def test_mismatched_dims():
f = np.arange(128 * 128, dtype=float).reshape((128, 128))
filter = np.arange(17, dtype=float) - 8
filter **= 2
filter /= -16
np.exp(filter, filter)
mahotas.convolve(f, filter)
def test_mismatched_dims():
f = np.arange(128*128, dtype=float).reshape((128,128))
filter = np.arange(17,dtype=float)-8
filter **= 2
filter /= -16
np.exp(filter,filter)
mahotas.convolve(f,filter)
def test_22():
A = np.arange(1024).reshape((32,32))
B = np.array([
[0,1],
[2,3],
])
C = np.array([
[0,1,0],
[2,3,0],
[0,0,0],
])
AB = mahotas.convolve(A,B)
AC = mahotas.convolve(A,C)
assert AB.shape == AC.shape
assert np.all(AB == AC)
def test_22():
A = np.arange(1024).reshape((32, 32))
B = np.array([
[0, 1],
[2, 3],
])
C = np.array([
[0, 1, 0],
[2, 3, 0],
[0, 0, 0],
])
AB = mahotas.convolve(A, B)
AC = mahotas.convolve(A, C)
assert AB.shape == AC.shape
assert np.all(AB == AC)
def test_compare_w_ndimage():
from scipy import ndimage
A = np.arange(34*340, dtype='float64').reshape((34,340))%3
B = np.ones((3,3), A.dtype)
for mode in mahotas._filters.modes:
if mode == 'ignore':
continue
assert np.all(mahotas.convolve(A, B, mode=mode) == ndimage.convolve(A, B, mode=mode))
def test_convolve1d():
ws = [
np.array([-.1, .5,.7,.7,.5]),
np.array([.1,.7,.5]),
]
for i in range(8):
for w in ws:
f = np.random.random((128,96))
ww = np.atleast_2d(w)
fw = mh.convolve(f, ww)
fww = mh.convolve(f, ww.T)
f0w = mh.convolve1d(f, w, 0)
f1w = mh.convolve1d(f, w, 1)
assert np.all(fw == f1w)
assert np.all(fww == f0w)
def test_compare_w_ndimage():
from scipy import ndimage
A = np.arange(34 * 340).reshape((34, 340)) % 3
B = np.ones((3, 3), A.dtype)
for mode in mahotas._filters.modes:
assert np.all(
mahotas.convolve(A, B, mode=mode) == ndimage.convolve(
A, B, mode=mode))
def test_convolve1d():
ws = [
np.array([-.1, .5, .7, .7, .5]),
np.array([.1, .7, .5]),
]
for i in range(8):
for w in ws:
f = np.random.random((128, 96))
ww = np.atleast_2d(w)
fw = mh.convolve(f, ww)
fww = mh.convolve(f, ww.T)
f0w = mh.convolve1d(f, w, 0)
f1w = mh.convolve1d(f, w, 1)
assert np.all(fw == f1w)
assert np.all(fww == f0w)
def perimeter(bwimage, n=4, mode="constant"):
"""
p = perimeter(bwimage, n=4, mode="constant")
Calculate total perimeter of all objects in binary image.
Parameters
----------
bwimage : array
binary image
n : int, optional
passed to ``bwperim`` as is
mode : str, optional
passed to ``bwperim`` as is
Returns
-------
p : float
total perimeter of all objects in binary image
See Also
--------
bwperim : function
Finds the perimeter region
References
----------
.. [1] K. Benkrid, D. Crookes. Design and FPGA Implementation of
a Perimeter Estimator. The Queen's University of Belfast.
http://www.cs.qub.ac.uk/~d.crookes/webpubs/papers/perimeter.doc
"""
global _perimeter_values
perim = bwperim(bwimage, n, mode)
perim = perim.astype(np.uint8)
histogram = mh.fullhistogram(
mh.convolve(perim, _perimeter_magic))
if _perimeter_values is None:
_perimeter_values = np.zeros(34, float)
_perimeter_values[[5, 7, 15, 17, 25, 27]] = 1
_perimeter_values[[21, 33]] = np.sqrt(2)
_perimeter_values[[13, 23]] = (1 + np.sqrt(2)) / 2
size = min(34, len(histogram))
return np.dot(histogram[:size], _perimeter_values[:size])
def perimeter(bwimage, n=4, mode="constant"):
"""
p = perimeter(bwimage, n=4, mode="constant")
Calculate total perimeter of all objects in binary image.
