion \'edge_confidence\'.'
assert Me.shape == (v_dim,
u_dim,), 'Me output has incorrect shape in fucntion \'edge_confidence\'.'
return Ce, Me
def get_rough_detection(self, img, bigsize=40.0, smallsize=4.0, thresh = 0):
diff = self.difference_of_gaussian(-img, bigsize, smallsize)
diff[diff>thresh] = 1
se = morphology.square(4)
ero = morphology.erosion(diff, se)
labimage = label(ero)
#rec = morphology.reconstruction(ero, img, method='dilation').astype(np.dtype('uint8'))
# connectivity=1 corresponds to 4-connectivity.
morphology.remove_small_objects(labimage, min_size=600, connectivity=1, in_place=True)
#res = np.zeros(img.shape)
ero[labimage==0] = 0
ero = 1 - ero
labimage = label(ero)
morphology.remove_small_objects(labimage, min_size=400, connectivity=1, in_place=True)
ero[labimage==0] = 0
res = 1 - ero
res[res>0] = 255
#temp = 255 - temp
#temp = morphology.remove_small_objects(temp, min_size=400, connectivity=1, in_place=True)
#res = 255 - temp
return res
def focus_score(self):
f_score = (color.rgb2grey(self.img) - erosion(color.rgb2grey(self.img), square(4)))
non_zero_pixel_area = self.get_nonzero_pixel_area(f_score)
#print("focus score: " + str(np.sum(f_score) / non_zero_pixel_area))
#plt.imshow(f_score)
#plt.show()
return np.sum(f_score) / non_zero_pixel_area
def segmentation(image): """Executes image segmentation based on various features of the video stream""" gray = cv2.cvtColor(image, cv2.cv.CV_RGB2GRAY) blurred = cv2.GaussianBlur(gray, (5, 5), 0) ret, bw = cv2.threshold(blurred, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU) # Close binary image result = cv2.dilate(bw, square(10), iterations = 1) result = cv2.erode(result, square(10), iterations = 1) # Open binary image result = cv2.erode(result, square(10), iterations = 1) result = cv2.dilate(result, square(10), iterations = 1) return label(result) * 50
def run3(self):
""" Cette fonction test des alternatives à SIFT et ORB. Ne fonctionne pas."""
for x in xrange(len(self.stack)-1):
print('Traitement image ' + str(x+1))
im1,im2 = 255.*gaussian_filter(self.stack[x,...], sqrt(self.initial_sigma**2 - 0.25)), 255.*gaussian_filter(self.stack[x+1,...], sqrt(self.initial_sigma**2 - 0.25))
im1,im2 = enhance_contrast(normaliser(im1), square(3)), enhance_contrast(normaliser(im2), square(3))
im1, im2 = normaliser(im1), normaliser(im2)
b = cv2.BRISK()
#b.create("Feature2D.BRISK")
k1,d1 = b.detectAndCompute(im1,None)
k2,d2 = b.detectAndCompute(im2,None)
bf = cv2.BFMatcher(cv2.NORM_HAMMING)
matches = bf.match(d1,d2)
g1,g2 = [],[]
for i in matches:
g1.append(k1[i.queryIdx].pt)
g2.append(k2[i.trainIdx].pt)
model, inliers = ransac((np.array(g1), np.array(g2)), AffineTransform, min_samples=3, residual_threshold=self.min_epsilon, max_trials=self.max_trials, stop_residuals_sum=self.min_inlier_ratio)
self.stack[x+1,...] = warp(self.stack[x+1,...], AffineTransform(rotation=model.rotation, translation=model.translation), output_shape=self.stack[x+1].shape)
self.stack = self.stack.astype(np.uint8)
def updateRasterInfo(self, **kwargs):
kwargs['output_info']['statistics'] = ()
kwargs['output_info']['histogram'] = ()
self.window = square(int(kwargs.get('size', 3)))
m = kwargs.get('measure', 'Mean').lower()
if m == 'minimum':
self.func = rank.minimum
elif m == 'maximum':
self.func = rank.maximum
elif m == 'mean':
self.func = rank.mean
elif m == 'bilateral mean':
self.func = rank.mean_bilateral
elif m == 'median':
self.func = rank.median
elif m == 'sum':
self.func = rank.sum
elif m == 'entropy':
self.func = rank.entropy
elif m == 'threshold':
self.func = rank.threshold
elif m == 'autolevel':
self.func = rank.autolevel
return kwargs
def plot_preprocessed_image(self):
"""
plots pre-processed image. The plotted image is the same as obtained at the end
of the get_text_candidates method.
"""
image = restoration.denoise_tv_chambolle(self.image, weight=0.1)
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(2))
cleared = bw.copy()
label_image = measure.label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(12, 12))
ax.imshow(image_label_overlay)
for region in regionprops(label_image):
if region.area < 10:
continue
minr, minc, maxr, maxc = region.bbox
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='red', linewidth=2)
ax.add_patch(rect)
plt.show()
def median_filter(image, selem=None):
if selem is None:
# default mask is 5x5 square
selem = square(5)
depth = image.shape[2]
return np.dstack(median(channel[...,0], selem)
for channel in np.dsplit(image, depth)) / 255.
def filter_img(img):
selem = square(11)
img[:, :, 0] = rank.mean(img[:, :, 0], selem=selem)
img[:, :, 1] = rank.mean(img[:, :, 1], selem=selem)
img[:, :, 2] = rank.mean(img[:, :, 2], selem=selem)
#return np.array(img, dtype=float)
return img_as_float(img)
def squareMask(maskImg, square_width): #both odd and even square_with are allowed
boxsize = maskImg.get_xsize()
maskArray = EMNumPy.em2numpy(maskImg)
if (boxsize <= square_width):
print "ERROR: the width of the square cannot be larger than the boxsize of particles."
sys.exit()
#from skimage.morphology import square
#Generates a flat, square-shaped structuring element.
#Every pixel along the perimeter has a chessboard distance no greater than radius (radius=floor(width/2)) pixels.
squareArray = square(square_width, dtype=np.uint8)
m, n = squareArray.shape
assert m==n
if (m%2 == 0):
pad_before = (boxsize - m)/2
pad_after = (boxsize - m)/2
else:
pad_before = (boxsize - m)/2
pad_after = (boxsize - m)/2+1
#pad_width = (boxsize - square_width)/2
#print "m, n, pad_before, pad_after", m, n, pad_before, pad_after
#squareArrayPad = np.pad(squareArray, pad_width, mode='constant')
squareArrayPad = np.pad(squareArray, (pad_before, pad_after), mode='constant')
squareImg = EMNumPy.numpy2em(squareArrayPad)
return squareImg
def roofRegion(edge):
"""Estimate region based on edges of roofRegion
"""
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(3))
# remove artifacts connected to image border
cleared = bw.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(6, 6))
ax.imshow(image_label_overlay)
for region in regionprops(label_image):
# skip small images
if region.area < 100:
continue
# draw rectangle around segmented coins
minr, minc, maxr, maxc = region.bbox
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='red', linewidth=2)
ax.add_patch(rect)
plt.show()
def blobs(image, remove_mb = None, val = 160, size = 100):
""" Convolve a kernel on the image and a gaussian filter to highligh blobs. Find blobs using the
Difference of Gaussian. Remove from the list of blobs the blobs that are at the membrane.
return 3 different list
"""
thresh = threshold_otsu(image)
#Find all the blobs in the image using Difference of Gaussian
blobs_in_image = feature.blob_dog(image, min_sigma=0.01,
max_sigma=3, threshold=thresh)
blob_list = []
for blob in blobs_in_image:
y, x, r = blob
blob_list.append((y, x))
if remove_mb == None:
blob_in_image_after_binary = set(blob_list)
else:
#Create a mask to remove blobs that are at the membrane and surrounded
#by bright big object
binary = image >= val*thresh/100
binary = dilation(binary, square(3))
binary = remove_small_objects(binary, min_size=size)
# Create a list of coordinate with the binary image
coor_binary = np.nonzero(binary)
list_blob_masked = zip(*coor_binary)
#Substract the list of coordinate from the binary image to the list of blobs
blob_in_image_after_binary = (set(blob_list) - set (list_blob_masked))
return blob_in_image_after_binary
def main():
for file_path in glob.glob("/home/lucas/Downloads/Lucas/GSK 10uM/*.JPG"):
img = data.imread(file_path, as_grey=True)
img = transform.resize(img, [600, 600])
img_color = transform.resize(data.imread(file_path), [600, 600])
img[img >img.mean()-0.1] = 0
# io.imshow(img)
# io.show()
#
edges = canny(img)
bordas_fechadas = closing(img > 0.1, square(15)) # fechando gaps
fill_cells = ndi.binary_fill_holes(bordas_fechadas)
# io.imshow(fill_cells)
# io.show()
img_label = label(fill_cells, background=0)
n= 0
for x in regionprops(img_label):
if x.area < 2000 and x.area > 300:
n +=1
print x.area
minr, minc, maxr, maxc = x.bbox
try:
out_path_name = file_path.split("/")[-1].rstrip(".JPG")
io.imsave("out/cell_{}_pic_{}_area_{}.png".format(n, out_path_name, str(round(x.area))),img_color[minr-3: maxr+3, minc-3: maxc+3])
#io.show()
except:
pass
def threshold_image(image, threshold=0): """ This function takes out any values in an image's RGB matrix that are below the threshold value. Inputs: - image: a matrix describing an image with only one channel represented. - threshold: a value, between 0 and 1, for which if an image matrix's value is below, will be set to 0, and if above, will be set to 1. If the threshold is set to 0, then an Otsu thresholding will be returned. Outputs: - thresholded_image: a matrix representation of the thresholded image. this is essentially a black and white image. - thresh: the threshold value To screen: the black-and-white image representation. - """ if threshold == 0: thresh = threshold_otsu(image) if threshold != 0: thresh = threshold thresholded_image = closing(image > thresh, square(3), out=None) imshow(thresholded_image) return thresholded_image, thresh
def mask_to_objects_2d(mask, background=0, offset=None):
"""Convert 2D (binary or label) mask to polygons. Generates borders fitting in the objects.
Parameters
----------
mask: ndarray
2D mask array. Expected shape: (height, width).
background: int
Value used for encoding background pixels.
offset: tuple (optional, default: None)
(x, y) coordinate offset to apply to all the extracted polygons.
Returns
-------
extracted: list of AnnotationSlice
Each object slice represent an object from the image. Fields time and depth of AnnotationSlice are set to None.
"""
if mask.ndim != 2:
raise ValueError("Cannot handle image with ndim different from 2 ({} dim. given).".format(mask.ndim))
if offset is None:
offset = (0, 0)
# opencv only supports contour extraction for binary masks: clean mask and binarize
mask_cpy = np.zeros(mask.shape, dtype=np.uint8)
mask_cpy[mask != background] = 255
# create artificial separation between adjacent touching each other + clean
contours = dilation(mask, square(3)) - mask
mask_cpy[np.logical_and(contours > 0, mask > 0)] = background
mask_cpy = clean_mask(mask_cpy, background=background)
# extract polygons and labels
polygons = _locate(mask_cpy, offset=offset)
objects = list()
for polygon in polygons:
# loop for handling multipart geometries
for curr in flatten_geoms(polygon.geoms) if hasattr(polygon, "geoms") else [polygon]:
x, y = get_polygon_inner_point(curr)
objects.append((polygon, mask[y - offset[1], x - offset[0]]))
return objects
def label_particles_edge(im, sigma=2, closing_size=0, **extra_args):
""" Segment image using Canny edge-finding filter.
