def segment_cells(frame, mask=None):
"""
Compute the initial segmentation based on ridge detection + watershed.
This works reasonably well, but is not robust enough to use by itself.
"""
blurred = filters.gaussian_filter(frame, 2)
ridges = enhance_ridges(frame)
# threshold ridge image
thresh = filters.threshold_otsu(ridges)
thresh_factor = 0.6
prominent_ridges = ridges > thresh_factor*thresh
prominent_ridges = morphology.remove_small_objects(prominent_ridges, min_size=256)
prominent_ridges = morphology.binary_closing(prominent_ridges)
prominent_ridges = morphology.binary_dilation(prominent_ridges)
# skeletonize
ridge_skeleton = morphology.medial_axis(prominent_ridges)
ridge_skeleton = morphology.binary_dilation(ridge_skeleton)
ridge_skeleton *= mask
ridge_skeleton -= mask
# label
cell_label_im = measure.label(ridge_skeleton)
# morphological closing to fill in the cracks
for cell_num in range(1, cell_label_im.max()+1):
cell_mask = cell_label_im==cell_num
cell_mask = morphology.binary_closing(cell_mask, disk(3))
cell_label_im[cell_mask] = cell_num
return cell_label_im
def tissue_region_from_rgb(_img, _min_area=150, _g_th=None):
"""
TISSUE_REGION_FROM_RGB detects the region(s) of the image containing the
tissue. The original image is supposed to represent a haematoxylin-eosin
-stained pathology slide.
The main purpose of this function is to detect the parts of a large image
which most probably contain tissue material, and to discard the background.
Usage:
tissue_mask = tissue_from_rgb(img, _min_area=150, _g_th=None)
Args:
img (numpy.ndarray): the original image in RGB color space
_min_area (int, default: 150): any object with an area smaller than
the indicated value, will be discarded
_g_th (int, default: None): the processing is done on the GREEN channel
and all pixels below _g_th are considered candidates for "tissue
pixels". If no value is given to _g_th, one is computed by K-Means
clustering (K=2), and is returned.
Returns:
numpy.ndarray: a binary image containing the mask of the regions
considered to represent tissue fragments
int: threshold used for GREEN channel
"""
if _g_th is None:
# Apply vector quantization to remove the "white" background - work in the
# green channel:
vq = MiniBatchKMeans(n_clusters=2)
_g_th = int(np.round(0.95 * np.max(vq.fit(_G(_img).reshape((-1,1)))
.cluster_centers_.squeeze())))
mask = _G(_img) < _g_th
skm.binary_closing(mask, skm.disk(3), out=mask)
mask = img_as_bool(mask)
mask = skm.remove_small_objects(mask, min_size=_min_area, in_place=True)
# Some hand-picked rules:
# -at least 5% H and E
# -at most 25% background
# for a region to be considered tissue
h, e, b = rgb2he2(_img)
mask &= (h > np.percentile(h, 5)) | (e > np.percentile(e, 5))
mask &= (b < np.percentile(b, 50)) # at most at 50% of "other components"
mask = mh.close_holes(mask)
return img_as_bool(mask), _g_th
def closing3D(data, selem=skimor.disk(3), slicewise=False, sliceId=0):
if slicewise:
if sliceId == 0:
for i in range(data.shape[0]):
data[i, :, :] = skimor.binary_closing(data[i, :, :], selem)
elif sliceId == 2:
for i in range(data.shape[2]):
data[:, :, i] = skimor.binary_closing(data[:, :, i], selem)
else:
data = scindimor.binary_closing(data, selem)
return data
def segment_lung_mask(image, fill_lung_structures=True):
LUNG_HU_VAL = -320
# not actually binary, but 1 and 2.
# 0 is treated as background, which we do not want
binary_image = np.array(image < LUNG_HU_VAL, dtype=np.int8)
labels = measure.label(binary_image, connectivity=2)
# Pick the pixel in the very corner to determine which label is air.
# Improvement: Pick multiple background labels from around the patient
# More resistant to "trays" on which the patient lays cutting the air
# around the person in half
background_label = labels[0, 0, 0]
# Fill the air around the person
binary_image[labels == background_label] = 0
# Method of filling the lung structures (that is superior to something like
# morphological closing)
if fill_lung_structures:
l_max = largest_label_volume(labels, bg=0)
if l_max is not None: # This slice contains some lung
mask = np.zeros_like(binary_image)
mask[labels == l_max] = 1
# Remove other air pockets insid of body
mask = morphology.binary_closing(mask)
return mask
def test9(self):
fig, ax = plt.subplots()
plt.imshow(self.mask)
plt.show()
shape = self.mask.shape
for y in range(20, shape[0], 20):
for x in range(20, shape[1], 20):
if self.mask[y][x] == True:
continue
print(y, x)
slice = self.prepareSliceForDot(y, x)
lengthsArray = self.convertSliceDotsToLenths(y, x, slice)
if self.calculateVariationForLengthsArray(
lengthsArray) > self.VARIATION_LIMIT_1:
continue
derivativeArray = self.prepareDerivativeArray(lengthsArray)
new_lengths_array, new_derivative_array = self.process_dot_border(
y, x, slice, lengthsArray, derivativeArray)
self.drawBorderInMask(y, x, new_lengths_array, slice)
fig, ax = plt.subplots()
plt.imshow(self.mask)
plt.show()
self.mask = binary_closing(self.mask, square(25))
self.mask = remove_small_objects(self.mask)
fig, ax = plt.subplots()
plt.imshow(self.mask)
io.imsave('data/output/mask_with_borders_1.jpg',
img_as_ubyte(self.mask))
plt.close('all')
def merge_and_save(label_file_name, expected_file_name):
try:
label_image = io.imread(label_file_name, as_grey=True)
merged_image = label_image < 2.0/255.0
merged_image = binary_fill_holes(merged_image)
selem = disk(7)
for i in range(20):
components, number_of_components = label(merged_image)
if number_of_components < 2:
break
merged_image = binary_closing(merged_image, selem=selem)
merged_image = binary_fill_holes(merged_image)
if i > 10 :
merged_image = remove_small_objects(merged_image, min_size=10)
try:
expected_image = io.imread(expected_file_name, as_grey=True)
merged_image = merged_image | (expected_image != 0)
except IOError:
pass
with warnings.catch_warnings():
warnings.simplefilter("ignore")
io.imsave(expected_file_name, img_as_ubyte(merged_image))
except IOError:
pass
def nucleiBinarySplit(mask, thr):
mask00 = ndi.binary_fill_holes(mask)
maskConv = convex_hull_image(mask00)
maskB = tinyDottsRemove(maskConv - mask)
notConv = np.sum(maskB) / np.sum(mask00)
if (notConv < thr):
return mask00
nn = np.max(label(maskB))
if nn > 1:
while (np.max(label(maskB)) == nn):
maskB = binary_closing(binary_dilation(maskB, selem=disk(1)),
selem=disk(2))
pass
maskC = binary_dilation(skeletonize(maskB), selem=disk(1))
maskD = tinyDottsRemove(binary_erosion(
imgToMask(binary_dilation(maskConv, selem=disk(1)) + (-1) * maskC),
selem=disk(1)),
minimum=10)
maskE = binary_opening(maskD, selem=disk(1))
#maskE = imgToMask(maskD - maskConv)
#maskF = ndi.binary_fill_holes(maskE)
markers = ndi.label(maskE)[0]
markers[np.where(mask00 == 0)] = 0
labels = watershed(-mask, markers, mask=mask)
return labels
def closing(gray_img, kernel=None):
"""Wrapper for scikit-image closing functions. Opening can remove small dark spots (i.e. pepper).