Parameters
----------
bwimage : array
binary image
n : int, optional
passed to ``bwperim`` as is
mode : str, optional
passed to ``bwperim`` as is
Returns
-------
p : float
total perimeter of all objects in binary image
See Also
--------
bwperim : function
Finds the perimeter region
References
----------
.. [1] K. Benkrid, D. Crookes. Design and FPGA Implementation of
a Perimeter Estimator. The Queen's University of Belfast.
http://www.cs.qub.ac.uk/~d.crookes/webpubs/papers/perimeter.doc
"""
global _perimeter_values
perim = bwperim(bwimage, n, mode)
perim = perim.astype(np.uint8)
histogram = mh.fullhistogram(
mh.convolve(perim, _perimeter_magic))
if _perimeter_values is None:
_perimeter_values = np.zeros(34, float)
_perimeter_values[[5, 7, 15, 17, 25, 27]] = 1
_perimeter_values[[21, 33]] = np.sqrt(2)
_perimeter_values[[13, 23]] = (1 + np.sqrt(2)) / 2
size = min(34, len(histogram))
return np.dot(histogram[:size], _perimeter_values[:size])
from pylab import imshow
import mahotas
import numpy as np
wally = mahotas.imread('data/DepartmentStore.jpg')
wfloat = wally.astype(float)
r, g, b = wfloat.transpose((2, 0, 1))
w = wfloat.mean(2)
pattern = np.ones((24, 16), float)
for i in range(2):
pattern[i::4] = -1
v = mahotas.convolve(r - w, pattern)
mask = (v == v.max())
mask = mahotas.dilate(mask, np.ones((48, 24)))
wally -= .8 * wally * ~mask[:, :, None]
imshow(wally)
gap_completion_distances * gap_completion_factor
combined_outflow = outflow_smooth * smoothing_factor + \
outflow_gap * gap_completion_factor
combined_inflow = inflow_smooth * smoothing_factor + \
inflow_gap * gap_completion_factor
# Find ignorable nodes - those where full 3x3 neighborhood has
# source_sink_cap > 0 and sum of source_sink_cap in
# neighborhood (except center) is greater than neighborhood
# outflow. Similar for inflow.
hollow = np.ones((3, 3))
hollow[1, 1] = 0
ignorable = np.logical_and(
mahotas.erode(source_sink_cap > 0, np.ones((3, 3))),
(mahotas.convolve(source_sink_cap,
hollow,
mode='ignore') > combined_outflow))
np.logical_or(
ignorable,
np.logical_and(
mahotas.erode(source_sink_cap < 0, np.ones(
(3, 3))),
(mahotas.convolve(
source_sink_cap, hollow, mode='ignore') <
-combined_inflow)), # careful with signs
out=ignorable)
print "Can ignore {0} of {1}".format(
np.sum(ignorable), ignorable.size)
## Load the adjacency matrix
combined_distances = smooth_distances * smoothing_factor + \
gap_completion_distances * gap_completion_factor
combined_outflow = outflow_smooth * smoothing_factor + \
outflow_gap * gap_completion_factor
combined_inflow = inflow_smooth * smoothing_factor + \
inflow_gap * gap_completion_factor
# Find ignorable nodes - those where full 3x3 neighborhood has
# source_sink_cap > 0 and sum of source_sink_cap in
# neighborhood (except center) is greater than neighborhood
# outflow. Similar for inflow.
hollow = np.ones((3, 3))
hollow[1, 1] = 0
ignorable = np.logical_and(mahotas.erode(source_sink_cap > 0, np.ones((3,3))),
(mahotas.convolve(source_sink_cap, hollow, mode='ignore') >
combined_outflow))
np.logical_or(ignorable,
np.logical_and(mahotas.erode(source_sink_cap < 0, np.ones((3,3))),
(mahotas.convolve(source_sink_cap, hollow, mode='ignore') <
- combined_inflow)), # careful with signs
out=ignorable)
print "Can ignore {0} of {1}".format(np.sum(ignorable), ignorable.size)
## Load the adjacency matrix
for di, direction in enumerate(directions[:4]):
dest_coords = shift_coords(coords, direction)
source_coords, dest_coords = validate_and_broadcast(coords, dest_coords)
mask = np.logical_or(ignorable[source_coords],
from pylab import imshow
import numpy as np
import mahotas
wally = mahotas.imread('waldo.jpg')
imshow(wally)
wfloat = wally.astype(float)
r,g,b = wfloat.transpose((2,0,1)) # split into rgb channels, better to use floats
w = wfloat.mean(2) # w is the white channel
pattern = np.ones((24,16),float)
for i in xrange(2):
pattern[i::4] = -1 # build a pattern of +1,+1,-1,-1 on vertical axis -> Wally's shirt.