parameters
----------
im : image in which to find particles
sigma : size of the Canny filter
closing_size : size of the closing filter
returns
-------
labels : an image array of uniquely labeled segments
"""
from skimage.morphology import square, binary_closing, skeletonize
if skimage_version < StrictVersion('0.11'):
from skimage.filter import canny
else:
from skimage.filters import canny
edges = canny(im, sigma=sigma)
if closing_size > 0:
edges = binary_closing(edges, square(closing_size))
edges = skeletonize(edges)
labels = sklabel(edges)
print "found {} segments".format(labels.max())
# in ma.array mask, False is True, and vice versa
labels = np.ma.array(labels, mask=edges == 0)
return labels
def _get_batches_of_transformed_samples(self, index_array):
batch_x = []
batch_y = []
for batch_index, image_index in enumerate(index_array):
_idx = self.image_ids[image_index]
img0 = all_images[_idx].copy()
msk0 = all_masks[_idx].copy()
lbl0 = all_labels[_idx].copy()
good4copy = all_good4copy[_idx]
x0 = random.randint(0, img0.shape[1] - input_shape[1])
y0 = random.randint(0, img0.shape[0] - input_shape[0])
img = img0[y0:y0 + input_shape[0], x0:x0 + input_shape[1], :]
msk = msk0[y0:y0 + input_shape[0], x0:x0 + input_shape[1], :]
if len(good4copy) > 0 and random.random() > 0.75:
num_copy = random.randrange(1, min(6, len(good4copy) + 1))
lbl_max = lbl0.max()
for i in range(num_copy):
lbl_max += 1
l_id = random.choice(good4copy)
lbl_msk = all_labels[_idx] == l_id
row, col = np.where(lbl_msk)
y1, x1 = np.min(np.where(lbl_msk), axis=1)
y2, x2 = np.max(np.where(lbl_msk), axis=1)
lbl_msk = lbl_msk[y1:y2 + 1, x1:x2 + 1]
lbl_img = img0[y1:y2 + 1, x1:x2 + 1, :]
if random.random() > 0.5:
lbl_msk = lbl_msk[:, ::-1, ...]
lbl_img = lbl_img[:, ::-1, ...]
rot = random.randrange(4)
if rot > 0:
lbl_msk = np.rot90(lbl_msk, k=rot)
lbl_img = np.rot90(lbl_img, k=rot)
x1 = random.randint(
max(0, x0 - lbl_msk.shape[1] // 2),
min(img0.shape[1] - lbl_msk.shape[1],
x0 + input_shape[1] - lbl_msk.shape[1] // 2))
y1 = random.randint(
max(0, y0 - lbl_msk.shape[0] // 2),
min(img0.shape[0] - lbl_msk.shape[0],
y0 + input_shape[0] - lbl_msk.shape[0] // 2))
tmp = erosion(lbl_msk, square(5))
lbl_msk_dif = lbl_msk ^ tmp
tmp = dilation(lbl_msk, square(5))
lbl_msk_dif = lbl_msk_dif | (tmp ^ lbl_msk)
lbl0[y1:y1 + lbl_msk.shape[0],
x1:x1 + lbl_msk.shape[1]][lbl_msk] = lbl_max
img0[y1:y1 + lbl_msk.shape[0],
x1:x1 + lbl_msk.shape[1]][lbl_msk] = lbl_img[lbl_msk]
full_diff_mask = np.zeros_like(img0[..., 0], dtype='bool')
full_diff_mask[y1:y1 + lbl_msk.shape[0],
x1:x1 + lbl_msk.shape[1]] = lbl_msk_dif
img0[..., 0][full_diff_mask] = median(
img0[..., 0], mask=full_diff_mask)[full_diff_mask]
img0[..., 1][full_diff_mask] = median(
img0[..., 1], mask=full_diff_mask)[full_diff_mask]
img0[..., 2][full_diff_mask] = median(
img0[..., 2], mask=full_diff_mask)[full_diff_mask]
img = img0[y0:y0 + input_shape[0], x0:x0 + input_shape[1], :]
lbl = lbl0[y0:y0 + input_shape[0], x0:x0 + input_shape[1]]
msk = create_mask(lbl)
if 'ic100_' in all_ids[_idx] or 'gnf_' in all_ids[_idx]:
data = self.random_transformers[1](image=img[..., ::-1],
mask=msk)
else:
data = self.random_transformers[0](image=img[..., ::-1],
mask=msk)
img = data['image'][..., ::-1]
msk = data['mask']
msk = msk.astype('float')
msk[..., 0] = (msk[..., 0] > 127) * 1
msk[..., 1] = (msk[..., 1] > 127) * (msk[..., 0] == 0) * 1
msk[..., 2] = (msk[..., 1] == 0) * (msk[..., 0] == 0) * 1
otp = msk
img = np.concatenate([img, bgr_to_lab(img)], axis=2)
batch_x.append(img)
batch_y.append(otp)
batch_x = np.array(batch_x, dtype="float32")
batch_y = np.array(batch_y, dtype="float32")
batch_x = preprocess_inputs(batch_x)
return self.transform_batch_x(batch_x), self.transform_batch_y(batch_y)
'''
Created on Aug 6, 2019
@author: jsaavedr
Filtro Mediana
'''
import matplotlib.pyplot as plt
import skimage.filters as filters
import skimage.morphology as morphology
import scipy.ndimage.filters as nd_filters
import utils
import pai_io
if __name__ == '__main__':
filename = '../images/gray/ruido.tif'
image = pai_io.imread(filename, as_gray=True)
strel = morphology.square(3)
image_median = filters.median(image, strel)
g_kernel = utils.get_gaussian2d(2, 6)
image_g = nd_filters.convolve(image, g_kernel, mode='constant', cval=0)
fig, xs = plt.subplots(1, 3)
for i in range(3):
xs[i].set_axis_off()
xs[0].imshow(image, cmap='gray', vmin=0, vmax=255)
xs[0].set_title('Image')
xs[1].imshow(image_g, cmap='gray', vmin=0, vmax=255)
xs[1].set_title('Filtro Gaussiano')
xs[2].imshow(image_median, cmap='gray', vmin=0, vmax=255)
xs[2].set_title('Filtro Mediana')
plt.show()
M = dict_imp.transform(M)
M = normalize(M)
print('Number of samples in Dictionary', len(names))
M = remove_bands(M, bands)
data = remove_bands(data, bands)
recon_img = np.reshape(data.transpose(),
(data.shape[1], img.shape[0], img.shape[1]))
#spec.view_cube(recon_img)
print('Dictionary Shape', M.shape)
print('Data reduced shape', data.shape)
pad_img = add_padding(recon_img, 3)
print('Padded image', pad_img.shape)
M = M.transpose()
data = data.transpose()
mu = .004
lamb = .1
gamma = .006
n_iter = 300
width = 5
strel = square(width)
#data = np.transpose(data)
X = morph_opt(M, data, lamb, gamma, mu, strel, n_iter=300)
#M = np.transpose(M)
print(X.shape)
recon = np.dot(M, X)
#recon = np.transpose(recon)
recon_img = np.reshape(recon, (250, 190, 188))
def erosion(img):
# return greyscale morphological erosion of an image
return mp.erosion(img, mp.square(2, dtype=np.uint8))
def remove_dead_pixels(vid, thresh=1.1):
for frame in tqdm(range(vid.shape[0]), desc='Removing Dead Pixels'):
med = skimage.filters.median(vid[frame, :, :], square(10)).ravel()
img = vid[frame, :, :].ravel()
img[img > thresh * med] = med[img > thresh * med]
vid[frame, :, :] = img.reshape(vid.shape[1], vid.shape[2])
def Bfx_lbp(I, R=None, options={}):
"""
X, Xn, options = Bfx_lbp(I, R, options)
Toolbox: Balu
Local Binary Patterns features
X is the features vector, Xn is the list of feature names (see Example
to see how it works).
It calculates the LBP over the a regular grid of patches. The function
uses scikit-image's local_binary_pattern implementation
(see http://scikit-image.org/docs/dev/api/skimage.feature.html#local-binary-pattern).
It returns a matrix of uniform lbp82 descriptors for I, made by
concatenating histograms of each grid cell in the image.
Grid size is options['hdiv'] * options['vdiv']
R is a binary image or empty. If R is given the lbp will be computed
the corresponding pixles R==0 in image I will be set to 0.
options['mappingtype'] can have one of this options: {'nri_uniform', 'uniform', 'ror', 'default'}.
If not options is provided 'nri_uniform' which produces histograms of 59 bins will be used.
Output:
X is a matrix of size ((hdiv*vdiv) x 59), each row has a
histogram corresponding to a grid cell. We use 59 bins.
options['x'] of size hdiv*vdiv is the x coordinates of center of ith grid cell
options['y'] of size hdiv*vdiv is the y coordinates of center of ith grid cell
Both coordinates are calculated as if image was a square of side length 1.
References:
Ojala, T.; Pietikainen, M. & Maenpaa, T. Multiresolution gray-scale
and rotation invariant texture classification with local binary
patterns. IEEE Transactions on Pattern Analysis and Machine
Intelligence, 2002, 24, 971-987.
Mu, Y. et al (2008): Discriminative Local Binary Patterns for Human
Detection in Personal Album. CVPR-2008.
Example 1:
import numpy as np
from balu.ImagesAndData import balu_imageload
from balu.FeatureExtraction import Bfx_lbp
from balu.InputOutput import Bio_printfeatures
from matplotlib.pyplot import bar, figure, show
options = {
'weight': 0, # Weigth of the histogram bins
'vdiv': 3, # one vertical divition
'hdiv': 3, # one horizontal divition
'samples': 8, # number of neighbor samples
'mappingtype': 'nri_uniform' # uniform LBP
}
I = balu_imageload('testimg1.jpg') # input image
J = I[119:219, 119:239, 1] # region of interest (green)
figure(1)
imshow(J, cmap='gray') # image to be analyzed
X, Xn = Bfx_lbp(J, None, options) # LBP features
figure(2);
bar(np.arange(X.shape[1]), X[0, :])
Bio_printfeatures(X, Xn)
show()
Example 2:
import numpy as np
from balu.ImagesAndData import balu_imageload
from balu.FeatureExtraction import Bfx_lbp
from balu.InputOutput import Bio_printfeatures
from matplotlib.pyplot import bar, figure, show
options = {
'weight': 0, # Weigth of the histogram bins
'vdiv': 3, # one vertical divition
'hdiv': 3, # one horizontal divition
'samples': 8, # number of neighbor samples
'mappingtype': 'uniform' # uniform LBP
}
I = balu_imageload('testimg1.jpg') # input image
J = I[119:219, 119:239, 1] # region of interest (green)
figure(1)
imshow(J, cmap='gray') # image to be analyzed
X, Xn = Bfx_lbp(J, None, options) # LBP features
figure(2);
bar(np.arange(X.shape[1]), X[0, :])
Bio_printfeatures(X, Xn)
show()
See also Bfx_gabor, Bfx_clp, Bfx_fourier, Bfx_dct.
(c) GRIMA-DCCUC, 2011
http://grima.ing.puc.cl
With collaboration from:
Diego Patiño ([email protected]) -> Translated implementation into python (2017)
"""
if R is None:
R = np.ones(I.shape)
if 'show' not in options:
options['show'] = False
if 'normalize' not in options:
options['normalize'] = False
if options['show']:
print('--- extracting local binary patterns features...')