Inputs:
gray_img = input image (grayscale or binary)
kernel = optional neighborhood, expressed as an array of 1s and 0s. If None, use cross-shaped structuring element.
:param gray_img: ndarray
:param kernel = ndarray
:return filtered_img: ndarray
"""
params.device += 1
# Make sure the image is binary/grayscale
if len(np.shape(gray_img)) != 2:
fatal_error("Input image must be grayscale or binary")
# If image is binary use the faster method
if len(np.unique(gray_img)) == 2:
bool_img = morphology.binary_closing(image=gray_img, selem=kernel)
filtered_img = np.copy(bool_img.astype(np.uint8) * 255)
# Otherwise use method appropriate for grayscale images
else:
filtered_img = morphology.closing(gray_img, kernel)
if params.debug == 'print':
print_image(filtered_img, os.path.join(params.debug_outdir, str(params.device) + '_opening' + '.png'))
elif params.debug == 'plot':
plot_image(filtered_img, cmap='gray')
return filtered_img
def repair(self, mask):
"""Apply binary closure using selection elements specified in the class
constructor. OR the results together.
Parameters
----------
mask : ndarray
2D rejection mask for spectrograph images.
Returns
-------
repaired_mask : ndarray
2D spectrograph cosmic ray mask with binary closure applied.
"""
# Convert mask to binary.
bmask = np.zeros(mask.shape, dtype=mask.dtype)
bmask[mask > 0] = 1
# Apply binary closure using each selection element. OR results.
bc = np.zeros(mask.shape, dtype=mask.dtype)
for se in self.selems:
bc = bc | binary_closing(bmask, selem=se.se)
return bc
def compute_hull_mask(faces,
vertices,
scale=config.HULL_SCALE,
remove_holes=True,
closing=False):
transformed = vertices.copy()
transformed[:, 0] -= vertices[:, 0].min()
transformed[:, 2] -= vertices[:, 2].min()
transformed *= scale
xmin = vertices[:, 0].min()
zmin = vertices[:, 2].min()
xmax = vertices[:, 0].max()
zmax = vertices[:, 2].max()
width = int(
math.ceil(vertices[:, 0].max() - vertices[:, 0].min()) * scale) + 1
height = int(
math.ceil(vertices[:, 2].max() - vertices[:, 2].min()) * scale) + 1
im = Image.new('L', (width, height))
draw = ImageDraw.Draw(im)
for face in faces:
p = [(int(transformed[i, 0]), int(transformed[i, 2])) for i in face]
draw.polygon(p, fill='#fff')
im = np.array(im) == 255
if closing:
imsave(os.path.join(config.IMAGE_SAVE_DIR, 'test.png'), im)
im = morphology.binary_closing(im, morphology.square(40))
imsave(os.path.join(config.IMAGE_SAVE_DIR, 'test2.png'), im)
if remove_holes and len(np.unique(im) >= 2):
im = morphology.remove_small_holes(im, min_size=scale**2)
return im.T, xmin, zmin, xmax, zmax
def remove_noise_from_segmented_lungs(segmented_ct_scan):
selem = ball(2)
binary = binary_closing(segmented_ct_scan, selem)
label_scan = label(binary)
areas = [r.area for r in regionprops(label_scan)]
areas.sort()
for r in regionprops(label_scan):
max_x, max_y, max_z = 0, 0, 0
min_x, min_y, min_z = 1000, 1000, 1000
for c in r.coords:
max_z = max(c[0], max_z)
max_y = max(c[1], max_y)
max_x = max(c[2], max_x)
min_z = min(c[0], min_z)
min_y = min(c[1], min_y)
min_x = min(c[2], min_x)
if (min_z == max_z or min_y == max_y or min_x == max_x or r.area > areas[-3]):
for c in r.coords:
segmented_ct_scan[c[0], c[1], c[2]] = 0
else:
index = (max((max_x - min_x), (max_y - min_y), (max_z - min_z))) / (min((max_x - min_x), (max_y - min_y) , (max_z - min_z)))
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 refine_aseg(aseg, ball_size=4):
"""
First step to reconcile ANTs' and FreeSurfer's brain masks.
Here, the ``aseg.mgz`` mask from FreeSurfer is refined in two
steps, using binary morphological operations:
1. With a binary closing operation the sulci are included
into the mask. This results in a smoother brain mask
that does not exclude deep, wide sulci.
2. Fill any holes (typically, there could be a hole next to
the pineal gland and the corpora quadrigemina if the great
cerebral brain is segmented out).
"""
# Read aseg data
bmask = aseg.copy()
bmask[bmask > 0] = 1
bmask = bmask.astype(np.uint8)
# Morphological operations
selem = sim.ball(ball_size)
newmask = sim.binary_closing(bmask, selem)
newmask = binary_fill_holes(newmask.astype(np.uint8), selem).astype(np.uint8)
return newmask.astype(np.uint8)
def get_segmented_lungs(im):
binary = im < -320
cleared = clear_border(binary)
cleared=morph(cleared,5)
label_image = label(cleared)
areas = [r.area for r in regionprops(label_image)]
areas.sort()
if len(areas) > 2:
for region in regionprops(label_image):
if region.area < areas[-2]:
for coordinates in region.coords:
label_image[coordinates[0], coordinates[1]] = 0
binary = label_image > 0
selem = disk(2)
binary = binary_erosion(binary, selem)
selem = disk(10)
binary = binary_closing(binary, selem)
edges = roberts(binary)
binary = ndi.binary_fill_holes(edges)
get_high_vals = binary == 0
im[get_high_vals] = 0
binary = morphology.dilation(binary,np.ones([5,5]))
return binary
def compute_binary_mask_lasseck(spectrogram, threshold):
# normalize to [0, 1)
norm_spectrogram = normalize(spectrogram)
# median clipping
binary_image = median_clipping(norm_spectrogram, threshold)
# closing binary image (dilation followed by erosion)
binary_image = morphology.binary_closing(binary_image,
selem=np.ones((4, 4)))
# dialate binary image
binary_image = morphology.binary_dilation(binary_image,
selem=np.ones((4, 4)))
# apply median filter
binary_image = filters.median(binary_image, selem=np.ones((2, 2)))
# remove small objects
binary_image = morphology.remove_small_objects(binary_image,
min_size=32,
connectivity=1)
mask = np.array([np.max(col) for col in binary_image.T])
mask = smooth_mask(mask)
return mask
def extend_mask_2d(imagemask, disk_size=4, iterations=15): padding = disk_size * iterations mask = np.zeros(shape=np.array(imagemask.shape)+2*padding, dtype=bool) mask[padding:imagemask.shape[0]+padding, padding:imagemask.shape[1]+padding][imagemask==1] = 1 struct = disk(disk_size) mask = binary_closing(mask, structure=struct, iterations=iterations) return mask[padding:imagemask.shape[0]+padding, padding:imagemask.shape[1]+padding]
def morphological_transform(roi: DenseROI,
shape: Tuple[int, int]) -> Union[DenseROI, None]:
"""performs a closing followed by an opening to clean up pixelated
appearance of ROIs
Parameters
----------
roi: DenseROI
roi to transform
shape: Tuple[int, int]
The frame shape of the movie from which ROIs were extracted in order
of: (height, width).