v = mahotas.convolve(r-w, pattern) # convolve red-white, will give strong response where shirt
mask = (v == v.max())
mask = mahotas.dilate(mask,np.ones((48,24))) # look for max and dilate it to make it visible
wally -= .8*wally * ~mask[:,:,None]
imshow(wally)# imshow(wally)
def _patch_ms(patch, args):
histogram = np.histogram(patch,bins=256,range=(0,256))[0]
# np.set_printoptions(precision=2,threshold=256)
# print(histogram)
thresholds = threshold.multi_kapur(histogram, 2)
tee.log('Maximum entropy discretization (Kapur et al. 1985, 3 bins):', thresholds)
minint = thresholds[0]
if minint != thresholds[0]:
tee.log('Warning: minint was lowered')
if minint <= 1:
tee.log('minint threshold too low (%d) - I believe there are no cells in this substack' % minint)
return None
if thresholds[1] < args.min_second_threshold:
tee.log('thresholds[1] threshold too low (%d) - I believe there are no cells in this substack' % thresholds[1])
return None
(Lx,Ly,Lz) = np.where(patch > minint)
intensities = patch[(Lx,Ly,Lz)]
L = np.array(list(zip(Lx,Ly,Lz)), dtype=np.uint16)
tee.log('Found', len(L), 'voxels above the threshold', minint)
if len(L) < 10:
tee.log('Too few points (%d) - I believe there are no cells in this substack' % len(L))
return None
bandwidth = args.mean_shift_bandwidth
radius = args.hi_local_max_radius
reg_maxima = mh.regmax(patch.astype(np.int))
if args.seeds_filtering_mode == 'hard':
xx, yy, zz = np.mgrid[:2*radius+1, :2*radius+1, :2*radius+1]
sphere = (xx - radius) ** 2 + (yy - radius) ** 2 + (zz - radius) ** 2
se = sphere <= radius*radius
f = se.astype(np.float64)
elif args.seeds_filtering_mode == 'soft':
f=np.zeros((int(radius+1)*2+1,int(radius+1)*2+1,int(radius+1)*2+1), dtype=np.float64);f[int(radius+1),int(radius+1),int(radius+1)]=1
f=gaussian_filter(f, radius/2.,mode='constant', cval=0.0);f=f/np.amax(f)
else:
raise ValueError("Invalid seeds filtering mode", args.seeds_filtering_mode)
min_mass = np.sum(f)*minint
local_mass = mh.convolve(patch, weights=f, mode='constant', cval=0.0)
above = local_mass > min_mass
himaxima = np.logical_and(reg_maxima,above)
if np.sum(himaxima) > args.max_expected_cells:
tee.log('Too many candidates,', np.sum(himaxima), 'I believe this substack is messy and give up')
return None
C = [volume.Center(x,y,z) for (x,y,z) in zip(*np.where(himaxima))]
if len(C) == 0:
tee.log('No maxima above. #himaxima=', np.sum(himaxima), '#above=', np.sum(above), '. Giving up')
return None
seeds = np.array([[c.x, c.y, c.z] for c in C])
# Save seeds with some info for debugging purposes
for c in C:
c.name = 'seed'
c.mass = patch[c.x,c.y,c.z]
c.volume = thresholds[0]
cluster_centers, labels, volumes, masses, trajectories = mean_shift(L, intensities=intensities,
bandwidth=bandwidth, seeds=seeds)
if cluster_centers is None:
return None
masses = np.zeros(len(cluster_centers))
for i,c in enumerate(cluster_centers):
masses[i] = local_mass[int(c[0]+0.5),int(c[1]+0.5),int(c[2]+0.5)]
PatchMSRet = namedtuple('PatchMSRet',
['cluster_centers','labels','masses','L','seeds'])
r = PatchMSRet(cluster_centers=cluster_centers,
labels=labels, masses=masses, L=L, seeds=C)
return r
def sujoy(img, kernel_nhood=0, just_filter=False):
'''
edges = sujoy(img, kernel_nhood=0, just_filter=False)
Compute edges using Sujoy's algorithm
`edges` is a binary image of edges computed according to Sujoy's algorithm.
PAPER LINK: https://www.ijert.org/research/a-better-first-derivative-approach-for-edge-detection-IJERTV2IS110616.pdf
Parameters
----------
img : Any 2D-ndarray
kernel_nhood : 0(default) or 1
if 0, kernel is based on 4-neighborhood
else , kernel is based on 8-neighborhood
just_filter : boolean, optional
If true, then return the result of filtering the image with the Sujoy's
filters, but do not threshold (default is False).