if 'samples' not in options:
options['samples'] = 8
if 'integral' not in options:
options['integral'] = False
if 'radius' not in options:
options['radius'] = np.log(options['samples']) / np.log(2.0) - 1
if 'weight' not in options:
options['weight'] = 0
LBPst = 'LBP'
if 'mappingtype' not in options:
options['mappingtype'] = 'nri_uniform'
if options['mappingtype'] == 'ror':
num_patterns = 256
elif options['mappingtype'] == 'uniform':
num_patterns = 10
elif options['mappingtype'] == 'nri_uniform':
num_patterns = 59
else:
options['mappingtype'] = 'default'
num_patterns = 256
st = '{0},{1}'.format(options['samples'], options['mappingtype'])
# Get lbp image
if R is not None:
I[np.where(R == 0)] = 0
radius = options['radius']
P = options['samples']
LBP = local_binary_pattern(I, P=P, R=radius, method=options['mappingtype'])
n1, n2 = LBP.shape
options['Ilbp'] = LBP
if options['integral']:
options['Hx'] = Bim_inthist(LBP, num_patterns)
vdiv = options['vdiv']
hdiv = options['hdiv']
modn1 = n1 % vdiv
if modn1 != 0:
LBP = np.concatenate((LBP.T, np.zeros((LBP.shape[1], vdiv - modn1))),
1).T
I = np.concatenate((I.T, np.zeros((I.shape[1], vdiv - modn1))), 1).T
modn2 = n2 % hdiv
if modn2 != 0:
LBP = np.concatenate((LBP, np.zeros((LBP.shape[0], hdiv - modn2))), 1)
I = np.concatenate((I, np.zeros((I.shape[0], hdiv - modn2))), 1)
n1, n2 = LBP.shape
ylen = int(np.round(n1 / vdiv))
xlen = int(np.round(n2 / hdiv))
# split image into blocks (saved as columns)
grid_img = view_as_blocks(LBP, block_shape=(ylen, xlen))
if options['weight'] > 0:
LBPst = 'w' + LBPst
mt = int(2 * radius - 1)
mt2 = float(mt**2)
Id = I.astype(int)
weight = options['weight']
if weight == 1:
W = np.abs(
convolve2d(Id, np.ones((mt, mt)) / mt2, mode='same') - Id)
elif weight == 2:
W = (np.abs(
convolve2d(Id, np.ones((mt, mt)) / mt2, mode='same') -
Id)) / (Id + 1)
elif weight == 3:
W = np.abs(median(Id, square(mt)) - Id)
elif weight == 4:
W = np.abs(median(Id, square(mt)) - Id) / (Id + 1)
elif weight == 5:
W = np.abs(order_filter(Id, np.ones((mt, mt)), 0) - Id)
elif weight == 6:
W = np.abs(order_filter(Id, np.ones((mt, mt)), 0) - Id) / (Id + 1)
elif weight == 7:
Id = convolve2d(Id, np.ones((mt, mt)) / mt2, mode='same')
W = np.abs(order_filter(Id, np.ones((mt, mt)), 0) - Id) / (Id + 1)
elif weight == 8:
Id = median(Id, square(mt))
W = np.abs(order_filter(Id, np.ones((mt, mt)), 0) - Id) / (Id + 1)
elif weight == 9:
Id = median(Id, square(mt))
W = np.abs(order_filter(Id, np.ones((mt, mt)), 1) - Id) / (Id + 1)
else:
print("Bfx_lbp does not recognize options['weight'] = {0}.".format(
options['weight']))
grid_W = view_as_blocks(W, block_shape=(ylen, xlen))
num_rows_blocks, num_cols_blocks = grid_W.shape[0:2]
desc = np.zeros((num_patterns, num_cols_blocks * num_rows_blocks))
p = 0
for br in range(num_rows_blocks):
for bc in range(num_cols_blocks):
x = grid_img[br, bc].astype(int).ravel()
y = grid_W[br, bc].ravel()
d = np.zeros(num_patterns)
for k in range(ylen * xlen):
d[x[k]] += y[k]
desc[:, p] = d
p += 1
else:
desc = (np.histogram(grid_img.ravel(), num_patterns)[0])[None]
# calculate coordinates of descriptors as if it was square w/ side=1
dx = 1.0 / float(hdiv)
dy = 1.0 / float(vdiv)
x = np.linspace(dx / 2.0, 1 - dx / 2.0, hdiv)
y = np.linspace(dy / 2.0, 1 - dy / 2.0, vdiv)
options['x'] = x
options['y'] = y
D = desc.T
M, N = D.shape
Xn = (N * M) * [None]
X = np.zeros((1, N * M))
k = 0
for i in range(M):
for j in range(N):
Xn[k] = '{0}({1},{2})[{3}] '.format(
LBPst, i, j, st)
X[0, k] = D[i, j]
k += 1
if options['normalize']:
X = X / np.sum(X)
return X, Xn
plt.savefig(path + '/outlines/' + input_no_ext + '.jpg')
plt.close()
path = sys.argv[1]
input_images = sorted([f for f in os.listdir(path) if f.endswith('.tif')])
print(input_images)
mask_images = sorted([f for f in os.listdir(path) if f.endswith('ties_.png')])
all_dfs = []
print('Paths are correct')
for image_name, mask_name in zip(input_images, mask_images) :
mask= io.imread(path +'/' + mask_name, as_gray = True)
mask_bw = rgb2gray(mask)
thresh = threshold_otsu(mask_bw)
bw = closing(mask_bw > thresh, square(3))
cleared = clear_border(bw)
label_image = measure.label(cleared)
area = []
length = []
width = []
solidity = []
centroid = []
for region in measure.regionprops(label_image):
area.append(region.area)
length.append(region.major_axis_length)
width.append(region.minor_axis_length)
solidity.append(region.solidity)
centroid.append(region.centroid)
def boundary_mask(footprint_msk=None,
out_file=None,
reference_im=None,
boundary_width=3,
boundary_type='inner',
burn_value=255,
**kwargs):
"""Convert a dataframe of geometries to a pixel mask.
Note
----
This function requires creation of a footprint mask before it can operate;
therefore, if there is no footprint mask already present, it will create
one. In that case, additional arguments for :func:`footprint_mask` (e.g.
``df``) must be passed.
By default, this function draws boundaries *within* the edges of objects.
To change this behavior, use the `boundary_type` argument.
Arguments
---------
footprint_msk : :class:`numpy.array`, optional
A filled in footprint mask created using :func:`footprint_mask`. If not
provided, one will be made by calling :func:`footprint_mask` before
creating the boundary mask, and the required arguments for that
function must be provided as kwargs.
out_file : str, optional
Path to an image file to save the output to. Must be compatible with
:class:`rasterio.DatasetReader`. If provided, a `reference_im` must be
provided (for metadata purposes).
reference_im : :class:`rasterio.DatasetReader` or `str`, optional
An image to extract necessary coordinate information from: the
affine transformation matrix, the image extent, etc. If provided,
`affine_obj` and `shape` are ignored
boundary_width : int, optional
The width of the boundary to be created **in pixels.** Defaults to 3.
boundary_type : ``"inner"`` or ``"outer"``, optional
Where to draw the boundaries: within the object (``"inner"``) or
outside of it (``"outer"``). Defaults to ``"inner"``.
burn_value : `int`, optional
The value to use for labeling objects in the mask. Defaults to 255 (the
max value for ``uint8`` arrays). The mask array will be set to the same
dtype as `burn_value`. Ignored if `burn_field` is provided.
**kwargs : optional
Additional arguments to pass to :func:`footprint_mask` if one needs to
be created.
Returns
-------
boundary_mask : :class:`numpy.array`
A pixel mask with 0s for non-object pixels and the same value as the
footprint mask `burn_value` for the boundaries of each object.
"""
if out_file and not reference_im:
raise ValueError(
'If saving output to file, `reference_im` must be provided.')
if reference_im:
reference_im = _check_rasterio_im_load(reference_im)
# need to have a footprint mask for this function, so make it if not given
if footprint_msk is None:
footprint_msk = footprint_mask(reference_im=reference_im,
burn_value=burn_value,
**kwargs)
# perform dilation or erosion of `footprint_mask` to get the boundary
strel = square(boundary_width)
if boundary_type == 'outer':
boundary_mask = dilation(footprint_msk, strel)
elif boundary_type == 'inner':
boundary_mask = erosion(footprint_msk, strel)
# use xor operator between border and footprint mask to get _just_ boundary
boundary_mask = boundary_mask ^ footprint_msk
# scale the `True` values to burn_value and return
boundary_mask = boundary_mask > 0 # need to binarize to get burn val right
output_arr = boundary_mask.astype('uint8') * burn_value
if out_file:
meta = reference_im.meta.copy()
meta.update(count=1)
meta.update(dtype='uint8')
with rasterio.open(out_file, 'w', **meta) as dst:
dst.write(output_arr, indexes=1)
return output_arr
F = I[1525:3000, 1450:1800]
imshow(F, cmap='gray')
show()
print("imagen recortada binarizada")
borde2 = sobel(F, mask=None)
Z = (borde2 > 0.1).astype('uint32')
imshow(Z, cmap='gray')
show()
plt.hist(borde2.ravel(), 256, [0, 1])
plt.show()
selSquare = square(14)
selDisk = disk(12)
selRectangle = rectangle(6, 20)
IDilationSquare = dilation(Z, selem=selSquare)
#imshow(IDilationSquare, cmap='gray')
#show()
IDilationDisk = dilation(Z, selem=selDisk)
#imshow(IDilationDisk, cmap='gray')
#show()
IDilationRectangle = dilation(Z, selem=selRectangle)
imshow(IDilationRectangle, cmap='gray')
show()
IClosingSquare = closing(IDilationDisk, selem=selSquare)
#imshow(IClosingSquare, cmap='gray')
def optimalThreshold(self,
color_im,
method='r_small_objects',
remove_spots=True,
level=200,
debug=True):
im = cv2.cvtColor(color_im, cv2.COLOR_BGR2GRAY)
ret, thresh = cv2.threshold(im, 0, 255,
cv2.THRESH_BINARY + cv2.THRESH_OTSU)
if debug:
cv2.imwrite('binary.jpg', thresh)
thresh = filters.median(thresh, morphology.square(7))
cv2.imwrite('binary_med.jpg', thresh)
#MORPHOLOGICAL_REMOVE_SMALL_OBJECTS
imglab = morphology.label(thresh) # create labels in segmented image
min_s = (int)(im.shape[0])
try:
cleaned = morphology.remove_small_objects(imglab,
min_size=min_s,
connectivity=8)
except UserWarning:
pass
res_small = np.zeros((cleaned.shape)) # create array of size cleaned
res_small[cleaned > 0] = 255
res_small = np.uint8(res_small)
if debug:
cv2.imwrite("cleaned.jpg", res_small)
#MORPOLOGICAL_OPENING_OPENCV
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (32, 32))
opened_mask = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
if debug:
cv2.imwrite("opened_mask.jpg", opened_mask)
if remove_spots:
blurred = cv2.GaussianBlur(im, (11, 11), 0)
spots = cv2.threshold(blurred, level, 255, cv2.THRESH_BINARY)[1]
res_small = res_small - spots
opened_mask = opened_mask - spots
if debug:
cv2.imwrite("cleaned_spots.jpg", res_small)
cv2.imwrite("opened_mask_spots.jpg", opened_mask)
img, contours, h = cv2.findContours(res_small, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
max_c = []
max_a = 0
result = np.zeros(img.shape)
for contour in contours:
if cv2.contourArea(contour) > max_a:
max_c = contour
max_a = cv2.contourArea(contour)
bouding = cv2.boundingRect(max_c)
print(bouding)
if debug:
masked_img = cv2.bitwise_and(color_im, color_im, mask=opened_mask)
masked_img2 = cv2.bitwise_and(color_im, color_im, mask=res_small)
cv2.imwrite("masked_img.jpg", masked_img)
cv2.imwrite("masked_img_small.jpg", masked_img2)
min_x = bouding[1]
min_y = bouding[0]
w_x = bouding[1] + bouding[3]
h_y = bouding[0] + bouding[2]
return res_small, min_x, min_y, w_x, h_y
def binary_image(folder, image_file, threshold=2, figsize=(10, 10),
ajar=False, close=False, show=False,
channel=None, imname=None):
"""Create binary image from input image with optional opening step.
Parameters
----------
folder : string
Directory containing image_file
image_file : string
Filename of image to be analyzed.
threshold : int or float
Intensity threshold of binary image.
figsize : tuple of int or float
Size of output figure.
ajar : bool
If True, opens binary image by performing a dilation followed by
an erosion.
close : bool
If True, closes binary image by performing an erosion followed by a
dilation.
show : bool
If True, outputs image to Jupyter notebook display.
channel : int
Channel of image to read in for multichannel images e.g.
testim[:, :, channel]
imname : string
Desired name of output file. Defaults to 'test.png'.
Returns
-------
op_image : numpy.ndarray
Output image.
Examples
--------
"""
fname = '{}/{}'.format(folder, image_file)
if channel is None:
test_image = sio.imread(fname)
else:
test_image = sio.imread(fname)[:, :, channel]
bi_image = test_image > threshold
if ajar is True:
op_image = opening(bi_image, square(3))
else:
op_image = bi_image
if close is True:
op_image = closing(op_image, square(3))
if show:
fig, ax = plt.subplots(figsize=figsize)
ax.imshow(op_image, cmap='gray')
ax.axis('off')
op_image = op_image.astype('uint8')*255
if imname is None:
output = "clean_{}".format(image_file)
else:
output = imname
sio.imsave('{}/{}'.format(folder, output), op_image)
return op_image
def remove_background(self, method, *args, **kwargs):
"""Perform background subtraction via multiple methods.
Parameters
----------
method : string
Specify the method used to determine the direct beam position.
* 'h-dome' -
* 'gaussian_difference' - Uses a difference between two gaussian
convolutions to determine where the peaks are,
and sets all other pixels to 0.
* 'median' - Use a median filter for background removal
* 'reference_pattern' - Subtract a user-defined reference patterns
from every diffraction pattern.
sigma_min : int, float
Standard deviation for the minimum gaussian convolution
(gaussian_difference only)
sigma_max : int, float
Standard deviation for the maximum gaussian convolution
(gaussian_difference only)
footprint : int
Size of the window that is convoluted with the array to determine
the median. Should be large enough that it is about 3x as big as the
size of the peaks (median only).
implementation : 'scipy' or 'skimage'
(median only) see expt_utils.subtract_background_median
for details, if not selected 'scipy' is used
bg : array
Background array extracted from vacuum. (subtract_reference only)
*args:
Arguments to be passed to map().