Returns
-------
roi: DenseROI
transformed roi or None if empty after transform
"""
mask = full_mask_constructor(roi['mask_matrix'], roi['x'], roi['y'], shape)
structuring_element = disk(radius=1)
mask = binary_closing(mask, selem=structuring_element)
mask = binary_opening(mask, selem=structuring_element)
new_roi = roi_from_full_mask(roi, mask)
return new_roi
def morphology(binarized):
if morph_method == 'legacy':
morph = binary_dilation(binarized, disk(1))
morph = binary_erosion(morph, disk(morph_disk))
elif morph_method == 'instamatic':
morph = remove_small_objects(binarized,
min_size=4 * 4,
connectivity=0) # remove noise
morph = binary_closing(morph,
disk(morph_disk)) # dilation + erosion
morph = binary_erosion(morph, disk(morph_disk)) # erosion
if remove_carbon_lacing:
morph = remove_small_objects(morph,
min_size=8 * 8,
connectivity=0)
morph = remove_small_holes(morph,
min_size=32 * 32,
connectivity=0)
morph = binary_dilation(morph, disk(morph_disk)) # dilation
elif (morph_method is None) or (morph_method == 'none'):
morph = binarized
else:
raise ValueError(
'Unknown morphology method {}.Choose legacy or instamatic.'
.format(morph_method))
return morph
def get_segmented_lungs(im, plot=False):
# Step 1: Convert into a binary image.
binary = im < -400
# Step 2: Remove the blobs connected to the border of the image.
cleared = clear_border(binary)
# Step 3: Label the image.
label_image = label(cleared)
# Step 4: Keep the labels with 2 largest areas.
areas = [r.area for r in regionprops(label_image)]
areas.sort()
if len(areas) > 2:
for region in regionprops(label_image):
if region.area < areas[-2]:
for coordinates in region.coords:
label_image[coordinates[0], coordinates[1]] = 0
binary = label_image > 0
# Step 5: Erosion operation with a disk of radius 2. This operation is seperate the lung nodules attached to the blood vessels.
selem = disk(2)
binary = binary_erosion(binary, selem)
# Step 6: Closure operation with a disk of radius 10. This operation is to keep nodules attached to the lung wall.
selem = disk(10) # CHANGE BACK TO 10
binary = binary_closing(binary, selem)
# Step 7: Fill in the small holes inside the binary mask of lungs.
edges = roberts(binary)
binary = ndi.binary_fill_holes(edges)
# Step 8: Superimpose the binary mask on the input image.
get_high_vals = binary == 0
im[get_high_vals] = -2000
return im, binary
def fill_raster_holes(self, array, thresh, ndval):
"""
Fills in holes and gaps in an array of 1s and NoData
:param array: 2-D array of 1s and NoData
:param thresh: hole size (cells) below which should be filled
:param ndval: NoData value
:return: 2-D array like input array but with holes filled
"""
binary = np.zeros_like(array, dtype=bool)
for j in range(0, array.shape[0] - 1):
for i in range(0, array.shape[1] - 1):
if array[j, i] == 1:
binary[j, i] = 1
b = mo.remove_small_holes(binary, thresh, 1)
c = mo.binary_closing(b, selem=np.ones((7, 7)))
d = mo.remove_small_holes(c, 500, 1)
out_array = np.full(d.shape, ndval, dtype=np.float32)
for j in range(0, d.shape[0] - 1):
for i in range(0, d.shape[1] - 1):
if d[j, i] is True:
out_array[j, i] = 1.
return out_array
def close(B): neiDia = 20 # neighborhood square side # expanding image C = [0] * (2 * neiDia + len(B[0])) C = [C] * (2 * neiDia + len(B)) C = np.array(C) C[neiDia:-neiDia, neiDia:-neiDia] = B[:, :] # creating a 2d array of ones ones = [1] * neiDia ones = [ones] * neiDia C = binary_closing(C, ones) # returning to original size C = C[neiDia:-neiDia, neiDia:-neiDia] if showProcess: viewer = ImageViewer(C) viewer.show() if writeProcessImages: folder = str(runParameters.stepNumber) + "_closing"; if not os.path.exists(folder): os.makedirs(folder) io.imsave(folder + "/" + str(imageNumber) + ".png", C*255) runParameters.stepNumber += 1 return C
def morp(arr, selema=diamond(8), selemb=diamond(4)):
"""Apply the morphology transformation over the image array."""
# res = morphology.binary_(arr, selem=selema)
# res = morphology.binary_opening(arr, selem=selema)
res = morphology.binary_dilation(arr, selem=selemb)
res = morphology.binary_closing(res, selem=selema)
return res
def binaryPostProcessing(BinaryImage, removeArea):
BinaryImage[BinaryImage > 0] = 1
###9s
# Img_BW = pymorph.binary(BinaryImage)
# Img_BW = pymorph.areaopen(Img_BW, removeArea)
# Img_BW = pymorph.areaclose(Img_BW, 50)
# Img_BW = np.uint8(Img_BW)
###2.5 s
# Img_BW = np.uint8(BinaryImage)
# Img_BW = ITK_LabelImage(Img_BW, removeArea)
# Img_BW[Img_BW >0] = 1
Img_BW = BinaryImage.copy()
BinaryImage_Label = measure.label(Img_BW)
for i, region in enumerate(measure.regionprops(BinaryImage_Label)):
if region.area < removeArea:
Img_BW[BinaryImage_Label == i + 1] = 0
else:
pass
Img_BW = morphology.binary_closing(Img_BW, morphology.disk(3))
Img_BW = remove_small_holes(Img_BW, 50)
Img_BW = np.uint8(Img_BW)
return Img_BW
def segm_2d(image, spacing=1.0):
"""This funtion segments the lungs from the given 2D slice."""