Returns
-------
edges : ndarray
Binary image of edges, unless `just_filter`, in which case it will be
an array of floating point values.
'''
img = np.array(img, dtype=np.float)
if img.ndim != 2:
raise ValueError(
'mahotas.sujoy: Only available for 2-dimensional images')
img -= img.min()
ptp = img.ptp()
if ptp == 0:
return img
img /= ptp
if kernel_nhood:
krnl_h = np.array([[0, -1, -1, -1, 0], [0, -1, -1, -1, 0],
[0, 0, 0, 0, 0], [0, 1, 1, 1, 0], [0, 1, 1, 1, 0]
]) / 12.
krnl_v = np.array([[0, 0, 0, 0, 0], [-1, -1, 0, 1, 1], [
-1, -1, 0, 1, 1
], [-1, -1, 0, 1, 1], [0, 0, 0, 0, 0]]) / 12.
else:
krnl_h = np.array([[0, 0, -1, 0, 0], [0, -1, -1, -1, 0], [
0, 0, 0, 0, 0
], [0, 1, 1, 1, 0], [0, 0, 1, 0, 0]]) / 8.
krnl_v = np.array([[0, 0, 0, 0, 0], [0, -1, 0, 1, 0], [
-1, -1, 0, 1, 1
], [0, -1, 0, 1, 0], [0, 0, 0, 0, 0]]) / 8.
grad_h = mh.convolve(img, krnl_h, mode='nearest')
grad_v = mh.convolve(img, krnl_v, mode='nearest')
grad_h **= 2
grad_v **= 2
grad = grad_h
grad += grad_v
if just_filter:
return grad
t = np.sqrt(grad.mean())
return mh.regmax(grad) * (np.sqrt(grad) > t)
import mahotas
import mahotas.demos
from pylab import gray, imshow, show
import numpy as np
# loading image(input image file name inplace of 'lena')
img = mahotas.demos.load('lena')
img = img.max(2)
T_otsu = mahotas.otsu(img)
img = img > T_otsu
print("Image threshold using Otsu Mehtod")
imshow(img)
show()
weight = np.ones((5, 5), float)
new_img = mahotas.convolve(img, weight)
print("Convolved Image")
imshow(new_img)
show()
wally = mahotas.demos.load('Wally')
imshow(wally)
show()
wfloat = wally.astype(float)
r, g, b = wfloat.transpose((2,0,1)) #transpose 시킴. 인덱스 번호는 0, 1, 2 순서로 갑니다. 그런데 지금 '2'가 면으로 왔습니다. ???????????????
w = wfloat.mean(2)# 2개씩 평균을 취해감.
pattern = np.ones((24, 16), float)#직삭각형을 만든 것 입니다. 직사각형 패턴
#셔츠의 패턴
for i in np.arange(2): # i에는 0, 1
pattern[i::4] = -1 # 4칸씩 건너뛰면서 -1
v = mahotas.convolve(r-w, pattern) #컨볼루션 연산을 패턴을 가지고 합니다. 위에 셔츠의 패턴이 '필터'가 됩니다. #여기에는 stride 개념이 있습니다. 몇칸씩 건너뛸것이냐. 지금 지정이 없으니까 '1픽셀씩 건너뛰면서 = -1 '
mask = (v == v.max()) # v값과, v최고값인 것
mask = mahotas.dilate(mask, np.ones((48, 24))) #dilate 확장=키우라. 원래 24,16인데 48,24로 키웠음.