**kwargs:
Keyword arguments to be passed to map().
Returns
-------
bg_subtracted : :obj:`ElectronDiffraction2D`
A copy of the data with the background subtracted. Be aware that
this function will only return inplace.
"""
if method == 'h-dome':
scale = self.data.max()
self.data = self.data / scale
bg_subtracted = self.map(regional_filter,
inplace=False,
*args,
**kwargs)
bg_subtracted.map(filters.rank.mean, selem=square(3))
bg_subtracted.data = bg_subtracted.data / bg_subtracted.data.max()
elif method == 'gaussian_difference':
bg_subtracted = self.map(subtract_background_dog,
inplace=False,
*args,
**kwargs)
elif method == 'median':
if 'implementation' in kwargs.keys():
if kwargs['implementation'] != 'scipy' and kwargs[
'implementation'] != 'skimage':
raise NotImplementedError(
"Unknown implementation `{}`".format(
kwargs['implementation']))
bg_subtracted = self.map(subtract_background_median,
inplace=False,
*args,
**kwargs)
elif method == 'reference_pattern':
bg_subtracted = self.map(subtract_reference,
inplace=False,
*args,
**kwargs)
else:
raise NotImplementedError(
"The method specified, '{}', is not implemented. See"
"documentation for available implementations.".format(method))
return bg_subtracted
def clean_image(folder, image_file, threshold=2, figsize=(10, 10),
ajar=False, close=False, show=False,
area_thresh=50, channel=None, imname=None):
"""Create binary image from input image with optional opening step.
Parameters
----------
folder : string
Directory containing image_file
image_file : string
Filename of image to be analyzed.
threshold : int or float
Intensity threshold of binary image.
figsize : tuple of int or float
Size of output figure.
ajar : bool
If True, opens binary image by performing a dilation followed by
an erosion.
close : bool
If True, closes binary image by performing an erosion followed by a
dilation.
show : bool
If True, outputs image to Jupyter notebook display.
area_thresh : int or float
Minimum square pixels for object to be included in final image.
channel : int
Channel of image to read in for multichannel images e.g.
testim[:, :, channel]
imname : string
Desired name of output file. Defaults to 'test.png'.
Returns
-------
short_image : numpy.ndarray
Output binary image. All small objects (area < area_thresh) are
filtered out.
short_props : skimage.object
Contains all properties of objects identified in image.
Examples
--------
"""
fname = '{}/{}'.format(folder, image_file)
if channel is None:
test_image = sio.imread(fname)
else:
test_image = sio.imread(fname)[:, :, channel]
bi_image = test_image > threshold
if ajar is True:
op_image = opening(bi_image, square(3))
else:
op_image = bi_image
if close is True:
op_image = closing(op_image, square(3))
op_image = op_image.astype('uint8')*255
# if default_name:
# output = "clean_{}.png".format(image_file.split('.')[0])
# else:
# output = fname
# sio.imsave(folder+'/'+output, op_image)
# Labelling and cleaning up image.
test_image = op_image
labels = label(test_image)
props = regionprops(labels)
short_image = np.zeros(labels.shape)
counter = 0
skip = 0
short_props = []
for i in range(0, len(props)):
area = props[i]['area']
if area < area_thresh:
skip = skip + 1
else:
short_props.append(props[i])
test_coords = props[i]['coords'].tolist()
for coord in test_coords:
short_image[coord[0], coord[1]] = True
counter = counter + 1
if show:
fig, ax = plt.subplots(figsize=figsize)
ax.imshow(short_image, cmap='gray')
ax.axis('off')
short_image = short_image.astype('uint8')*255
if imname is None:
output = "short_{}".format(image_file)
else:
output = imname
sio.imsave(folder+'/'+output, short_image)
return short_image, short_props
def dilation(img):
# return greyscale morphological dilation of an image
return mp.dilation(img, mp.square(2, dtype=np.uint8))
def merge_overlapping_images(metadata, inputs):
"""
Merge simultaneous overlapping images that cover the area of interest.
When the area of interest is located at the boundary between 2 images, there
will be overlap between the 2 images and both will be downloaded from Google
Earth Engine. This function merges the 2 images, so that the area of interest
is covered by only 1 image.
KV WRL 2018
Arguments:
-----------
metadata: dict
contains all the information about the satellite images that were downloaded
inputs: dict with the following keys
'sitename': str
name of the site
'polygon': list
polygon containing the lon/lat coordinates to be extracted,
longitudes in the first column and latitudes in the second column,
there are 5 pairs of lat/lon with the fifth point equal to the first point:
```
polygon = [[[151.3, -33.7],[151.4, -33.7],[151.4, -33.8],[151.3, -33.8],
[151.3, -33.7]]]
```
'dates': list of str
list that contains 2 strings with the initial and final dates in
format 'yyyy-mm-dd':
```
dates = ['1987-01-01', '2018-01-01']
```
'sat_list': list of str
list that contains the names of the satellite missions to include:
```
sat_list = ['L5', 'L7', 'L8', 'S2']
```
'filepath_data': str
filepath to the directory where the images are downloaded
Returns:
-----------
metadata_updated: dict
updated metadata
"""
# only for Sentinel-2 at this stage (not sure if this is needed for Landsat images)
sat = 'S2'
filepath = os.path.join(inputs['filepath'], inputs['sitename'])
filenames = metadata[sat]['filenames']
# find the pairs of images that are within 5 minutes of each other
time_delta = 5 * 60 # 5 minutes in seconds
dates = metadata[sat]['dates'].copy()
pairs = []
for i, date in enumerate(metadata[sat]['dates']):
# dummy value so it does not match it again
dates[i] = pytz.utc.localize(datetime(1, 1, 1) + timedelta(days=i + 1))
# calculate time difference
time_diff = np.array(
[np.abs((date - _).total_seconds()) for _ in dates])
# find the matching times and add to pairs list
boolvec = time_diff <= time_delta
if np.sum(boolvec) == 0:
continue
else:
idx_dup = np.where(boolvec)[0][0]
pairs.append([i, idx_dup])
# because they could be triplicates in S2 images, adjust the pairs for consecutive merges
for i in range(1, len(pairs)):
if pairs[i - 1][1] == pairs[i][0]:
pairs[i][0] = pairs[i - 1][0]
# for each pair of image, first check if one image completely contains the other
# in that case keep the larger image. Otherwise merge the two images.
for i, pair in enumerate(pairs):
# get filenames of all the files corresponding to the each image in the pair
fn_im = []
for index in range(len(pair)):
fn_im.append([
os.path.join(filepath, 'S2', '10m', filenames[pair[index]]),
os.path.join(filepath, 'S2', '20m',
filenames[pair[index]].replace('10m', '20m')),
os.path.join(filepath, 'S2', '60m',
filenames[pair[index]].replace('10m', '60m')),
os.path.join(
filepath, 'S2', 'meta',
filenames[pair[index]].replace('_10m',
'').replace('.tif', '.txt'))
])
# get polygon for first image
polygon0 = SDS_tools.get_image_bounds(fn_im[0][0])
im_epsg0 = metadata[sat]['epsg'][pair[0]]
# get polygon for second image
polygon1 = SDS_tools.get_image_bounds(fn_im[1][0])
im_epsg1 = metadata[sat]['epsg'][pair[1]]
# check if epsg are the same
if not im_epsg0 == im_epsg1:
print(
'WARNING: there was an error as two S2 images do not have the same epsg,'
+
' please open an issue on Github at https://github.com/kvos/CoastSat/issues'
+ ' and include your script so we can find out what happened.')
break
# check if one image contains the other one
if polygon0.contains(polygon1):
# if polygon0 contains polygon1, remove files for polygon1
for k in range(4): # remove the 3 .tif files + the .txt file
os.chmod(fn_im[1][k], 0o777)
os.remove(fn_im[1][k])
# print('removed 1')
continue
elif polygon1.contains(polygon0):
# if polygon1 contains polygon0, remove image0
for k in range(4): # remove the 3 .tif files + the .txt file
os.chmod(fn_im[0][k], 0o777)
os.remove(fn_im[0][k])
# print('removed 0')
# adjust the order in case of triplicates
if i + 1 < len(pairs):
if pairs[i + 1][0] == pair[0]: pairs[i + 1][0] = pairs[i][1]
continue
# otherwise merge the two images after masking the nodata values
else:
for index in range(len(pair)):
# read image
im_ms, georef, cloud_mask, im_extra, im_QA, im_nodata = SDS_preprocess.preprocess_single(
fn_im[index], sat, False)
# in Sentinel2 images close to the edge of the image there are some artefacts,
# that are squares with constant pixel intensities. They need to be masked in the
# raster (GEOTIFF). It can be done using the image standard deviation, which
# indicates values close to 0 for the artefacts.
if len(im_ms) > 0:
# calculate image std for the first 10m band
im_std = SDS_tools.image_std(im_ms[:, :, 0], 1)
# convert to binary
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
# dilate to fill the edges (which have high std)
mask10 = morphology.dilation(im_binary,
morphology.square(3))
# mask the 10m .tif file (add no_data where mask is True)
SDS_tools.mask_raster(fn_im[index][0], mask10)
# now calculate the mask for the 20m band (SWIR1)
# for the older version of the ee api calculate the image std again
if int(ee.__version__[-3:]) <= 201:
# calculate std to create another mask for the 20m band (SWIR1)
im_std = SDS_tools.image_std(im_extra, 1)
im_binary = np.logical_or(im_std < 1e-6,
np.isnan(im_std))
mask20 = morphology.dilation(im_binary,
morphology.square(3))
# for the newer versions just resample the mask for the 10m bands
else:
# create mask for the 20m band (SWIR1) by resampling the 10m one
mask20 = ndimage.zoom(mask10, zoom=1 / 2, order=0)
mask20 = transform.resize(mask20,
im_extra.shape,
mode='constant',
order=0,
preserve_range=True)
mask20 = mask20.astype(bool)
# mask the 20m .tif file (im_extra)
SDS_tools.mask_raster(fn_im[index][1], mask20)
# create a mask for the 60m QA band by resampling the 20m one
mask60 = ndimage.zoom(mask20, zoom=1 / 3, order=0)
mask60 = transform.resize(mask60,
im_QA.shape,
mode='constant',
order=0,
preserve_range=True)
mask60 = mask60.astype(bool)
# mask the 60m .tif file (im_QA)
SDS_tools.mask_raster(fn_im[index][2], mask60)
# make a figure for quality control/debugging
# im_RGB = SDS_preprocess.rescale_image_intensity(im_ms[:,:,[2,1,0]], cloud_mask, 99.9)
# fig,ax= plt.subplots(2,3,tight_layout=True)
# ax[0,0].imshow(im_RGB)
# ax[0,0].set_title('RGB original')
# ax[1,0].imshow(mask10)
# ax[1,0].set_title('Mask 10m')
# ax[0,1].imshow(mask20)
# ax[0,1].set_title('Mask 20m')
# ax[1,1].imshow(mask60)
# ax[1,1].set_title('Mask 60 m')
# ax[0,2].imshow(im_QA)
# ax[0,2].set_title('Im QA')
# ax[1,2].imshow(im_nodata)
# ax[1,2].set_title('Im nodata')
else:
continue
# once all the pairs of .tif files have been masked with no_data, merge the using gdal_merge
fn_merged = os.path.join(filepath, 'merged.tif')
for k in range(3):
# merge masked bands
gdal_merge.main(
['', '-o', fn_merged, '-n', '0', fn_im[0][k], fn_im[1][k]])
# remove old files
os.chmod(fn_im[0][k], 0o777)
os.remove(fn_im[0][k])
os.chmod(fn_im[1][k], 0o777)
os.remove(fn_im[1][k])
# rename new file
fn_new = fn_im[0][k].split('.')[0] + '_merged.tif'
os.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_new)
# open both metadata files
metadict0 = dict([])
with open(fn_im[0][3], 'r') as f:
metadict0['filename'] = f.readline().split('\t')[1].replace(
'\n', '')
metadict0['acc_georef'] = float(
f.readline().split('\t')[1].replace('\n', ''))
metadict0['epsg'] = int(f.readline().split('\t')[1].replace(
'\n', ''))
metadict1 = dict([])
with open(fn_im[1][3], 'r') as f:
metadict1['filename'] = f.readline().split('\t')[1].replace(
'\n', '')
metadict1['acc_georef'] = float(
f.readline().split('\t')[1].replace('\n', ''))
metadict1['epsg'] = int(f.readline().split('\t')[1].replace(
'\n', ''))
# check if both images have the same georef accuracy
if np.any(
np.array([
metadict0['acc_georef'], metadict1['acc_georef']
]) == -1):
metadict0['georef'] = -1
# add new name
metadict0['filename'] = metadict0['filename'].split(
'.')[0] + '_merged.tif'
# remove the old metadata.txt files
os.chmod(fn_im[0][3], 0o777)
os.remove(fn_im[0][3])
os.chmod(fn_im[1][3], 0o777)
os.remove(fn_im[1][3])
# rewrite the .txt file with a new metadata file
fn_new = fn_im[0][3].split('.')[0] + '_merged.txt'
with open(fn_new, 'w') as f:
for key in metadict0.keys():
f.write('%s\t%s\n' % (key, metadict0[key]))
# update filenames list (in case there are triplicates)
filenames[pair[0]] = metadict0['filename']
print(
'%d out of %d Sentinel-2 images were merged (overlapping or duplicate)'
% (len(pairs), len(filenames)))
# update the metadata dict
metadata_updated = get_metadata(inputs)
return metadata_updated
draw.set_color(img,[rr,cc],[255,0,0])
plt.imshow(img,plt.cm.gray)
'''8、空心椭圆'''
plt.subplot(428)
plt.title('hollow ellipse')
img=data.chelsea()
rr, cc=draw.ellipse_perimeter(150, 150, 30, 80)
draw.set_color(img,[rr,cc],[255,0,0])
plt.imshow(img,plt.cm.gray)
plt.show()
# =============================================================================
print('''十一、基本形态学滤波''')
# =============================================================================
img=data.checkerboard()
'''1、膨胀（dilation)'''
dst1=sm.dilation(img,sm.square(5)) #用边长为5的正方形滤波器进行膨胀滤波
dst2=sm.dilation(img,sm.square(15)) #用边长为15的正方形滤波器进行膨胀滤波
fig = plt.figure('morphology',figsize=(12,4))
fig.suptitle('dilation')
plt.subplot(131)
plt.title('origin image')
plt.imshow(img,plt.cm.gray)
plt.subplot(132)
plt.title('morphological image')
plt.imshow(dst1,plt.cm.gray)
plt.subplot(133)
plt.title('morphological image')
plt.imshow(dst2,plt.cm.gray)
plt.show()
'''2、腐蚀（erosion)'''
dst1=sm.erosion(img,sm.square(5)) #用边长为5的正方形滤波器进行膨胀滤波
def merge_overlapping_images(metadata, inputs):
"""
Merge simultaneous overlapping images that cover the area of interest.