# Step 1: Convert into a binary image.
binary = image < -400
# Step 2: Remove the blobs connected to the border of the image.
cleared = segmentation.clear_border(binary)
# Step 3: Label the image.
label_image = measure.label(cleared)
# Step 4: Keep the labels with 2 largest areas.
areas = [r.area for r in measure.regionprops(label_image)]
areas.sort()
if len(areas) > 2:
for region in measure.regionprops(label_image):
if region.area < areas[-2]:
for coordinates in region.coords:
label_image[coordinates[0], coordinates[1]] = 0
binary = label_image > 0
# Step 5: Erosion operation with a disk of radius 2. This operation is
# seperating the lung nodules attached to the blood vessels.
selem = morphology.disk(2.0 / spacing)
binary = morphology.binary_erosion(binary, selem)
# Step 6: Closure operation with a disk of radius 10. This operation is
# to keep nodules attached to the lung wall.
selem = morphology.disk(10.0 / spacing)
binary = morphology.binary_closing(binary, selem)
# Step 7: Fill in the small holes inside the binary mask of lungs.
edges = filters.roberts(binary)
binary = ndimage.binary_fill_holes(edges)
return binary
def get_compactness(self, labels):
nlabels = labels.max() + 1
# nlabels = len(np.unique(labels)) - 1
eccs = np.zeros(nlabels)
for lab in range(nlabels):
obj = labels == lab
if labels.ndim == 2:
strel = np.ones((3, 3), dtype=np.bool)
obj_c = skimor.binary_closing(obj, strel)
if obj_c.sum() >= obj.sum():
obj = obj_c
else:
strel = np.ones((3, 3, 3), dtype=np.bool)
obj_c = tools.closing3D(obj, strel)
if obj_c.sum() >= obj.sum():
obj = obj_c
if labels.ndim == 2:
ecc = skimea.regionprops(obj)[0]['eccentricity']
else:
ecc = tools.get_zunics_compatness(obj)
# if np.isnan(ecc):
# ecc = 0
eccs[lab] = ecc
return eccs
def getSegmentFeatures(segment):
side = segment.shape[0]
segment[0, 0] = 0
smooth_seg = binary_fill_holes(segment)
smooth_seg = binary_closing(smooth_seg, disk(side // 60))
dist_map = distance_transform_edt(smooth_seg)
skel = skeletonize(smooth_seg)
sG = skelgraph.SkelGraph(skel)
sG.trim(side // 12)
skel = sG.mask
num_endpoints = sG.get_num_endpoints()
length = skel.sum()
width_map = skel * dist_map
mean_width = width_map.sum() / length
std_width = (((width_map)**2).sum() / length - mean_width**2)**0.5
elongation = length * length / segment.sum()
features = [
mean_width / side, std_width / side, elongation / side, num_endpoints
]
return features
def download(name_file):
img = imread(name_file)
img_gray = rgb2gray(img)
binary_img = binary_closing(canny(img_gray, sigma=2),
selem=np.ones((6, 6))) # 1.5;2
img_segment = binary_fill_holes(binary_img)
mask_img = binary_opening(img_segment, selem=np.ones((40, 40))) # 16;25
plt.imshow(img)
# plt.imshow(label2rgb(mask_img, image=img_gray))
# Поиск контуров
contours_img = find_contours(mask_img, level=0.8)
# Отображение (слишком громоздко при запуске на всем датасете, поэтому закомментировано)
# fig, ax = plt.subplots()
# ax.imshow(mask_img, cmap=plt.cm.gray)
# for contour in contours_img:
# ax.plot(contour[:, 1], contour[:, 0], linewidth=2)
plt.show()
return contours_img, mask_img
def get_segmented_lungs(im):
# Convert into a binary image.
binary = im < 604
# Remove the blobs connected to the border of the image
cleared = clear_border(binary)
# Label the image
label_image = label(cleared)
# Keep the labels with 2 largest areas
areas = [r.area for r in regionprops(label_image)]
areas.sort()
if len(areas) > 2:
for region in regionprops(label_image):
if region.area < areas[-2]:
for coordinates in region.coords:
label_image[coordinates[0], coordinates[1]] = 0
binary = label_image > 0
# Closure operation with disk of radius 12
selem = disk(2)
binary = binary_erosion(binary, selem)
selem = disk(10)
binary = binary_closing(binary, selem)
# Fill in the small holes inside the lungs
edges = roberts(binary)
binary = ndi.binary_fill_holes(edges)
# Superimpose the mask on the input image
get_high_vals = binary == 0
im[get_high_vals] = 0
return im
def clean_mask_v2(m, c):
# threshold
m_b = m > threshold_otsu(m)
c_b = c > threshold_otsu(c)
# combine contours and masks and fill the cells
m_ = np.where(m_b | c_b, 1, 0)
m_ = ndi.binary_fill_holes(m_)
# close what wasn't closed before
area, radius = mean_blob_size(m_b)
struct_size = int(1.25 * radius)
struct_el = morph.disk(struct_size)
m_padded = pad_mask(m_, pad=struct_size)
m_padded = morph.binary_closing(m_padded, selem=struct_el)
m_ = crop_mask(m_padded, crop=struct_size)
# open to cut the real cells from the artifacts
area, radius = mean_blob_size(m_b)
struct_size = int(0.75 * radius)
struct_el = morph.disk(struct_size)
m_ = np.where(c_b & (~m_b), 0, m_)
m_padded = pad_mask(m_, pad=struct_size)
m_padded = morph.binary_opening(m_padded, selem=struct_el)
m_ = crop_mask(m_padded, crop=struct_size)
# join the connected cells with what we had at the beginning
m_ = np.where(m_b | m_, 1, 0)
m_ = ndi.binary_fill_holes(m_)
# drop all the cells that weren't present at least in 25% of area in the initial mask
m_ = drop_artifacts(m_, m_b, min_coverage=0.25)
return m_
def get_segmented_lungs(im, plot=False):
# Step 1: Convert into a binary image.
binary = im < -400
# Step 2: Remove the blobs connected to the border of the image.
cleared = clear_border(binary)
# Step 3: Label the image.
label_image = label(cleared)
# Step 4: Keep the labels with 2 largest areas.
areas = [r.area for r in regionprops(label_image)]
areas.sort()
if len(areas) > 2:
for region in regionprops(label_image):
if region.area < areas[-2]:
for coordinates in region.coords:
label_image[coordinates[0], coordinates[1]] = 0
binary = label_image > 0
# Step 5: Erosion operation with a disk of radius 2. This operation is seperate the lung nodules attached to the blood vessels.
selem = disk(2)
binary = binary_erosion(binary, selem)
# Step 6: Closure operation with a disk of radius 10. This operation is to keep nodules attached to the lung wall.
selem = disk(10) # CHANGE BACK TO 10
binary = binary_closing(binary, selem)
# Step 7: Fill in the small holes inside the binary mask of lungs.
edges = roberts(binary)
binary = ndi.binary_fill_holes(edges)
# Step 8: Superimpose the binary mask on the input image.
get_high_vals = binary == 0
im[get_high_vals] = -2000
return im, binary
def refine_aseg(aseg, ball_size=4):
"""
First step to reconcile ANTs' and FreeSurfer's brain masks.