np.subtract(wally, .8*wally * ~mask[:, :, None], out=wally, casting='unsafe')
imshow(wally)
show()
##
from PIL import Image
img = Image.open('C:/Users/Hyungi/Desktop/workplace/img/image.png')
dim = (100, 100, 400, 400)
crop_img = img.crop(dim)
crop_img.show()
def _patch_ms(patch, args):
histogram = np.histogram(patch,bins=256,range=(0,256))[0]
# np.set_printoptions(precision=2,threshold=256)
# print(histogram)
thresholds = threshold.multi_kapur(histogram, 2)
tee.log('Maximum entropy discretization (Kapur et al. 1985, 3 bins):', thresholds)
minint = thresholds[0]
if minint != thresholds[0]:
tee.log('Warning: minint was lowered')
if minint <= 1:
tee.log('minint threshold too low (%d) - I believe there are no cells in this substack' % minint)
return None
if thresholds[1] < args.min_second_threshold:
tee.log('thresholds[1] threshold too low (%d) - I believe there are no cells in this substack' % thresholds[1])
return None
(Lx,Ly,Lz) = np.where(patch > minint)
intensities = patch[(Lx,Ly,Lz)]
L = np.array(zip(Lx,Ly,Lz), dtype=np.uint16)
tee.log('Found', len(L), 'voxels above the threshold', minint)
if len(L) < 10:
tee.log('Too few points (%d) - I believe there are no cells in this substack' % len(L))
return None
bandwidth = args.mean_shift_bandwidth
radius = args.hi_local_max_radius
reg_maxima = mh.regmax(patch.astype(np.int))
if args.seeds_filtering_mode == 'hard':
xx, yy, zz = np.mgrid[:2*radius+1, :2*radius+1, :2*radius+1]
sphere = (xx - radius) ** 2 + (yy - radius) ** 2 + (zz - radius) ** 2
se = sphere <= radius*radius
f = se.astype(np.float64)
elif args.seeds_filtering_mode == 'soft':
f=np.zeros((int(radius+1)*2+1,int(radius+1)*2+1,int(radius+1)*2+1), dtype=np.float64);f[int(radius+1),int(radius+1),int(radius+1)]=1
f=gaussian_filter(f, radius/2.,mode='constant', cval=0.0);f=f/np.amax(f)
else:
raise ValueError("Invalid seeds filtering mode", args.seeds_filtering_mode)
min_mass = np.sum(f)*minint
local_mass = mh.convolve(patch, weights=f, mode='constant', cval=0.0)
above = local_mass > min_mass
himaxima = np.logical_and(reg_maxima,above)
if np.sum(himaxima) > args.max_expected_cells:
tee.log('Too many candidates,', np.sum(himaxima), 'I believe this substack is messy and give up')
return None
C = [volume.Center(x,y,z) for (x,y,z) in zip(*np.where(himaxima))]
if len(C) == 0:
tee.log('No maxima above. #himaxima=', np.sum(himaxima), '#above=', np.sum(above), '. Giving up')
return None
seeds = np.array([[c.x, c.y, c.z] for c in C])
# Save seeds with some info for debugging purposes
for c in C:
c.name = 'seed'
c.mass = patch[c.x,c.y,c.z]
c.volume = thresholds[0]
cluster_centers, labels, volumes, masses, trajectories = mean_shift(L, intensities=intensities,
bandwidth=bandwidth, seeds=seeds)
if cluster_centers is None:
return None
masses = np.zeros(len(cluster_centers))
for i,c in enumerate(cluster_centers):
masses[i] = local_mass[int(c[0]+0.5),int(c[1]+0.5),int(c[2]+0.5)]
PatchMSRet = namedtuple('PatchMSRet',
['cluster_centers','labels','masses','L','seeds'])
r = PatchMSRet(cluster_centers=cluster_centers,
labels=labels, masses=masses, L=L, seeds=C)
return r
def main(image, mask, threshold=25,
mean_size=6, min_size=10,
filter_type='log_2d',
minimum_bead_intensity=150,
z_step=0.333, pixel_size=0.1625,
alpha=0, plot=False):
'''Converts an image stack with labelled cell surface to a cell
`volume` image
Parameters
----------
image: numpy.ndarray[Union[numpy.uint8, numpy.uint16]]
grayscale image in which beads should be detected (3D)
mask: numpy.ndarray[Union[numpy.int32, numpy.bool]]
binary or labeled image of cell segmentation (2D)
threshold: int, optional
intensity of bead in filtered image (default: ``25``)
mean_size: int, optional
mean size of bead (default: ``6``)
min_size: int, optional
minimal number of connected voxels per bead (default: ``10``)
filter_type: str, optional
filter used to emphasise the beads in 3D
(options: ``log_2d`` (default) or ``log_3d``)
minimum_bead_intensity: int, optional
minimum intensity in the original image of an identified bead
centre. Use to filter low intensity beads.