When the area of interest is located at the boundary between 2 images, there
will be overlap between the 2 images and both will be downloaded from Google
Earth Engine. This function merges the 2 images, so that the area of interest
is covered by only 1 image.
KV WRL 2018
Arguments:
-----------
metadata: dict
contains all the information about the satellite images that were downloaded
inputs: dict with the following keys
'sitename': str
name of the site
'polygon': list
polygon containing the lon/lat coordinates to be extracted,
longitudes in the first column and latitudes in the second column,
there are 5 pairs of lat/lon with the fifth point equal to the first point:
```
polygon = [[[151.3, -33.7],[151.4, -33.7],[151.4, -33.8],[151.3, -33.8],
[151.3, -33.7]]]
```
'dates': list of str
list that contains 2 strings with the initial and final dates in
format 'yyyy-mm-dd':
```
dates = ['1987-01-01', '2018-01-01']
```
'sat_list': list of str
list that contains the names of the satellite missions to include:
```
sat_list = ['L5', 'L7', 'L8', 'S2']
```
'filepath_data': str
filepath to the directory where the images are downloaded
Returns:
-----------
metadata_updated: dict
updated metadata
"""
# only for Sentinel-2 at this stage (not sure if this is needed for Landsat images)
sat = 'S2'
filepath = os.path.join(inputs['filepath'], inputs['sitename'])
filenames = metadata[sat]['filenames']
# find the pairs of images that are within 5 minutes of each other
time_delta = 5 * 60 # 5 minutes in seconds
dates = metadata[sat]['dates'].copy()
pairs = []
for i, date in enumerate(metadata[sat]['dates']):
# dummy value so it does not match it again
dates[i] = pytz.utc.localize(datetime(1, 1, 1) + timedelta(days=i + 1))
# calculate time difference
time_diff = np.array(
[np.abs((date - _).total_seconds()) for _ in dates])
# find the matching times and add to pairs list
boolvec = time_diff <= time_delta
if np.sum(boolvec) == 0:
continue
else:
idx_dup = np.where(boolvec)[0][0]
pairs.append([i, idx_dup])
# for each pair of image, create a mask and add no_data into the .tif file (this is needed before merging .tif files)
for i, pair in enumerate(pairs):
fn_im = []
for index in range(len(pair)):
# get filenames of all the files corresponding to the each image in the pair
fn_im.append([
os.path.join(filepath, 'S2', '10m', filenames[pair[index]]),
os.path.join(filepath, 'S2', '20m',
filenames[pair[index]].replace('10m', '20m')),
os.path.join(filepath, 'S2', '60m',
filenames[pair[index]].replace('10m', '60m')),
os.path.join(
filepath, 'S2', 'meta',
filenames[pair[index]].replace('_10m',
'').replace('.tif', '.txt'))
])
# read that image
im_ms, georef, cloud_mask, im_extra, im_QA, im_nodata = SDS_preprocess.preprocess_single(
fn_im[index], sat, False)
# im_RGB = SDS_preprocess.rescale_image_intensity(im_ms[:,:,[2,1,0]], cloud_mask, 99.9)
# in Sentinel2 images close to the edge of the image there are some artefacts,
# that are squares with constant pixel intensities. They need to be masked in the
# raster (GEOTIFF). It can be done using the image standard deviation, which
# indicates values close to 0 for the artefacts.
if len(im_ms) > 0:
# calculate image std for the first 10m band
im_std = SDS_tools.image_std(im_ms[:, :, 0], 1)
# convert to binary
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
# dilate to fill the edges (which have high std)
mask10 = morphology.dilation(im_binary, morphology.square(3))
# mask all 10m bands
for k in range(im_ms.shape[2]):
im_ms[mask10, k] = np.nan
# mask the 10m .tif file (add no_data where mask is True)
SDS_tools.mask_raster(fn_im[index][0], mask10)
# create another mask for the 20m band (SWIR1)
im_std = SDS_tools.image_std(im_extra, 1)
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
mask20 = morphology.dilation(im_binary, morphology.square(3))
im_extra[mask20] = np.nan
# mask the 20m .tif file (im_extra)
SDS_tools.mask_raster(fn_im[index][1], mask20)
# use the 20m mask to create a mask for the 60m QA band (by resampling)
mask60 = ndimage.zoom(mask20, zoom=1 / 3, order=0)
mask60 = transform.resize(mask60,
im_QA.shape,
mode='constant',
order=0,
preserve_range=True)
mask60 = mask60.astype(bool)
# mask the 60m .tif file (im_QA)
SDS_tools.mask_raster(fn_im[index][2], mask60)
else:
continue
# make a figure for quality control
# fig,ax= plt.subplots(2,2,tight_layout=True)
# ax[0,0].imshow(im_RGB)
# ax[0,0].set_title('RGB original')
# ax[1,0].imshow(mask10)
# ax[1,0].set_title('Mask 10m')
# ax[0,1].imshow(mask20)
# ax[0,1].set_title('Mask 20m')
# ax[1,1].imshow(mask60)
# ax[1,1].set_title('Mask 60 m')
# once all the pairs of .tif files have been masked with no_data, merge the using gdal_merge
fn_merged = os.path.join(filepath, 'merged.tif')
# merge masked 10m bands and remove duplicate file
gdal_merge.main(
['', '-o', fn_merged, '-n', '0', fn_im[0][0], fn_im[1][0]])
os.chmod(fn_im[0][0], 0o777)
os.remove(fn_im[0][0])
os.chmod(fn_im[1][0], 0o777)
os.remove(fn_im[1][0])
os.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_im[0][0])
# merge masked 20m band (SWIR band)
gdal_merge.main(
['', '-o', fn_merged, '-n', '0', fn_im[0][1], fn_im[1][1]])
os.chmod(fn_im[0][1], 0o777)
os.remove(fn_im[0][1])
os.chmod(fn_im[1][1], 0o777)
os.remove(fn_im[1][1])
os.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_im[0][1])
# merge QA band (60m band)
gdal_merge.main(
['', '-o', fn_merged, '-n', '0', fn_im[0][2], fn_im[1][2]])
os.chmod(fn_im[0][2], 0o777)
os.remove(fn_im[0][2])
os.chmod(fn_im[1][2], 0o777)
os.remove(fn_im[1][2])
os.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_im[0][2])
# remove the metadata .txt file of the duplicate image
os.chmod(fn_im[1][3], 0o777)
os.remove(fn_im[1][3])
print('%d pairs of overlapping Sentinel-2 images were merged' % len(pairs))
# update the metadata dict
metadata_updated = copy.deepcopy(metadata)
idx_removed = []
idx_kept = []
for pair in pairs:
idx_removed.append(pair[1])
for idx in np.arange(0, len(metadata[sat]['dates'])):
if not idx in idx_removed: idx_kept.append(idx)
for key in metadata_updated[sat].keys():
metadata_updated[sat][key] = [
metadata_updated[sat][key][_] for _ in idx_kept
]
return metadata_updated
def main():
parser=argparse.ArgumentParser(description='Image-file processing to identify total number of droplets',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input_image', type=str,
help='input image file')
parser.add_argument('template_image', type=str,
help='template image file')
parser.add_argument('--outfile', type=str,
help='output image name. Will default to input_image_processed.png')
parser.add_argument('--cutoff_area', type=int,
help='rectangle size. only detected rectangles above this size will be displayed')
parser.add_argument('--include', action='store_true', dest="include_edge",
help='Include edge or boundary or border droplets; incomplete droplets found on the edge of the picture will be included too.')
parser.add_argument("--exclude", action="store_false", dest="include_edge",
help='Exclude edge or boundary or border droplets; incomplete droplets found on the edge of the picture will be excluded.')
parser.add_argument('--threshold', type=float, default=0.6,
help='thresholding parameter, tweak from 0 to 1 and visually examine results, depends on the image, default is 0.6')
args=parser.parse_args()
if args.outfile==None:
args.outfile=''.join([path.splitext(args.input_image)[0],"_border_",str(args.include_edge),'_processed']) ## leaving out the file extension; adding it later just before writing out the image file
filename=args.input_image
rectsize=args.cutoff_area
print "...."
print "image file being processed..."
print "..."
from skimage import img_as_float
image = io.imread(filename, flatten=True) # conver 3d to 2d image by using flatten=True
image = img_as_float(image)
#io.imshow(image) ## check the image
#io.show() ## check the image
from skimage.color import rgb2gray
img_gray = rgb2gray(image)
#io.imshow(img_gray) ## check the image
#io.show() ## check the image
image = gaussian_filter(image, 1)
seed = np.copy(image)
seed[1:-1, 1:-1] = image.min()
mask = image
dilated = reconstruction(seed, mask, method='dilation')
"""
fig, (ax0, ax1, ax2) = plt.subplots(nrows=1,
ncols=3,
figsize=(8, 2.5),
sharex=True,
sharey=True)
ax0.imshow(image, cmap='gray')
ax0.set_title('original image')
ax0.axis('off')
ax0.set_adjustable('box-forced')
ax1.imshow(dilated, vmin=image.min(), vmax=image.max(), cmap='gray')
ax1.set_title('dilated')
ax1.axis('off')
ax1.set_adjustable('box-forced')
ax2.imshow(image - dilated, cmap='gray')
ax2.set_title('image - dilated')
ax2.axis('off')
ax2.set_adjustable('box-forced')
fig.tight_layout()
"""
print "...."
print "background correction..."
print "..."