Here, the ``aseg.mgz`` mask from FreeSurfer is refined in two
steps, using binary morphological operations:
1. With a binary closing operation the sulci are included
into the mask. This results in a smoother brain mask
that does not exclude deep, wide sulci.
2. Fill any holes (typically, there could be a hole next to
the pineal gland and the corpora quadrigemina if the great
cerebral brain is segmented out).
"""
# Read aseg data
bmask = aseg.copy()
bmask[bmask > 0] = 1
bmask = bmask.astype(np.uint8)
# Morphological operations
selem = sim.ball(ball_size)
newmask = sim.binary_closing(bmask, selem)
newmask = binary_fill_holes(newmask.astype(np.uint8),
selem).astype(np.uint8)
return newmask.astype(np.uint8)
def calculate_oct_roi_mask(img, tresh=1e-10):
"""
Calculate the interesting region MASK of the image using entropy
:param img:
:param tresh: entropy cutoff threshold
:return: mask of the interesting region (MASK = 1 interesting)
"""
if img.ndim == 2:
im_slice = skimage.img_as_float(img.astype(np.float32) / 128. - 1.)
elif img.ndim == 3:
im_slice = skimage.img_as_float(img[:, :, 1].astype(np.float32) /
128. - 1.)
assert img.ndim in {2, 3}
im_slice_ = entropy(im_slice, disk(11))
im_slice_ = im_slice_ / (np.max(im_slice_) + 1e-16)
im_slice_ = np.asarray(im_slice_ > tresh, dtype=np.int8)
selem = disk(35)
im_slice_ = binary_closing(im_slice_, selem=selem)
im_slice_ = convex_hull_image(im_slice_)
plt.imshow(im_slice, cmap='gray')
plt.imshow(im_slice_, cmap='jet', alpha=0.5)
plt.pause(.1)
return im_slice_
def fill_minor_holes(img, closing_kernel=disk(10), dilation_kernel=disk(10)):
"""
Run simple heuristic to fill small holes in tissue.
It's 3 morphological operation applied in order:
1. binary_closing: used to connect tissue edges
2. binary dilation: makes tissue edges bolder (holes smaller)
3. binary_fill_holes: fill in small holes
In effect this algorithm identifies a "tissue convex hull".
Parameters
----------
img : an binary image as a numpy array
closing_kernel : image kernel used for closing
dilation_kernel : image kernel used for dilation
Returns
-------
numpy.ndarray :
transformed binary image of the same size
"""
img = binary_closing(img, closing_kernel) # connects edges
img = binary_dilation(img, dilation_kernel) # make tissue bolder
img = binary_fill_holes(img) # fills in holes
return img
def tissue_mask_generation(img_rgb, rgb_min=50):
"""
This function is used to generate tissue masks
works for patches too i guess
input :
image : type : numpy.array : BGR format usually ex
i
"""
img_rgb = np.array(img_rgb)
background_r = img_rgb[:, :, 0] > threshold_otsu(img_rgb[:, :, 0])
background_g = img_rgb[:, :, 1] > threshold_otsu(img_rgb[:, :, 1])
background_b = img_rgb[:, :, 2] > threshold_otsu(img_rgb[:, :, 2])
tissue_rgb = np.logical_not(background_r & background_g & background_b)
del background_b, background_g, background_r
min_r = img_rgb[:, :, 0] > rgb_min
min_g = img_rgb[:, :, 1] > rgb_min
min_b = img_rgb[:, :, 2] > rgb_min
tissue_mask = tissue_rgb & min_r & min_g & min_b
del min_r, min_g, min_b
close_kernel = np.ones((7, 7), dtype=np.uint8)
image_close = binary_closing(np.array(tissue_mask), close_kernel)
tissue_mask = binary_fill_holes(image_close)
del image_close, close_kernel
#Apply median filter
tissue_mask = median(tissue_mask, disk(7))
tissue_mask = np.array(tissue_mask).astype(np.uint8)
tissue_mask = tissue_mask > 0
return tissue_mask
def count_ships(path, seg, date_mask):
struct = disk(2)
seg = binary_closing(seg, struct).astype(np.bool)
im = imread(path)
im = rgba2rgb(im)
grayscale = rgb2gray(im)
thresh = threshold_yen(grayscale)
yen = grayscale > thresh
eroded = binary_erosion(seg, struct).astype(np.bool)
grayscale = grayscale > 0.6
grayscale[(eroded == 0) | (date_mask == 1) | (yen == 0)] = 0
grayscale[date_mask == 1] = 0
grayscale = binary_fill_holes(grayscale)
grayscale = clear_border(grayscale)
l = label(grayscale)
for region in regionprops(l):
if region.area > 100 or region.extent < 0.2:
grayscale = flood_fill(grayscale, tuple(region.coords[0, :]), 0)
label_image, num = label(grayscale, return_num=True)
return num, grayscale
def 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 needles2tips(needles, mri, number_of_slices=3):
"""
This function accepts a list of volumes (each volumes containing a needle) and returns a single volume containing just the tips.
Here there are a plenty of attempts of removing untrusted data.
"""
tips = np.zeros_like(mri).astype(np.int32)
#print(tips.shape)
for needle in needles:
needle = needle.astype(np.int32)
#print("MIN %f, MAX %f" % (needle.min(), needle.max()))
if np.sum(needle) < (np.shape(needle)[0] * np.shape(needle)[1] * np.shape(needle)[2]):
#print("Valid needle")
needle = binary_closing(needle, selem=np.ones((3,3,3)))
needle[needle!=0]=1
#print(" after closing: MIN %f, MAX %f " % (needle.min(), needle.max()))
for z in range(np.shape(mri)[0]-1, 0, -1):
if 200 > np.sum(needle[z,:,:]) > 0.5 and z-number_of_slices-1 >= 0:
#print(" valid slice %d" % z)
tmp = deepcopy(needle)
tmp[:z-number_of_slices-1,:,:] = 0
tips[tmp!=0] = 1
del(tmp)
break
tips[tips!=0]=1
return tips.astype(np.int32)
def segment_roi(roi):
# step 1. phase congruency (edge detection)
Mm = phasecong_Mm(roi)
# step 2. hysteresis thresholding (of edges)
B = hysthresh(Mm,HT_T1,HT_T2)
# step 3. trim pixels off border
B[B[:,1]==0,0]=0
B[B[:,-2]==0,-1]=0
B[0,B[1,:]==0]=0
B[-1,B[-2,:]==0]=0
# step 4. threshold to find dark areas
dark = dark_threshold(roi, DARK_THRESHOLD_ADJUSTMENT)
# step 5. add dark areas back to blob
B = B | dark
# step 6. binary closing
B = binary_closing(B,SE3)
# step 7. binary dilation
B = binary_dilation(B,SE2)
# step 8. thinning
B = bwmorph_thin(B,3)
# step 9. fill holes
B = binary_fill_holes(B)
# step 10. remove blobs smaller than BLOB_MIN
B = remove_small_objects(B,BLOB_MIN,connectivity=2)