z_step: float, optional
distance between consecutive z-planes (um) (default: ``0.333``)
pixel_size: float, optional
size of pixel (um) (default: ``0.1625``)
alpha: float, optional
value of parameter for 3D alpha shape calculation
(default: ``0``, no vertex filtering performed)
plot: bool, optional
whether a plot should be generated (default: ``False``)
Returns
-------
jtmodules.generate_volume_image.Output
'''
# Check that there are cells identified in image
if (np.max(mask) > 0):
volume_image_calculated = True
n_slices = image.shape[-1]
logger.debug('input image has z-dimension %d', n_slices)
# Remove high intensity pixels
detect_image = image.copy()
p = np.percentile(detect_image, 99.9)
detect_image[detect_image > p] = p
# Perform LoG filtering in 3D to emphasise beads
if filter_type == 'log_2d':
logger.info('using stacked 2D LoG filter to detect beads')
f = -1 * log_2d(size=mean_size, sigma=float(mean_size - 1) / 3)
filt = np.stack([f for _ in range(mean_size)], axis=2)
elif filter_type == 'log_3d':
logger.info('using 3D LoG filter to detect beads')
filt = -1 * log_3d(mean_size, (float(mean_size - 1) / 3,
float(mean_size - 1) / 3,
4 * float(mean_size - 1) / 3))
else:
logger.info('using unfiltered image to detect beads')
if filter_type == 'log_2d' or filter_type == 'log_3d':
logger.debug('convolve image with filter kernel')
detect_image = mh.convolve(detect_image.astype(float), filt)
detect_image[detect_image < 0] = 0
logger.debug('threshold beads')
labeled_beads, n_labels = mh.label(detect_image > threshold)
logger.info('detected %d beads', n_labels)
logger.debug('remove small beads')
sizes = mh.labeled.labeled_size(labeled_beads)
too_small = np.where(sizes < min_size)
labeled_beads = mh.labeled.remove_regions(labeled_beads, too_small)
mh.labeled.relabel(labeled_beads, inplace=True)
logger.info(
'%d beads remain after removing small beads', np.max(labeled_beads)
)
logger.debug('localise beads in 3D')
localised_beads = localise_bead_maxima_3D(
image, labeled_beads, minimum_bead_intensity
)
logger.debug('mask beads inside cells')
'''NOTE: localised_beads.coordinate image is used only for beads
outside cells and can therefore be modified here. For beads
inside cells, localised_beads.coordinates are used instead.
'''
# expand mask to ensure slide-beads are well away from cells
slide = localised_beads.coordinate_image
expand_mask = mh.dilate(
A=mask > 0,
Bc=np.ones([25,25], bool)
)
slide[expand_mask] = 0
logger.debug('determine coordinates of slide surface')
try:
bottom_surface = slide_surface_params(slide)
except InvalidSlideError:
logger.error('slide surface calculation is invalid' +
' returning empty volume image')
volume_image = np.zeros(shape=image[:,:,0].shape,
dtype=image.dtype)
figure = str()
return Output(volume_image, figure)
logger.debug('subtract slide surface to get absolute bead coordinates')
bead_coords_abs = []
for i in range(len(localised_beads.coordinates)):
bead_height = (
localised_beads.coordinates[i][2] -
plane(localised_beads.coordinates[i][0],
localised_beads.coordinates[i][1],
bottom_surface.x)
)
if bead_height > 0:
bead_coords_abs.append(
(localised_beads.coordinates[i][0],
localised_beads.coordinates[i][1],
bead_height)
)
logger.debug('convert absolute bead coordinates to image')
coord_image_abs = coordinate_list_to_array(
bead_coords_abs, shape=image[:,:,0].shape, dtype=np.float32
)
filtered_coords_global = filter_vertices_per_cell_alpha_shape(
coord_image_abs=coord_image_abs,
mask=mask,
alpha=alpha,
z_step=z_step,
pixel_size=pixel_size
)
logger.info('interpolate cell surface')
volume_image = interpolate_surface(
coords=np.asarray(filtered_coords_global, dtype=np.uint16),
output_shape=np.shape(image[:,:,0]),
method='linear'
)
volume_image = volume_image.astype(image.dtype)
logger.debug('set regions outside mask to zero')
volume_image[mask == 0] = 0
else:
logger.warn(
'no objects in input mask, skipping cell volume calculation.'