h = 0.4
seed = image - h
dilated = reconstruction(seed, mask, method='dilation')
hdome = image - dilated
#io.imshow(hdome) ## check the image
#io.show() ## check the image
"""
fig, (ax0, ax1, ax2) = plt.subplots(nrows=1, ncols=3, figsize=(8, 2.5))
yslice = 197
ax0.plot(mask[yslice], '0.5', label='mask')
ax0.plot(seed[yslice], 'k', label='seed')
ax0.plot(dilated[yslice], 'r', label='dilated')
ax0.set_ylim(-0.2, 2)
ax0.set_title('image slice')
ax0.set_xticks([])
ax0.legend()
ax1.imshow(dilated, vmin=image.min(), vmax=image.max(), cmap='gray')
ax1.axhline(yslice, color='r', alpha=0.4)
ax1.set_title('dilated')
ax1.axis('off')
ax2.imshow(hdome, cmap='gray')
ax2.axhline(yslice, color='r', alpha=0.4)
ax2.set_title('image - dilated')
ax2.axis('off')
fig.tight_layout()
plt.show()
"""
print "...."
print "edge detection..."
print "..."
im = hdome
edges1 = feature.canny(image, sigma=3)
edges2 = feature.canny(im, sigma=3)
#io.imshow(edges1) ## check the image
#io.show() ## check the image
#io.imshow(edges2) ## check the image
#io.show() ## check the image
"""
# display results
fig, (ax1, ax2, ax3) = plt.subplots(nrows=1, ncols=3, figsize=(8, 3),
sharex=True, sharey=True)
ax1.imshow(im, cmap=plt.cm.gray)
ax1.axis('off')
ax1.set_title('Original image', fontsize=10)
ax2.imshow(edges1, cmap=plt.cm.gray)
ax2.axis('off')
ax2.set_title('Canny filter on original image, $\sigma=3$', fontsize=10)
ax3.imshow(edges2, cmap=plt.cm.gray)
ax3.axis('off')
ax3.set_title('Canny filter on background subtracted image, $\sigma=3$', fontsize=10)
fig.tight_layout()
plt.show()
"""
#
### check how good are the original and processed images by selecting corresponding image here
#
image=image
#image=edges2
#image=hdome
## apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(2))
#io.imshow(bw) ## check the image
#io.show() ## check the image
print "... are we including incomplete droplets at the edge of image?..."
print ".............................................................", args.include_edge
if args.include_edge is False:
## remove artifacts connected to image border
cleared = clear_border(bw) ## use this option to avoid the incomplete droplets at boundary/edge of picture frame
else:
cleared = bw ## use this to use all droplets in the image; even incomplete ones at the boundary/edge of pciture frame
#io.imshow(cleared) ## check the image
#io.show() ## check the image
# label image regions
label_image = label(cleared)
image_label_overlay = label2rgb(label_image, image=image)
#io.imshow(image_label_overlay) ## check the image
#io.show() ## check the image
fig, ax = plt.subplots(figsize=(10, 6))
#ax.imshow(label_image)
#ax.imshow(image_label_overlay)
targetimagefile=args.input_image
templateimagefile=args.template_image
thresholdval=args.threshold
beads_count=0
droplet_count=0
outfile=0
for region in regionprops(label_image):
# take regions with large enough areas; should correspond to droplets
if region.area >= rectsize:
# draw rectangle around segmented droplets
droplet_count=droplet_count+1
minr, minc, maxr, maxc = region.bbox
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='yellow', linewidth=2)
#print region.bbox
try:
crop_image = image[minr-50:maxr+50, minc-50:maxc+50] ## offset the bounding box in all directions; seems better this way based on visual examination
except ValueError: #raised if this subtraction takes it out of bounds
pass
finally:
crop_image = image[minr:maxr, minc:maxc]
#io.imshow(crop_image) ## check the image
#io.show() ## check the image
outfile=outfile+1
## improve this and instead of passing file names of whole images to the findtemplate function
## pass the cropped image that already exists here
## for now, not changing too drastically on something that works
## slow tweaks ensuring what works functionally well doesnt break down
beads=findtemplate(templateimagefile, targetimagefile, region.bbox, outfile, thresholdval)
ax.add_patch(rect)
ax.set_axis_off()
plt.tight_layout()
outfile=args.outfile + "_totaldroplets-" + str(droplet_count) + ".png"
print "...saving image file...."
print outfile
print "........................"
plt.savefig(outfile)
#plt.show() ## activate this if you want to examine how the processed images are turning out and stop/start with different input parameters; key one being --cutoff_area
print "...total droplets identified in the image:"
print droplet_count
print "..."
def __getitem__(self, idx):
fileName = self.fileList[idx]
# load image
imgName = os.path.join(self.dataFolder, fileName + '_mlt.png')
image = io.imread(imgName)
if len(image.shape) == 2:
image = np.tile(image[..., None], (1, 3))
image = np.float32(image) / 255.0
# load albedo
albedoName = os.path.join(self.albedoFolder,
fileName + '_mlt_albedo.png')
albedo = io.imread(albedoName)
if len(albedo.shape) == 2:
albedo = np.tile(albedo[..., None], (1, 3))
albedo = np.float32(albedo) / 255.0
albedo[albedo < 1e-6] = 1e-6
# --------------------------------------------------------------------
# complicated code copied from CGI
# I don't really think this block of code is totally correct
# get shading and mask according to the code
maskName = os.path.join(self.dataFolder, fileName + "_mlt_mask.png")
mask = io.imread(maskName)
mask = np.float32(mask) / 255.0
gt_R_gray = np.mean(albedo, 2)
mask[gt_R_gray < 1e-6] = 0
mask[np.mean(image, 2) < 1e-6] = 0
mask = skimage.morphology.binary_erosion(mask, square(11))
mask = np.expand_dims(mask, axis=2)
mask = np.repeat(mask, 3, axis=2)
albedo[albedo < 1e-6] = 1e-6
rgb_img = image**2.2
shading = rgb_img / albedo
mask[
shading >
10] = 0 # CGI code this value is set to be 10, but I think it is wrong
#mask[shading > 20] = 0
mask[shading < 1e-4] = 0
shading[shading < 1e-4] = 1e-4
shading[shading > 20] = 20
if np.sum(mask) < 10:
max_S = 1.0
else:
max_S = np.percentile(shading[mask > 0.5], 90)
shading = shading / max_S
mask = np.float32(np.abs(np.sum(mask, axis=2) / 3.0 - 1.0) < 1e-6)
#------------------------------------------------------------------------
## shading saved as raw
#shadingName = os.path.join(self.shadingFolder, fileName + '.tiff')
#shading = imageio.imread(shadingName)
#if len(shading.shape)==2:
# shading = np.tile(shading[...,None], (1, 3))
#shading = shading/20.0
if fileName in self.missingList:
# no normal
imgHeight = image.shape[0]
imgWidth = image.shape[1]
normal = np.zeros((imgHeight, imgWidth, 3))
normalMask = np.zeros((imgHeight, imgWidth))
else:
normalName = os.path.join(self.normalFolder,
fileName + '_norm_camera.png')
normal = io.imread(normalName)
normalMaskName = os.path.join(self.normalFolder,
fileName + '_valid.png')
normalMask = io.imread(normalMaskName)
if self.transform:
image, albedo, shading, normal, mask, normalMask = \
self.transform([image, albedo, shading, normal, mask, normalMask])
return image, albedo, shading, normal, mask, normalMask
def _get_batches_of_transformed_samples(self, index_array):
batch_x = []
batch_y = []
#print(index_array)
for batch_index, image_index in enumerate(index_array):
row = self.image_table.iloc[image_index]
img_id = row.ImageId
if img_id in exclude_list:
continue
img0 = cv2.imread(path.join(images_folder, '{0}'.format(img_id)),
cv2.IMREAD_COLOR)
mask_path = path.join(masks_folder, '{0}.png'.format(img_id[:-4]))
if not os.path.exists(mask_path):
msk0 = np.zeros((768, 768, 3))
lbl0 = np.zeros((768, 768))
else:
msk0 = cv2.imread(mask_path, cv2.IMREAD_UNCHANGED)
lbl0 = cv2.imread(
path.join(labels_folder, '{0}.tif'.format(img_id[:-4])),
cv2.IMREAD_UNCHANGED)
if img0.shape[0] == 0 or msk0.shape[0] == 0 or lbl0.shape[
0] == 0:
img0 = np.zeros((768, 768, 3))
msk0 = np.zeros((768, 768, 3))
lbl0 = np.zeros((768, 768))
# print('mask_path', mask_path)
# print('img_shape', img0.shape, 'mask_shape', msk0.shape)
tmp = np.zeros_like(msk0[..., 0], dtype='uint8')
tmp[1:-1, 1:-1] = msk0[1:-1, 1:-1, 0]
good4copy = list(
set(np.unique(lbl0[lbl0 > 0])).symmetric_difference(
np.unique(lbl0[(lbl0 > 0) & (tmp == 0)])))
x0 = random.randint(0, img0.shape[1] - self.input_shape[1])
y0 = random.randint(0, img0.shape[0] - self.input_shape[0])
img = img0[y0:y0 + self.input_shape[0],
x0:x0 + self.input_shape[1], :]
msk = msk0[y0:y0 + self.input_shape[0],
x0:x0 + self.input_shape[1], :]
if len(good4copy) > 0 and random.random() > 0.75:
num_copy = random.randrange(1, min(6, len(good4copy) + 1))
lbl_max = lbl0.max()
for i in range(num_copy):
lbl_max += 1
l_id = random.choice(good4copy)
lbl_msk = lbl0 == l_id
row, col = np.where(lbl_msk)
y1, x1 = np.min(np.where(lbl_msk), axis=1)
y2, x2 = np.max(np.where(lbl_msk), axis=1)
lbl_msk = lbl_msk[y1:y2 + 1, x1:x2 + 1]
lbl_img = img0[y1:y2 + 1, x1:x2 + 1, :]
if random.random() > 0.5:
lbl_msk = lbl_msk[:, ::-1, ...]
lbl_img = lbl_img[:, ::-1, ...]
rot = random.randrange(4)
if rot > 0:
lbl_msk = np.rot90(lbl_msk, k=rot)
lbl_img = np.rot90(lbl_img, k=rot)
x1 = random.randint(
max(0, x0 - lbl_msk.shape[1] // 2),
min(img0.shape[1] - lbl_msk.shape[1],
x0 + self.input_shape[1] - lbl_msk.shape[1] // 2))
y1 = random.randint(
max(0, y0 - lbl_msk.shape[0] // 2),
min(img0.shape[0] - lbl_msk.shape[0],
y0 + self.input_shape[0] - lbl_msk.shape[0] // 2))
tmp = erosion(lbl_msk, square(5))
lbl_msk_dif = lbl_msk ^ tmp
tmp = dilation(lbl_msk, square(5))
lbl_msk_dif = lbl_msk_dif | (tmp ^ lbl_msk)
lbl0[y1:y1 + lbl_msk.shape[0],
x1:x1 + lbl_msk.shape[1]][lbl_msk] = lbl_max
img0[y1:y1 + lbl_msk.shape[0],
x1:x1 + lbl_msk.shape[1]][lbl_msk] = lbl_img[lbl_msk]
full_diff_mask = np.zeros_like(img0[..., 0], dtype='bool')
full_diff_mask[y1:y1 + lbl_msk.shape[0],
x1:x1 + lbl_msk.shape[1]] = lbl_msk_dif
img0[..., 0][full_diff_mask] = median(
img0[..., 0], mask=full_diff_mask)[full_diff_mask]
img0[..., 1][full_diff_mask] = median(
img0[..., 1], mask=full_diff_mask)[full_diff_mask]
img0[..., 2][full_diff_mask] = median(
img0[..., 2], mask=full_diff_mask)[full_diff_mask]
img = img0[y0:y0 + self.input_shape[0],
x0:x0 + self.input_shape[1], :]
lbl = lbl0[y0:y0 + self.input_shape[0],
x0:x0 + self.input_shape[1]]
msk = create_mask(lbl)
# return img, msk
data = self.random_transformers[0](image=img[..., ::-1], mask=msk)
img = data['image'][..., ::-1]
msk = data['mask']
msk = msk.astype('float')
msk[..., 0] = (msk[..., 0] > 127) * 1
msk[..., 1] = (msk[..., 1] > 127) * (msk[..., 0] == 0) * 1
msk[..., 2] = (msk[..., 1] == 0) * (msk[..., 0] == 0) * 1
otp = msk
img = np.concatenate([img, bgr_to_lab(img)], axis=2)
batch_x.append(img)
batch_y.append(otp)
batch_x = np.array(batch_x, dtype="float32")
batch_y = np.array(batch_y, dtype="float32")
batch_x = preprocess_input(batch_x)
return self.transform_batch_x(batch_x), self.transform_batch_y(batch_y)
add_image APIs
"""
from skimage import data
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label
from skimage.morphology import closing, square, remove_small_objects
from napari import ViewerApp
from napari.util import app_context
with app_context():
image = data.coins()[50:-50, 50:-50]
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(4))
# remove artifacts connected to image border
cleared = remove_small_objects(clear_border(bw), 20)
# label image regions
label_image = label(cleared)
# initialise viewer with astro image
viewer = ViewerApp(coins=image, multichannel=False)
viewer.layers[0].colormap = 'gray'
# add the labels
label_layer = viewer.add_labels(label_image, name='segmentation')
def __getitem__(self, idx):
_idx = self.train_idxs[idx]
fn = self.all_files[_idx]
img = cv2.imread(fn, cv2.IMREAD_COLOR)
img2 = cv2.imread(fn.replace('_pre_disaster', '_post_disaster'),
cv2.IMREAD_COLOR)
msk0 = cv2.imread(fn.replace('/images/', '/masks/'),
cv2.IMREAD_UNCHANGED)
lbl_msk1 = cv2.imread(
fn.replace('/images/', '/masks/').replace('_pre_disaster',
'_post_disaster'),
cv2.IMREAD_UNCHANGED)
msk1 = np.zeros_like(lbl_msk1)
msk2 = np.zeros_like(lbl_msk1)
msk3 = np.zeros_like(lbl_msk1)
msk4 = np.zeros_like(lbl_msk1)
msk2[lbl_msk1 == 2] = 255
msk3[lbl_msk1 == 3] = 255
msk4[lbl_msk1 == 4] = 255
msk1[lbl_msk1 == 1] = 255
if random.random() > 0.5:
img = img[::-1, ...]