# done.
return B
def fill_gaps(image, closing_radius=0, min_hole_size=0, median_radius=0.6):
"""
This function closes small gaps between and within objects and smooths edges. It is a
'finishing' step before skeletonization, and improves the quality of the skeleton by removing
gaps and minimizing bumps. It also enables removing close, parallel objects such as appear under
the microscope as a single, long, clear object with sharp, parallel edges. These spurrious objects would
otherwise pass earlier filters but are, in fact, spurrious. The function itself is a wrapper for
`skimage.morphology.binary_closing`, `skimage.morphology.remove_small_holes`, and `skimage.filters.median`
on a binary image.
Parameters
----------
image : ndarray
Binary image of candidate objects
closing_radius : ndarray
Binary structure to perform binary closing. Defaults to 0 (skips).
min_hole_size : int
Holes with areas smaller than this (in pixels) are removed. Defaults to 0 (skips).
median_radius : ndarray
Binary structure to use for a median filter. Defaults at 0.6, giving square connectivity of 1
(manhattan = 1). 0 to skip.
Returns
-------
ndarray : Binary image of candidate objects.
"""
closing_structure = _disk(closing_radius)
median_structure = _disk(median_radius)
out = morphology.binary_closing(image, closing_structure)
out = morphology.remove_small_holes(out, min_size=min_hole_size)
out = filters.median(out, selem=median_structure)
return(out)
def main():
# read image
input_path, output_path = _get_args()
input_img = cv2.imread(input_path, cv2.IMREAD_GRAYSCALE)
img = _img2bin(input_img)
# text processing phase
img = _preprocess(img)
img = binary_closing(img, selem=cfg.POS_CLOSING_SELEM)
stats = _connected_components(img)
ratios = _calc_ratios(img, stats)
blobs_img = _draw(_bin2img(img), stats, ratios=ratios)
cv2.imwrite(os.path.join(output_path, 'blobs_img.png'), blobs_img)
text_stats = _apply_thr(stats, ratios)
text_blobs_img = _draw(input_img, text_stats)
cv2.imwrite(os.path.join(output_path, 'text_blobs_img.png'), text_blobs_img)
# segmentating words
words = _process_words(_img2bin(input_img))
cv2.imwrite(os.path.join(output_path, 'words_img.png'), _bin2img(words))
words_stats = _connected_components(words)
text_mask = _stats2mask(text_stats, img.shape)
words_mask = _stats2mask(words_stats, img.shape) & text_mask
words_stats = _connected_components(words_mask)
words_blobs_img = _draw(input_img, words_stats)
cv2.imwrite(os.path.join(output_path, 'words_blobs_img.png'), words_blobs_img)
print('number of lines: %d' % len(text_stats))
print('number of words: %d' % len(words_stats))
def image_filter(img):
img2 = img.copy();
img2[img2 < 30] = 100;
img2 = exp.smooth_image(img2, sigma = 1.0);
#plt.figure(6); plt.clf();
#plt.imshow(img2);
# threshold image and take zero smaller components..
th = img2 < 92;
th2 = morph.binary_closing(th, morph.diamond(1))
label = meas.label(th2, background=0)
#plt.imshow(mask)
bs = meas.regionprops(label+1);
area = np.array([prop.area for prop in bs]);
if len(area) > 0:
mask = np.logical_and(label > -1, label != np.argsort(area)[-1]);
img2[mask] = 100;
img2[:2,:] = 100; img2[-2:,:] = 100;
img2[:,:2] = 100; img2[:,-2:] = 100;
#plt.figure(6); plt.clf();
#plt.subplot(1,2,1);
#plt.imshow(img2, vmin = 84, vmax = 92, cmap = plt.cm.gray)
#plt.subplot(1,2,2);
#plt.imshow(img2);
return img2;
def segment_watershed(seg, centers, post_morph=False):
""" perform watershed segmentation on input imsegm
and optionally run some postprocessing using morphological operations
:param ndarray seg: input image / segmentation
:param [[int, int]] centers: position of centres / seeds
:param bool post_morph: apply morphological postprocessing
:return ndarray, [[int, int]]: resulting segmentation, updated centres
"""
logging.debug('segment: watershed...')
seg_binary = (seg > 0)
seg_binary = ndimage.morphology.binary_fill_holes(seg_binary)
# thr_area = int(0.05 * np.sum(seg_binary))
# seg_binary = morphology.remove_small_holes(seg_binary, min_size=thr_area)
distance = ndimage.distance_transform_edt(seg_binary)
markers = np.zeros_like(seg)
for i, pos in enumerate(centers):
markers[int(pos[0]), int(pos[1])] = i + 1
segm = morphology.watershed(-distance, markers, mask=seg_binary)
# if morphological postprocessing was not selected, ends here
if not post_morph:
return segm, centers, None
segm_clean = np.zeros_like(segm)
for lb in range(1, np.max(segm) + 1):
seg_lb = (segm == lb)
# some morphology operartion for cleaning
seg_lb = morphology.binary_closing(seg_lb, selem=morphology.disk(5))
seg_lb = ndimage.morphology.binary_fill_holes(seg_lb)
# thr_area = int(0.15 * np.sum(seg_lb))
# seg_lb = morphology.remove_small_holes(seg_lb, min_size=thr_area)
seg_lb = morphology.binary_opening(seg_lb, selem=morphology.disk(15))
segm_clean[seg_lb] = lb
return segm_clean, centers, None
def otsu(difference, closing=True):
thresh = threshold_otsu(difference)
print(f'Otsu threshold: {thresh}')
result = difference > thresh
if closing:
result = morphology.binary_closing(result, np.ones((5, 5)))
return result
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 = binary_erosion(lines, square(13))
# Remove major lines and close shape paths
removedChessboard = binary_closing(edges * lines, square(8))
return removedChessboard
def get_segmented_lungs(im, plot=False):
cleared = clear_border(im)
label_image = measure.label(cleared)
areas = [r.area for r in measure.regionprops(label_image)]
areas.sort()
#print areas
if len(areas) > 2:
for region in measure.regionprops(label_image):
if region.area < areas[-2]:
for coordinates in region.coords:
label_image[coordinates[0], coordinates[1]] = 0
binary = label_image > 0
selem = morphology.disk(2)
binary = morphology.binary_erosion(binary, selem)
selem = morphology.disk(15)
binary = morphology.binary_closing(binary, selem)
edges = filters.roberts(binary)
binary = binary_fill_holes(edges)
get_high_vals = binary == 0
im[get_high_vals] = 0
return im
def mask_numpy_array(channel1, channel2, thresh_o = 20):
channel2_Otsu = threshold_otsu(channel2)
channel2_thresh = channel2 > ((channel2_Otsu*thresh_o)/100)
channel2_thresh = binary_closing(channel2_thresh, square(5))
channel1_channel2_masked = ma.masked_array(channel1, mask=~channel2_thresh)
channel1_channel2 = channel1_channel2_masked.filled(0)
return channel1_channel2, channel2_thresh
def get_rois(im_array, markers):
"""Return the regions of interest."""
