def run_one(fname, outname):
N = 1
im = img.open(fname)
#im = im.filter(ImageFilter.BLUR)
im = im.resize((600, 600), img.ANTIALIAS)
im = im.convert('L')
im = invert(im)
x = np.asarray(im)
y = x
size = 3
for i in range(N):
y = morph.dilate(y, morph.sedisk(size))
y = morph.close(y, morph.sedisk(size))
jm = img.fromarray(y)
jm = invert(jm)
jm = jm.resize((400, 400), img.ANTIALIAS)
jm.save(outname)
def buildSeedPoints(image, mode='com'):
""" Successive set of filters to take a still image, isolate cell-like ROIs, and return a
list of points representing center points to pass into core.segmentation.pickCells.
Filters are, in order: thresholding, morphological closing, and then a connected pixel cutoff filter.
Often, the best thing to pass into this image as a high pass filtered version of your field of view.
:param image: a 2d numpy array to build points from
:param mode: an optional string, either: 'centriod' or 'com'
:returns: tuple, (seedPoints, seedPointImage) 2d and 3d numpy array, containing coordinates and an image of points, respectively
"""
# seedMask = ipg.binaryErode(ipg.connectedPixelFilter(pymorph.label(ipg.threshold(ipg.subGaussian(image))>0)))
# binarySeedMask = ipg.connectedPixelFilter(pymorph.label(pymorph.close(ipg.threshold(ipg.subGaussian(image))>0)))
binarySeedMask = ipg.connectedPixelFilter(pymorph.label(pymorph.close(ipg.threshold(image))))
seedMask = pymorph.label(binarySeedMask)
seedingRegionProps = regionProps(image, seedMask)
if mode is 'centroid':
seedPoints = [r['centroid'] for r in sorted(seedingRegionProps, key=lambda x: x['meanIntensity'],reverse=True)]
elif mode is 'com':
seedPoints = [r['com'] for r in sorted(seedingRegionProps, key=lambda x: x['meanIntensity'],reverse=True)]
# pdb.set_trace()
seedPoints = np.floor(np.array(seedPoints))
seedPointImage = np.zeros_like(seedMask)
for point in seedPoints:
seedPointImage[point] = 255
return seedPoints, seedPointImage
def GradBasedSegmentation(im):
blur = nd.gaussian_filter(im, 16)
rmax = pymorph.regmax(blur)
T = mahotas.thresholding.otsu(blur)
bImg0 = im > T
# bImg01=nd.binary_closing(bImg0,iterations=2)
bImg01 = pymorph.close(bImg0, pymorph.sedisk(3))
bImg = pymorph.open(bImg01, pymorph.sedisk(4))
# bImg=nd.binary_opening(bImg01,iterations=3)
b = pymorph.edgeoff(bImg)
d = distanceTranform(b)
seeds, nr_nuclei = nd.label(rmax)
lab = mahotas.cwatershed(d, seeds)
return lab
def GradBasedSegmentation(im):
blur=nd.gaussian_filter(im, 16)
rmax = pymorph.regmax(blur)
T = mahotas.thresholding.otsu(blur)
bImg0=im>T
#bImg01=nd.binary_closing(bImg0,iterations=2)
bImg01=pymorph.close(bImg0, pymorph.sedisk(3))
bImg=pymorph.open(bImg01, pymorph.sedisk(4))
#bImg=nd.binary_opening(bImg01,iterations=3)
b=pymorph.edgeoff(bImg)
d=distanceTranform(b)
seeds,nr_nuclei = nd.label(rmax)
lab=mahotas.cwatershed(d,seeds)
return lab
import cv2
import numpy
import numpy as np
import scipy
import pylab as pl
import pylab
import pymorph
from scipy import misc
def s(fig): pl.imshow(fig); pl.gray(); pl.show()
e = lambda fig: pymorph.erode(fig)
d = lambda fig: pymorph.dilate(fig)
o = lambda fig: pymorph.open(fig)
c = lambda fig: pymorph.close(fig)
a = lambda fun, n: reduce(lambda f1, f2: lambda x: f1(f2(x)), [fun]*n, lambda x: x)
img= 255-cv2.imread('reps/2/2.png', cv2.CV_LOAD_IMAGE_GRAYSCALE)
imgb = img > 128
BW=imgb
# grab contours
cs,_ = cv2.findContours( BW.astype('uint8'), mode=cv2.RETR_LIST,
method=cv2.CHAIN_APPROX_SIMPLE )
# set up the 'FilledImage' bit of regionprops.
filledI = np.zeros(BW.shape[0:2]).astype('uint8')
# set up the 'ConvexImage' bit of regionprops.
convexI = np.zeros(BW.shape[0:2]).astype('uint8')
# for each contour c in cs:
# will demonstrate with cs[0] but you could use a loop.
import pylab as pl
import pylab
import pymorph
from scipy import misc
def s(fig):
pl.imshow(fig)
pl.gray()
pl.show()
e = lambda fig: pymorph.erode(fig)
d = lambda fig: pymorph.dilate(fig)
o = lambda fig: pymorph.open(fig)
c = lambda fig: pymorph.close(fig)
a = lambda fun, n: reduce(lambda f1, f2: lambda x: f1(f2(x)), [fun] * n, lambda
x: x)
img = 255 - cv2.imread('reps/2/2.png', cv2.CV_LOAD_IMAGE_GRAYSCALE)
imgb = img > 128
BW = imgb
# grab contours
cs, _ = cv2.findContours(BW.astype('uint8'),
mode=cv2.RETR_LIST,
method=cv2.CHAIN_APPROX_SIMPLE)