)
volume_image_calculated = False
volume_image = np.zeros(shape=image[:,:,0].shape, dtype=image.dtype)
if (plot and volume_image_calculated):
logger.debug('convert bottom surface plane to image for plotting')
dt = np.dtype(float)
bottom_surface_image = np.zeros(slide.shape, dtype=dt)
for ix in range(slide.shape[0]):
for iy in range(slide.shape[1]):
bottom_surface_image[ix, iy] = plane(
ix, iy, bottom_surface.x)
logger.info('create plot')
from jtlib import plotting
plots = [
plotting.create_intensity_image_plot(
np.max(image, axis=-1), 'ul', clip=True
),
plotting.create_float_image_plot(
bottom_surface_image, 'll', clip=True
),
plotting.create_intensity_image_plot(
volume_image, 'ur', clip=True
)
]
figure = plotting.create_figure(
plots, title='Convert stack to volume image'
)
else:
figure = str()
return Output(volume_image, figure)
from pylab import imshow
import mahotas as mh
import numpy as np
wally = mh.demos.load('DepartmentStore')
wfloat = wally.astype(float)
r, g, b = wfloat.transpose((2, 0, 1))
w = wfloat.mean(2)
pattern = np.ones((24, 16), float)
for i in range(2):
pattern[i::4] = -1
v = mh.convolve(r - w, pattern)
mask = (v == v.max())
mask = mh.dilate(mask, np.ones((48, 24)))
wally -= np.array(.8 * wally * ~mask[:, :, None], dtype=wally.dtype)
imshow(wally)
def main(image,
mask,
threshold=1,
min_area=3,
mean_area=5,
max_area=1000,
clip_percentile=99.999,
plot=False):
'''Detects blobs in `image` using an implementation of
`SExtractor <http://www.astromatic.net/software/sextractor>`_ [1].
The `image` is first convolved with a Laplacian of Gaussian filter of size
`mean_area` to enhance blob-like structures. The enhanced image is
then thresholded at `threshold` level and connected pixel components are
subsequently deplended.
Parameters
----------
image: numpy.ndarray[Union[numpy.uint8, numpy.uint16]]
grayscale image in which blobs should be detected
mask: numpy.ndarray[Union[numpy.int32, numpy.bool]]
binary or labeled image that specifies pixel regions of interest
in which blobs should be detected
threshold: int, optional
threshold level for pixel values in the convolved image
(default: ``1``)
min_area: int, optional
minimal size a blob is allowed to have (default: ``3``)
mean_area: int, optional
estimated average size of a blob (default: ``5``)
max_area: int, optional
maximal size a blob is allowed to have to be subject to deblending;
no attempt will be made to deblend blobs larger than `max_area`
(default: ``100``)
clip_percentile: float, optional
clip intensity values in `image` above the given percentile; this may
help in attenuating artifacts
plot: bool, optional
whether a plot should be generated (default: ``False``)
Returns
-------
jtmodules.detect_blobs.Output[Union[numpy.ndarray, str]]
References
----------
.. [1] Bertin, E. & Arnouts, S. 1996: SExtractor: Software for source
extraction, Astronomy & Astrophysics Supplement 317, 393
'''
logger.info('detect blobs above threshold {0}'.format(threshold))
detect_image = image.copy()
p = np.percentile(image, clip_percentile)
detect_image[image > p] = p
# Enhance the image for blob detection by convoling it with a LOG filter
f = -1 * log_2d(size=mean_area, sigma=float(mean_area - 1) / 3)
detect_image = mh.convolve(detect_image.astype(float), f)
detect_image[detect_image < 0] = 0
# Mask regions of too big blobs
pre_blobs = mh.label(detect_image > threshold)[0]
bad_blobs, n_bad = mh.labeled.filter_labeled(pre_blobs, min_size=max_area)
logger.info(
'remove {0} blobs because they are bigger than {1} pixels'.format(
n_bad, max_area))
detect_mask = np.invert(mask > 0)
detect_mask[bad_blobs > 0] = True
detect_image[bad_blobs > 0] = 0
logger.info('deblend blobs')
blobs, centroids = detect_blobs(image=detect_image,
mask=detect_mask,
threshold=threshold,
min_area=min_area)
n = len(np.unique(blobs[blobs > 0]))
logger.info('{0} blobs detected'.format(n))
if plot:
logger.info('create plot')
from jtlib import plotting
colorscale = plotting.create_colorscale('Spectral',
n=n,
permute=True,
add_background=True)
plots = [
plotting.create_float_image_plot(detect_image, 'ul', clip=True),
plotting.create_mask_image_plot(blobs, 'ur', colorscale=colorscale)
]
figure = plotting.create_figure(
plots,
title=('detected #{0} blobs above threshold {1}'
' in LOG filtered image'.format(n, threshold)))
else:
figure = str()
return Output(centroids, blobs, figure)
import mahotas as mh
import numpy as np
import cv2
# Imported mahotas & numpy with standard abbreviations
im = mh.imread('./images/pool-table-above-17031042.jpg', as_grey=1)
# Load the image & convert to gray
# im2 = im[::2,::2]
im2 = mh.gaussian_filter(im, 1.2)
cv2.imshow('gaussian', im)
# save first step
# mh.imsave('1.png', im2.astype(np.uint8))
# Mean filtering is implemented "by hand" with a convolution.
mean_filtered = mh.convolve(im2.astype(float), np.ones((9, 9))/81.)