salem = disk(3)
im = get_thresholded_image(im_array)
im = remove_small_objects(im, min_size=50)
im = binary_closing(im, salem)
im = watershed(-im_array, markers, mask=im)
return im
def outlineSmoothing(image, radius=1):
"""Smooth outlines of foreground object using morphological operations."""
struct = median(disk(radius), disk(1))
label_image = binary_closing(image, struct)
label_image = binary_opening(label_image, struct)
return label_image.astype(image.dtype)
def ProcessImage(im, targetDim = 250, doDenoiseOpening = True):
#Resize to specified pixels max edge size
scaling = 1.
if im.shape[0] > im.shape[1]:
if im.shape[0] != targetDim:
scaling = float(targetDim) / im.shape[0]
im = misc.imresize(im, (targetDim, int(round(im.shape[1] * scaling))))
else:
if im.shape[1] != targetDim:
scaling = float(targetDim) / im.shape[1]
im = misc.imresize(im, (int(round(im.shape[0] * scaling)), targetDim))
#print "scaling", scaling
greyim = 0.2126 * im[:,:,0] + 0.7152 * im[:,:,1] + 0.0722 * im[:,:,2]
#Highlight number plate
imnorm = np.array(greyim, dtype=np.uint8)
se = np.ones((3, 30), dtype=np.uint8)
opim = morph.opening(imnorm, se)
diff = greyim - opim + 128.
misc.imsave("diff.png", diff)
#Binarize image
vals = diff.copy()
vals = vals.reshape((vals.size))
meanVal = vals.mean()
stdVal = vals.std()
threshold = meanVal + stdVal
#print "Threshold", threshold
binIm = diff > threshold
misc.imsave("threshold.png", binIm)
#print vals.shape
#plt.plot(vals)
#plt.show()
#Denoise
diamond = morph.diamond(2)
if doDenoiseOpening:
currentIm = morph.binary_opening(binIm, diamond)
else:
currentIm = binIm
denoiseIm2 = morph.binary_closing(currentIm, np.ones((3, 13)))
#print "currentIm", currentIm.min(), currentIm.max(), currentIm.mean()
#print "denoiseIm2", denoiseIm2.min(), denoiseIm2.max(), currentIm.mean()
#misc.imsave("denoised1.png", currentIm * 255)
#misc.imsave("denoised2.png", denoiseIm2 * 255)
#Number candidate regions
#print "Numbering regions"
numberedRegions, maxRegionNum = morph.label(denoiseIm2, 4, 0, return_num = True)
return numberedRegions, scaling
def rotate_blob(blob, theta):
"""rotate a blob and smooth out rotation artifacts"""
blob = rotate(blob,-1*theta,resize=True)
blob = binary_closing(blob,SE3)
blob = binary_dilation(blob,SE2)
# note that H Sosik's version does one iteration
# of thinning but 3 is closer to area-preserving
blob = bwmorph_thin(blob,3)
return blob
def close_holes(image, salem=None, name='close_holes'):
if salem is None:
salem = disk(3)
closed = binary_closing(image.image_array, salem)
ia = ImageArray(closed, name)
ia.history = image.history + [name]
return ia
def crop_by_saliency(saliency_map, closing_size=11, border=50):
binary_image = threshold(saliency_map)
selem = np.ones((closing_size, closing_size))
binary_image = binary_closing(binary_image, selem)
labels = label(binary_image)
roi = max(regionprops(labels), key=attrgetter('filled_area'))
border = 50
return (slice(roi.bbox[0] - border, roi.bbox[2] + 2 * border),
slice(roi.bbox[1] - border, roi.bbox[3] + 2 * border))
def morphological_clean_sp(image, segments, diameter=4):
# remove small / thin segments by morphological closing + watershed
# extract boundaries
boundary = boundaries.find_boundaries(segments)
closed = morphology.binary_closing(boundary, np.ones((diameter, diameter)))
# extract regions
labels = morphology.label(closed, neighbors=4, background=1)
# watershed to get rid of boundaries
# interestingly we can't use gPb here. It is to sharp.
edge_image = sobel(rgb2gray(image))
result = morphology.watershed(edge_image, labels + 1)
# we want them to start at zero!
return result - 1
def extract_properties(image, closing_size=2):
selem = morphology.disk(radius=closing_size)
thresholded = image > filters.threshold_otsu(image)
closed = morphology.binary_closing(thresholded, selem)
regions = ndi.label(closed)[0]
propnames = ['area', 'convex_area', 'eccentricity', 'euler_number',
'extent', 'min_intensity', 'mean_intensity', 'max_intensity',
'minor_axis_length', 'major_axis_length']
props = measure.regionprops(regions, image)
data_table = []
for obj in props:
data_point = [getattr(obj, p) for p in propnames]
data_table.append(data_point)
return propnames, np.array(data_table), props
def noise_removal(img, radius_1=1, radius_2=2, median_iterations=3):
"""
Cleans a binary image by separating loosely connected objects, eliminating
small objects, and finally smoothing edges of the remaining objects.
The method is ``binary_opening``, ``binary_closing``, and two rounds of
``median_filter``.
Parameters
----------
img : array
a boolean ndarray
radius_1 : int
Radius of disk structuring element for opening and closing.
Default = 1, which gives 3x3 square connectivity (manhattan distance = 1).
Can also supply own boolean array.
structure_2 : int
Radius of disk structuring element for smoothing with a median filter.
Default = 2, which gives a is euclidean distance < 2*sqrt(2).
Can also supply own boolean array.
Returns
-------
A boolean ndarray of the same dimensions as ``img``.