img2 = img2[::-1, ...]
msk0 = msk0[::-1, ...]
msk1 = msk1[::-1, ...]
msk2 = msk2[::-1, ...]
msk3 = msk3[::-1, ...]
msk4 = msk4[::-1, ...]
if random.random() > 0.05:
rot = random.randrange(4)
if rot > 0:
img = np.rot90(img, k=rot)
img2 = np.rot90(img2, k=rot)
msk0 = np.rot90(msk0, k=rot)
msk1 = np.rot90(msk1, k=rot)
msk2 = np.rot90(msk2, k=rot)
msk3 = np.rot90(msk3, k=rot)
msk4 = np.rot90(msk4, k=rot)
if random.random() > 0.9:
shift_pnt = (random.randint(-320, 320), random.randint(-320, 320))
img = shift_image(img, shift_pnt)
img2 = shift_image(img2, shift_pnt)
msk0 = shift_image(msk0, shift_pnt)
msk1 = shift_image(msk1, shift_pnt)
msk2 = shift_image(msk2, shift_pnt)
msk3 = shift_image(msk3, shift_pnt)
msk4 = shift_image(msk4, shift_pnt)
if random.random() > 0.6:
rot_pnt = (img.shape[0] // 2 + random.randint(-320, 320),
img.shape[1] // 2 + random.randint(-320, 320))
scale = 0.9 + random.random() * 0.2
angle = random.randint(0, 20) - 10
if (angle != 0) or (scale != 1):
img = rotate_image(img, angle, scale, rot_pnt)
img2 = rotate_image(img2, angle, scale, rot_pnt)
msk0 = rotate_image(msk0, angle, scale, rot_pnt)
msk1 = rotate_image(msk1, angle, scale, rot_pnt)
msk2 = rotate_image(msk2, angle, scale, rot_pnt)
msk3 = rotate_image(msk3, angle, scale, rot_pnt)
msk4 = rotate_image(msk4, angle, scale, rot_pnt)
if random.random() > 0.985:
img = shift_channels(img, random.randint(-5, 5),
random.randint(-5, 5), random.randint(-5, 5))
elif random.random() > 0.985:
img2 = shift_channels(img2, random.randint(-5, 5),
random.randint(-5, 5), random.randint(-5, 5))
if random.random() > 0.985:
img = change_hsv(img, random.randint(-5, 5), random.randint(-5, 5),
random.randint(-5, 5))
elif random.random() > 0.985:
img2 = change_hsv(img2, random.randint(-5, 5),
random.randint(-5, 5), random.randint(-5, 5))
if random.random() > 0.98:
if random.random() > 0.985:
img = clahe(img)
elif random.random() > 0.985:
img = gauss_noise(img)
elif random.random() > 0.985:
img = cv2.blur(img, (3, 3))
elif random.random() > 0.98:
if random.random() > 0.985:
img = saturation(img, 0.9 + random.random() * 0.2)
elif random.random() > 0.985:
img = brightness(img, 0.9 + random.random() * 0.2)
elif random.random() > 0.985:
img = contrast(img, 0.9 + random.random() * 0.2)
if random.random() > 0.98:
if random.random() > 0.985:
img2 = clahe(img2)
elif random.random() > 0.985:
img2 = gauss_noise(img2)
elif random.random() > 0.985:
img2 = cv2.blur(img2, (3, 3))
elif random.random() > 0.98:
if random.random() > 0.985:
img2 = saturation(img2, 0.9 + random.random() * 0.2)
elif random.random() > 0.985:
img2 = brightness(img2, 0.9 + random.random() * 0.2)
elif random.random() > 0.985:
img2 = contrast(img2, 0.9 + random.random() * 0.2)
if random.random() > 0.983:
el_det = self.elastic.to_deterministic()
img = el_det.augment_image(img)
if random.random() > 0.983:
el_det = self.elastic.to_deterministic()
img2 = el_det.augment_image(img2)
msk0 = msk0[..., np.newaxis]
msk1 = msk1[..., np.newaxis]
msk2 = msk2[..., np.newaxis]
msk3 = msk3[..., np.newaxis]
msk4 = msk4[..., np.newaxis]
msk = np.concatenate([msk0, msk1, msk2, msk3, msk4], axis=2)
msk = (msk > 127)
msk[..., 0] = False
msk[..., 1] = dilation(msk[..., 1], square(5))
msk[..., 2] = dilation(msk[..., 2], square(5))
msk[..., 3] = dilation(msk[..., 3], square(5))
msk[..., 4] = dilation(msk[..., 4], square(5))
msk[..., 1][msk[..., 2:].max(axis=2)] = False
msk[..., 3][msk[..., 2]] = False
msk[..., 4][msk[..., 2]] = False
msk[..., 4][msk[..., 3]] = False
msk[..., 0][msk[..., 1:].max(axis=2)] = True
msk = msk * 1
lbl_msk = msk.argmax(axis=2)
img = np.concatenate([img, img2], axis=2)
img = preprocess_inputs(img)
img = torch.from_numpy(img.transpose((2, 0, 1))).float()
msk = torch.from_numpy(msk.transpose((2, 0, 1))).long()
sample = {'img': img, 'msk': msk, 'lbl_msk': lbl_msk, 'fn': fn}
return sample
sharey=True)
ax0.imshow(np.squeeze(test_img).astype('uint8'), cmap='gray')
ax1.imshow(overlay)
plt.show()
# # general way
# In[19]:
# the rest defects
defects_
# In[20]:
start_time = time.time()
bin_img = morphology.binary_closing((pred_img > 0), morphology.square(3))
label_img = measure.label(bin_img > 0)
regions = measure.regionprops(label_img)
proc_time = time.time() - start_time
print('proc time = ', proc_time)
overlay = np.squeeze(test_img).copy().astype('uint8')
for region in regions:
label = region.label
area = region.area
if area < 0:
continue
y0, x0, y1, x1 = region.bbox
def use_mask_tif():
for one_color in unique_colors:
# print("one_color",one_color)
# (0, 255, 127)
# new_img=np.where(loaded_img_mask[:,:,:3]==np.array(one_color),1.0,0.0)
loaded_img_mask_proc = loaded_img_mask[:, :, :3]
# (0, 255, 127) locations are True
new_img = np.all(loaded_img_mask_proc == np.array(one_color),
axis=2)
# print("new_img",new_img.shape)
# print("new_img",new_img)
new_img = skimage.morphology.binary_dilation(new_img, square(3))
new_img = new_img[:, :, np.newaxis].astype("uint8")
# None (0, 255, 127) locations are 1
new_img = np.where(new_img == 0, 1, 0)
# print("new_img",new_img)
masked_img = loaded_img_crop * new_img
stacked = np.vstack(masked_img)
# # print("stacked",stacked.shape)
# # (234971, 3)
# # afaf
# # stacked=loaded_img_crop_mask.reshape((-1,3))
# # print("stacked",stacked.shape)
# # (234971, 3)
idx = np.all(stacked == [0, 0, 0], 1)
# # print("idx",idxs.shape)
# # idx (234971,)
# # print("idx",idx)
# # afaf
# a1=np.vstack(loaded_img_crop)
stacked[idx] = [0, 255, 0]
# # print("a1",a1.shape)
# # a1 (234971, 3)
loaded_img_crop_new = stacked.reshape(loaded_img_crop.shape[0],
loaded_img_crop.shape[1], 3)
# print("loaded_img_crop",loaded_img_crop.shape)
# loaded_img_crop_masked=loaded_img_crop[loaded_img_crop_mask]
# print("loaded_img_crop_masked",loaded_img_crop_masked)
# # loaded_img_crop[loaded_img_crop_mask] (18, 3)
# # loaded_img_crop[loaded_img_crop_mask] (387, 3)
# # loaded_img_crop[loaded_img_crop_mask] (234971, 3)
# # loaded_img_crop[loaded_img_crop_mask] (1629, 3)
# loaded_img_crop[loaded_img_crop_mask]=[0,250,0]
# # print("loaded_img_crop",loaded_img_crop)
# plt.imshow(loaded_img_crop*nesw_img)
plt.imshow(loaded_img_crop_new)
plt.title("File: 1_Region 1_mask.tif, " + str(one_color))
# /home/young/Pictures/2019_04_14_10:01:03.png
# /home/young/Pictures/2019_04_14_10:01:18.png
# /home/young/Pictures/2019_04_14_10:01:34.png
plt.show()
def dist_map(x, y, z, xmin, xmax, ymin, ymax, dx, delta_s):
"""function for centerline rasterization and distance map calculation
inputs:
x,y,z - coordinates of centerline
xmin, xmax, ymin, ymax - x and y coordinates that define the area of interest
dx - gridcell size (m)
delta_s - distance between points along centerline (m)
returns:
cl_dist - distance map (distance from centerline)
x_pix, y_pix, z_pix - x,y, and z pixel coordinates of the centerline
s_pix - along-channel distance in pixels
z_map - map of reference channel thalweg elevation (elevation of closest point along centerline)
x, y, z - x,y,z centerline coordinates clipped to the 3D model domain"""
y = y[(x > xmin) & (x < xmax)]
z = z[(x > xmin) & (x < xmax)]
x = x[(x > xmin) & (x < xmax)]
dummy, dy, dz, ds, s = compute_derivatives(x, y, z)
if len(np.where(ds > 2 * delta_s)[0]) > 0:
inds = np.where(ds > 2 * delta_s)[0]
inds = np.hstack((0, inds, len(x)))
lengths = np.diff(inds)
long_segment = np.where(lengths == max(lengths))[0][0]
start_ind = inds[long_segment] + 1
end_ind = inds[long_segment + 1]
if end_ind < len(x):
x = x[start_ind:end_ind]
y = y[start_ind:end_ind]
z = z[start_ind:end_ind]
else:
x = x[start_ind:]
y = y[start_ind:]
z = z[start_ind:]
xdist = xmax - xmin
ydist = ymax - ymin
iwidth = int((xmax - xmin) / dx)
iheight = int((ymax - ymin) / dx)
xratio = iwidth / xdist
# create list with pixel coordinates:
pixels = []
for i in range(0, len(x)):
px = int(iwidth - (xmax - x[i]) * xratio)
py = int(iheight - (ymax - y[i]) * xratio)
pixels.append((px, py))
# create image and numpy array:
img = Image.new("RGB", (iwidth, iheight), "white")
draw = ImageDraw.Draw(img)
draw.line(pixels, fill="rgb(0, 0, 0)") # draw centerline as black line
pix = np.array(img)
cl = pix[:, :, 0]
cl[cl == 255] = 1 # set background to 1 (centerline is 0)
y_pix, x_pix = np.where(cl == 0)
x_pix, y_pix = order_cl_pixels(x_pix, y_pix)