# iminv = 255 - mean_filtered
# mh.imsave('binarized1.png', iminv.astype(np.uint8))
# You might need to adjust the number 4 here, but it worked well for this image.
imc = im2 > mean_filtered - 4
# cv2.imshow('open circles', (imc*255).astype(np.uint8));
# cv2.waitKey(0)
# mh.imsave('1.png', im2.astype(np.uint8))
# print(im2)
# imc = mh.convolve(imc.astype(float), np.ones((9, 9))/81.)
# imc = im2 > mean_filtered - 6
from pylab import imshow
import mahotas
wally = mahotas.imread('data/DepartmentStore.jpg')
wfloat = wally.astype(float)
r,g,b = wfloat.transpose((2,0,1))
w = wfloat.mean(2)
pattern = np.ones((24,16), float)
for i in xrange(2):
pattern[i::4] = -1
v = mahotas.convolve(r-w, pattern)
mask = (v == v.max())
mask = mahotas.dilate(mask, np.ones((48,24)))
wally -= .8*wally * ~mask[:,:,None]
imshow(wally)
def main(image, mask, threshold=1, min_area=3, mean_area=5, max_area=1000,
clip_percentile=99.999, plot=False):
'''Detects blobs in `image` using an implementation of
`SExtractor <http://www.astromatic.net/software/sextractor>`_ [1].
The `image` is first convolved with a Laplacian of Gaussian filter of size
`mean_area` to enhance blob-like structures. The enhanced image is
then thresholded at `threshold` level and connected pixel components are
subsequently deplended.
Parameters
----------
image: numpy.ndarray[Union[numpy.uint8, numpy.uint16]]
grayscale image in which blobs should be detected
mask: numpy.ndarray[Union[numpy.int32, numpy.bool]]
binary or labeled image that specifies pixel regions of interest
in which blobs should be detected
threshold: int, optional
threshold level for pixel values in the convolved image
(default: ``1``)
min_area: int, optional
minimal size a blob is allowed to have (default: ``3``)
mean_area: int, optional
estimated average size of a blob (default: ``5``)
max_area: int, optional
maximal size a blob is allowed to have to be subject to deblending;
no attempt will be made to deblend blobs larger than `max_area`
(default: ``100``)
clip_percentile: float, optional
clip intensity values in `image` above the given percentile; this may
help in attenuating artifacts
plot: bool, optional
whether a plot should be generated (default: ``False``)
Returns
-------
jtmodules.detect_blobs.Output[Union[numpy.ndarray, str]]
References
----------
.. [1] Bertin, E. & Arnouts, S. 1996: SExtractor: Software for source
extraction, Astronomy & Astrophysics Supplement 317, 393
'''
logger.info('detect blobs above threshold {0}'.format(threshold))
detect_image = image.copy()
p = np.percentile(image, clip_percentile)
detect_image[image > p] = p
# Enhance the image for blob detection by convoling it with a LOG filter
f = -1 * log_2d(size=mean_area, sigma=float(mean_area - 1)/3)
detect_image = mh.convolve(detect_image.astype(float), f)
detect_image[detect_image < 0] = 0
# Mask regions of too big blobs
pre_blobs = mh.label(detect_image > threshold)[0]
bad_blobs, n_bad = mh.labeled.filter_labeled(pre_blobs, min_size=max_area)
logger.info(
'remove {0} blobs because they are bigger than {1} pixels'.format(
n_bad, max_area
)
)
detect_mask = np.invert(mask > 0)
detect_mask[bad_blobs > 0] = True
detect_image[bad_blobs > 0] = 0
logger.info('deblend blobs')
blobs, centroids = detect_blobs(
image=detect_image, mask=detect_mask, threshold=threshold,
min_area=min_area
)
n = len(np.unique(blobs[blobs>0]))
logger.info('{0} blobs detected'.format(n))
if plot:
logger.info('create plot')
from jtlib import plotting
colorscale = plotting.create_colorscale(
'Spectral', n=n, permute=True, add_background=True
)
plots = [
plotting.create_float_image_plot(
detect_image, 'ul', clip=True
),
plotting.create_mask_image_plot(
blobs, 'ur', colorscale=colorscale
)
]
figure = plotting.create_figure(
plots,
title=(
'detected #{0} blobs above threshold {1}'
' in LOG filtered image'.format(n, threshold)
)
)
else:
figure = str()
return Output(centroids, blobs, figure)