See Also
--------
In ``scipy.ndimage``, see ``skimage.morphology.binary_opening``,
``skimage.morphology.binary_closing``, and ``skimage.filters.median``
"""
if len(np.array([radius_1]).shape) == 1:
ELEMENT_1 = _disk(radius=radius_1)
else:
ELEMENT_1 = structure_1
if len(np.array([radius_2]).shape) == 1:
ELEMENT_2 = _disk(radius=radius_2)
else:
ELEMENT_2 = structure_2
out = morphology.binary_opening(img, selem=ELEMENT_1)
out = morphology.binary_closing(out, selem=ELEMENT_1)
i = 0
while i < median_iterations:
out = filters.median(out, selem=ELEMENT_2)
i += 1
return(out)
def remove_small_ccomponents(base_label_image, size_closing=2, hist_thres=1000):
# the number and lettering are a pain for a number of methods
# we tried to get rid of it
# to this end, we extract all markings, compute connected components,
# compute the number of pixels in each components, and remove the components
# with few pixels
from scipy import ndimage as ndi
from skimage.morphology import binary_closing, binary_opening, binary_dilation
from skimage.morphology import disk
from skimage.restoration import denoise_bilateral
from skimage import measure
from skimage.morphology import label
import matplotlib.pyplot as plt
import numpy as np
#dilate then retract using morph math to consolidate noisy results
#binclos = binary_dilation(jac_inverted)
binclos = binary_closing(base_label_image,disk(size_closing)).astype(float)
#binclos = binary_opening(binclos,disk(1))
#bil = denoise_bilateral(binclos, sigma_color=0.05, sigma_spatial=5, multichannel=False)
#find the connected components
markers, n_label = label(binclos, connectivity=1, background=0, return_num=True)
#plt.imshow(markers,vmin=-1, vmax=1)
hist, bins = np.histogram(markers, bins=n_label)
r_bins = bins[0:n_label]
print('hom much hist bins are we going to keep? : ',np.sum(hist>hist_thres) )
bins_to_remove = r_bins[hist<hist_thres]
#np.append(bins_to_remove)
to_remove_mask = np.in1d(markers, bins_to_remove.astype(int))
np.sum(to_remove_mask==True)
to_remove_mask_resh = np.reshape(to_remove_mask, markers.shape)
filtered_jac_inverted = np.copy(base_label_image)
filtered_jac_inverted[to_remove_mask_resh == True] = 0
return filtered_jac_inverted, to_remove_mask_resh
def _run_interface(self, runtime):
in_files = self.inputs.in_files
if self.inputs.enhance_t2:
in_files = [_enhance_t2_contrast(f, newpath=runtime.cwd)
for f in in_files]
masknii = compute_epi_mask(
in_files,
lower_cutoff=self.inputs.lower_cutoff,
upper_cutoff=self.inputs.upper_cutoff,
connected=self.inputs.connected,
opening=self.inputs.opening,
exclude_zeros=self.inputs.exclude_zeros,
ensure_finite=self.inputs.ensure_finite,
target_affine=self.inputs.target_affine,
target_shape=self.inputs.target_shape
)
if self.inputs.closing:
closed = sim.binary_closing(masknii.get_data().astype(
np.uint8), sim.ball(1)).astype(np.uint8)
masknii = masknii.__class__(closed, masknii.affine,
masknii.header)
if self.inputs.fill_holes:
filled = binary_fill_holes(masknii.get_data().astype(
np.uint8), sim.ball(6)).astype(np.uint8)
masknii = masknii.__class__(filled, masknii.affine,
masknii.header)
if self.inputs.no_sanitize:
in_file = self.inputs.in_files
if isinstance(in_file, list):
in_file = in_file[0]
nii = nb.load(in_file)
qform, code = nii.get_qform(coded=True)
masknii.set_qform(qform, int(code))
sform, code = nii.get_sform(coded=True)
masknii.set_sform(sform, int(code))
self._results['out_mask'] = fname_presuffix(
self.inputs.in_files[0], suffix='_mask', newpath=runtime.cwd)
masknii.to_filename(self._results['out_mask'])
return runtime
def estimate_ympp(self, line_img):
"""This implemenation of estimation meter-per-pixel on y axis
is very hard-coded and image dependent. Actually I am not aware
of a general way of doing it.
"""
# warp line_img by the estimated perspective transform
warped_img = self.binary_transform(line_img)
# close the gaps in image, focus on the right part that
# has the dotted line segments
right_lane_img = binary_closing(warped_img, selem=disk(5))
right_lane_img = right_lane_img[:,1000:]
# find the regions, find the length of dot-lane segment
# as the max-axis-length of the larget region
regions = regionprops(label(right_lane_img))
max_len = max([r.major_axis_length for r in regions])
# that segment is 3 meters in reality
y_mpp = 3 / max_len
return y_mpp
def split(name):
img = plt.imread(name)
img = img[205:495,255:980]
binary = np.logical_and(img[:,:,2] > 0.8,img[:,:,0] < 0.5)
binary = binary_closing(binary)
binary_index = binary[:212,:]
binary_news = binary[212:,:]
img = img[:,600:]
binary = img[:,:,2] < 0.9
digit_index = binary[10:200,50:116]
digit_news = binary[243:278,80:116]
c = 30
d = 12
digit_index_list = [digit_index[i*c:i*c+d,:] for i in range(7)]
digit_news_list = [digit_news[:11,:],digit_news[25:,:]]
return binary_index,binary_news,digit_index_list,digit_news_list
def remove_small_ccomponents(base_label_image, size_closing=2, hist_thres=1000):
# the number and lettering are a pain for a number of methods
# we tried to extract it
from skimage.morphology import binary_closing
from skimage.morphology import disk
from skimage.morphology import label
import numpy as np
import cv2
base_label_image_f = cv2.bilateralFilter(
(base_label_image).astype(np.uint8),
d=5, sigmaColor=0.05, sigmaSpace=5)
# dilate then retract using morph math to consolidate noisy results
# binclos = binary_dilation(jac_inverted)
binclos = binary_closing(base_label_image_f, disk(size_closing)).astype(float)
# find the connected components
markers, n_label = label(binclos, connectivity=1, background=0, return_num=True)
# plt.imshow(markers,vmin=-1, vmax=1)
hist, bins = np.histogram(markers, bins=n_label)
r_bins = bins[0:n_label]
print('hom much hist bins are we going to keep? : ', np.sum(hist > hist_thres))
bins_to_remove = r_bins[hist < hist_thres]
# np.append(bins_to_remove)
to_remove_mask = np.in1d(markers, bins_to_remove.astype(int))
np.sum(to_remove_mask is True)
to_remove_mask_resh = np.reshape(to_remove_mask, markers.shape)
filtered_jac_inverted = np.copy(base_label_image)
filtered_jac_inverted[to_remove_mask_resh == 1] = 0
return filtered_jac_inverted, to_remove_mask_resh