# This next block of code is kind of a hack. Looking for, and eliminating, 'bad' pixels.
img = np.array(img)
img = img[:, :, 0]
img[img == 255] = 1
img1 = morphology.binary_dilation(img,
morphology.square(2)).astype(np.uint8)
if len(np.where(img1 == 0)[0]) > 0:
x_pix, y_pix = eliminate_bad_pixels(img, img1)
x_pix, y_pix = order_cl_pixels(x_pix, y_pix)
img1 = morphology.binary_dilation(
img, np.array([[1, 0, 1], [1, 1, 1]], dtype=np.uint8)).astype(np.uint8)
if len(np.where(img1 == 0)[0]) > 0:
x_pix, y_pix = eliminate_bad_pixels(img, img1)
x_pix, y_pix = order_cl_pixels(x_pix, y_pix)
img1 = morphology.binary_dilation(
img, np.array([[1, 0, 1], [0, 1, 0], [1, 0, 1]],
dtype=np.uint8)).astype(np.uint8)
if len(np.where(img1 == 0)[0]) > 0:
x_pix, y_pix = eliminate_bad_pixels(img, img1)
x_pix, y_pix = order_cl_pixels(x_pix, y_pix)
#redo the distance calculation (because x_pix and y_pix do not always contain all the points in cl):
cl[cl == 0] = 1
cl[y_pix, x_pix] = 0
cl_dist, inds = ndimage.distance_transform_edt(cl, return_indices=True)
dx, dy, dz, ds, s = compute_derivatives(x, y, z)
# dx_pix,dy_pix,ds_pix,s_pix = compute_derivatives(x_pix,y_pix) # needed for s_pix only
dx_pix = np.gradient(x_pix)
dy_pix = np.gradient(y_pix)
ds_pix = np.sqrt(dx_pix**2 + dy_pix**2)
s_pix = np.cumsum(ds_pix)
f = scipy.interpolate.interp1d(s, z)
snew = s_pix * s[-1] / s_pix[-1]
if snew[-1] > s[-1]:
snew[-1] = s[-1]
snew[snew < s[0]] = s[0]
z_pix = f(snew)
# create z_map:
z_map = np.zeros(np.shape(cl_dist))
z_map[y_pix, x_pix] = z_pix
xinds = inds[1, :, :]
yinds = inds[0, :, :]
for i in range(0, len(x_pix)):
z_map[(xinds == x_pix[i]) & (yinds == y_pix[i])] = z_pix[i]
return cl_dist, x_pix, y_pix, z_pix, s_pix, z_map, x, y, z
def run_model(file_to_predict, cnn_model):
model = keras.models.load_model(cnn_model)
# notice: the image_path corresponds to certain image;
## for desinging user interface, image_path should be automatically as the imagepath of the image imported by the user.
## also could design for batch prediction
Predicting_image_path = file_to_predict
#related to whether the image normalized
image_path = Predicting_image_path
image = cv2.imread(image_path, 0)
image = cv2.resize(image, (576, 576))
image = img_as_float(image)
image *= 255.0/image.max()
image = image/255.0
image = np.array(image)
img = mpimg.imread(image_path)
# imgplot = plt.imshow(img)
y = np.expand_dims(image, axis=0)
result = model.predict(y)
result= np.squeeze(result, axis=0)
result= np.squeeze(result, axis=-1)
plt.imshow(result, cmap = 'gray', interpolation = 'bicubic')
plt.xticks([]), plt.yticks([])
dir_path = os.path.dirname(os.path.realpath(__file__))
print("Output for dir path: " , dir_path)
save_file = dir_path + "/" + "result_output_test.tif"
plt.gca().set_axis_off()
plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0,
hspace = 0, wspace = 0)
plt.margins(0,0)
plt.gca().xaxis.set_major_locator(plt.NullLocator())
plt.gca().yaxis.set_major_locator(plt.NullLocator())
plt.savefig(save_file, bbox_inches='tight', pad_inches=0)
prediction_data = result
# only show the boundary:
## Critical: must notice the output of CNN is pixel with continous numbers:
# higher accuracy, the closer it is to the pixel values designated in masks.
# thus, the number "0.6" made here is arbitary, depends on the accuracy of CNN, if Accuracy is high, it should be close to 1.0
### could influence the quantification result by thining or expending the boundary/membrane areas
## could also find ways to show other ROI predicted to make more options for the user.
prediction_data[prediction_data >= 0.7] = 1
prediction_data[prediction_data < 0.7] = 0
prediction_data = prediction_data.astype('int')
prediction_data = morphology.remove_small_objects(prediction_data.astype(bool),64)
prediction_data = prediction_data.astype('float32')
prediction_data = skimage.morphology.closing(prediction_data, square(3))
## add the row at the margin of image, because of bad annotation, the boundary in image margin would be miss classified.
ROW= [0,1,2,3,4,5]
for I in ROW:
prediction_data[I,:]=1
prediction_data[:,I]=1
prediction_data[-I,:]=1
prediction_data[:,-I]=1
#change the interior area to value 1
prediction_data[prediction_data == 1.0] = 0.5
prediction_data[prediction_data == 0.0] = 1.0
prediction_data[prediction_data == 0.5] = 0.0
s = generate_binary_structure(2,2)
# num_features
# how many ROI/unconnected object it find
labeled_array, num_features = label(prediction_data, structure=s)
unique, counts = np.unique(labeled_array, return_counts=True)
dict(zip(unique, counts))
for i in range(num_features+1):
if np.count_nonzero(labeled_array == i)>1000: #discard small ROI
a = np.count_nonzero(labeled_array == i)
# print('pixel area =',np.count_nonzero(labeled_array == i))
b = ndimage.sum(image, labeled_array, index=[i])
# print('pixel intensity =',ndimage.sum(image, labeled_array, index=[i]))
arr_1 = (labeled_array == i).astype(int)
a1=np.roll(arr_1, 8, axis=0)
a2=np.roll(arr_1, -8, axis=0)
a3=np.roll(arr_1, 8, axis=1)
a4=np.roll(arr_1, -8, axis=1)
a5=a1+a2+a3+a4
a5[a5 > i-0.1] = 1
c= ndimage.sum(image, a5, index=[1])-b
# print('pixel intensity in boundary =',c)
## Critical: the value "8" in np.rool meas to expand the region i by 8 pixels
### the value "8" corresponds to the length of the cell membranes.
## Critical: the prediction accuracy of CNN also would influence the parameter used in np.rool:
### also related to the parameter in "#only show the boundary:" lines
slice_x, slice_y = ndimage.find_objects(labeled_array == i)[0]
roi = labeled_array[slice_x, slice_y]
for z in range(1, 5):
first_patient = load_scan(INPUT_FOLDER + patients[z])
first_patient_pixels = get_pixels_hu(first_patient)
im = Image.fromarray(
(first_patient_pixels[np.shape(first_patient_pixels)[0] / 2] + 1024) /
8)
#im.show()
im = im.convert(mode="L")
im = im.filter(ImageFilter.MedianFilter(15))
#im.show()
pxl = np.array(im)
thresh = threshold_otsu(pxl)
pxl2 = 255 * (pxl > thresh)
#im2 = Image.fromarray(pxl2)
#im2.show()
selem = square(150)
closed = closing(pxl2, selem)
#im2 = Image.fromarray(closed)
#im2.show()
a = closed - pxl2
selem = square(20)
closed = closing(a, selem)
selem = disk(6)
#closed = erosion(closed, selem)
#im2 = Image.fromarray(closed)
#im2.show()
mul = (closed > 150) * pxl
mask = (255 - closed) + mul
mul = 255 * (mul > .44 * (np.max(mul) - np.min(mask)))
#mul = 255*(mul>thresh)
mul = opening(mul, selem)
def framefeats(movie, frame, labels, counter, ring_flag):
labels = labels.astype(int)
labels_bin = labels == 0
features_temp = []
ims = []
for j in range(movie.channels):
im = movie.read_raw(j, frame)
features_temp.append(regionprops(labels, im))
if ring_flag:
ims.append(im)
features = dict()
features['tracking'] = np.zeros((len(features_temp[0]), 13))
features['data'] = np.zeros((len(features_temp[0]), 22))
new_label = np.zeros((movie.dims[0], movie.dims[1]))
for j in range(len(features_temp[0])):
# Tracking Features
cell_temp = features_temp[0][j]
ypos = cell_temp.centroid[0]
xpos = cell_temp.centroid[1]
features['tracking'][j, 0] = counter
features['tracking'][j, 2] = xpos
features['tracking'][j, 3] = ypos
features['tracking'][j, 4] = min(
[ypos, movie.dims[0] - ypos, xpos, movie.dims[1] - xpos])
# Morphology Features
features['data'][j, 0] = cell_temp.area
features['data'][j, 1] = cell_temp.eccentricity
features['data'][j, 2] = cell_temp.major_axis_length
features['data'][j, 3] = cell_temp.perimeter
# Determine region for dilation
if ring_flag:
r = int(np.round(cell_temp.perimeter / 5))
bbox = cell_temp.bbox
bbox_dil = (np.maximum(0, bbox[0] - r), np.maximum(0, bbox[1] - r),
np.minimum(movie.dims[0], bbox[2] + r - 1),
np.minimum(movie.dims[1], bbox[3] + r - 1))
pad = ((bbox[0] - bbox_dil[0], bbox_dil[2] - bbox[2]),
(bbox[1] - bbox_dil[1], bbox_dil[3] - bbox[3]))
image_dil = np.pad(cell_temp.image, pad, 'constant')
image_dil = dilation(image_dil, square(r))
bin_roi = labels_bin[bbox_dil[0]:bbox_dil[2],
bbox_dil[1]:bbox_dil[3]]
ring_region = np.logical_and(image_dil, bin_roi)
# Intensity Measurements for classification
for k in range(0, movie.channels):
cell_temp = features_temp[k][j]
mu = cell_temp.mean_intensity
im_temp = cell_temp.intensity_image.flatten()
bin_temp = cell_temp.image.flatten()
im_temp = im_temp[bin_temp]
ind = k * 6 + 4
features['data'][j, ind] = mu
features['data'][j, ind + 1] = np.median(im_temp)
features['data'][j, ind + 2] = np.std(im_temp)
features['data'][j, ind + 3] = np.std(im_temp[im_temp > mu])
if ring_flag:
im_roi = ims[k][bbox_dil[0]:bbox_dil[2],
bbox_dil[1]:bbox_dil[3]]
ring_region_vals = im_roi[ring_region].flatten()
features['data'][j, ind + 4] = np.mean(ring_region_vals)
features['data'][j, ind + 5] = np.median(ring_region_vals)
new_label[labels == cell_temp.label] = counter
counter += 1
features['data'][np.isinf(features['data'])] = 0
features['data'][np.isnan(features['data'])] = 0
return features, new_label, counter
"/home/apages/pysrc/KernelPheno/data/DSC05389.jpeg",
"/home/apages/pysrc/KernelPheno/data/DSC05384.jpeg"]
br_thresh_sum = 0
num_images = 0
for path in img_files:
col = imread(path)
gray = rgb2gray(col)
thresh = threshold_otsu(gray)
num_images += 1
br_thresh_sum += thresh
print("Threshold: " + str(thresh))
bw = closing(gray > thresh, square(3))
masked = col.copy()
masked[np.where(bw)] = [0,0,0]
# plt.imshow(masked)
# plt.show()
avg = br_thresh_sum / num_images
print("Average: " + str(avg))
for path in img_files:
col = imread(path)
gray = rgb2gray(col)
thresh = threshold_otsu(gray)
bw = closing(gray > thresh, square(3))
import matplotlib.pyplot as plt import matplotlib.patches as mpatches from skimage import data, filters, segmentation, measure, morphology, color #加载并裁剪硬币图片 imgname1 = "009-b.jpg" imgname2 = "003-b.jpg" img1 = cv2.imread(imgname1) img2 = cv2.imread(imgname2) image = data.coins()[50:-50, 50:-50] gray1 = cv2.cvtColor(img1, cv2.COLOR_BGR2GRAY) image = gray1 thresh = filters.threshold_otsu(image) #阈值分割 bw = morphology.closing(image > thresh, morphology.square(3)) #闭运算 cleared = bw.copy() #复制 segmentation.clear_border(cleared) #清除与边界相连的目标物 label_image = measure.label(cleared) #连通区域标记 borders = np.logical_xor(bw, cleared) #异或 label_image[borders] = -1 image_label_overlay = color.label2rgb(label_image, image=image) #不同标记用不同颜色显示 fig, (ax0, ax1) = plt.subplots(1, 2, figsize=(8, 6)) ax0.imshow(cleared, plt.cm.gray) ax1.imshow(image_label_overlay) for region in measure.regionprops(label_image): #循环得到每一个连通区域属性集