# set up the 'FilledImage' bit of regionprops.
filledI = np.zeros(BW.shape[0:2]).astype('uint8')
# set up the 'ConvexImage' bit of regionprops.
convexI = np.zeros(BW.shape[0:2]).astype('uint8')
glom_hed = rgb2hed(glom_rgb) #hed
glom_h = glom_hed[:, :, 0] #hematoxylim
glom_h = ia.ianormalize(glom_h)
selem = disk(10) #elemento estruturante
glom_h = np.array(glom_h)
glom_h = 255 - uint8(glom_h)
#Segmentation
glom_by_reconsTopHat = morph.closerecth(glom_h,selem) #reconstrução morfológicas de fechamento
global_thresh = threshold_otsu(glom_by_reconsTopHat) #Otsu
glom_bin = glom_by_reconsTopHat > global_thresh + global_thresh*0.1
glom_bin = img_as_ubyte(glom_bin)
selem = disk(3)
glom_seg = morph.open(glom_bin, selem)
glom_seg = morph.close(glom_seg, selem) #Fechamento final
#Mostra as etapas
fig, axes = plt.subplots(2, 3, figsize=(14, 10))
fig.suptitle('Preprocessing, segmentation')
ax1, ax2, ax3, ax4, ax5, ax6 = axes.ravel()
ax1.imshow(glom_rgb, vmin=0, vmax=255, cmap=plt.cm.gray); ax1.set_title("RGB")
ax2.imshow(glom_hed, vmin=0, vmax=255, cmap=plt.cm.gray); ax2.set_title("HED")
ax3.imshow(glom_h, cmap=plt.cm.gray); ax3.set_title("255 - H (Hematoxylin)")
ax4.imshow(glom_by_reconsTopHat, vmin=0, vmax=255, cmap=plt.cm.gray); ax4.set_title("Closing-by-reconstruction top-hat")
ax5.imshow(glom_bin, vmin=0, vmax=255, cmap=plt.cm.gray); ax5.set_title("Otsu Thresholding")
ax6.imshow(glom_seg, vmin=0, vmax=255, cmap=plt.cm.gray); ax6.set_title("Opening")
#------------------------------------------------------------------------------------------------
#Feature Extraction
print "Feature Extraction:"
label_img = label(glom_seg) #Identifica formas através da vizinhaça 4 E 8
def alternative_solution(self,
a,
orientation='coronal',
linethickness=10,
outimg=False):
'''
Paramenters
-----------
a: original image in graylevel
'''
H, W = a.shape
if orientation == 'coronal':
# UL = mm.limits(a)[1] # upper limit
UL = 255
b = 1 - iacircle(a.shape, H / 3, (1.4 * H / 3, W / 2)) # Circle
b = b[0:70, W / 2 - 80:W / 2 + 80] # Rectangle
# if outimg:
# b_ = 0 * a; b_[0:70, W / 2 - 80:W / 2 + 80] = UL * b # b_ only for presentation
# b_[:, W / 2 - linethickness / 2:W / 2 + linethickness / 2] = UL # b_ only for presentation
c = a + 0
c[:, W / 2 - linethickness / 2:W / 2 + linethickness / 2] = UL
c[0:70, W / 2 - 80:W / 2 +
80] = (1 - b) * c[0:70, W / 2 - 80:W / 2 + 80] + b * UL
c[0:40, W / 2 - 70:W / 2 + 70] = UL
d = mm.open(c, mm.img2se(mm.binary(np.ones((20, 10)))))
e = mm.close(d, mm.seline(5))
f = mm.close_holes(e)
g = mm.subm(f, d)
h = mm.close_holes(g)
i = mm.areaopen(h, 1000)
j1, j2 = iaotsu(i)
# j = i > j1
ret, j = cv2.threshold(cv2.GaussianBlur(i, (7, 7), 0), j1, 255,
cv2.THRESH_BINARY)
k = mm.open(j, mm.seline(20, 90))
l = mm.areaopen(k, 1000)
# m = mm.label(l)
res = np.vstack(
[np.hstack([c, d, e, f, g]),
np.hstack([h, i, j, k, l])])
cv2.imshow('Result', res)
cv2.waitKey(0)
cv2.destroyAllWindows()
################################
# l_ = mm.blob(k,'AREA','IMAGE')
# l = l_ == max(ravel(l_))
# m = mm.open(l, mm.sedisk(3)) # VERIFICAR O MELHOR ELEMENTO ESTRUTURANTE AQUI
# n = mm.label(m)
if outimg:
if not os.path.isdir('outimg'):
os.mkdir('outimg')
def N(x):
# y = uint8(ianormalize(x, (0, 255)) + 0.5)
y = (ianormalize(x, (0, 255)) + 0.5).astype(np.uint8)
return y
adwrite('outimg/a.png', N(a))
adwrite('outimg/b.png', N(b_))
adwrite('outimg/c.png', N(c))
adwrite('outimg/d.png', N(d))
adwrite('outimg/e.png', N(e))
adwrite('outimg/f.png', N(f))
adwrite('outimg/g.png', N(g))
adwrite('outimg/h.png', N(h))
adwrite('outimg/i.png', N(i))
adwrite('outimg/j.png', N(j))
adwrite('outimg/k.png', N(k))
adwrite('outimg/l.png', N(l))
adwrite('outimg/m.png', N(m))
# adwrite('outimg/n.png', N(n))
return m
else:
b = mm.areaopen(a, 500)
c = mm.close(b, mm.sebox(3))
d = mm.close_holes(c)
e = mm.subm(d, c)
f = mm.areaopen(e, 1000)
# g = f > 5
ret, g = cv2.threshold(cv2.GaussianBlur(f, (5, 5), 0), 3, 255,
cv2.THRESH_BINARY)
# ret, g = cv2.threshold(
# cv2.GaussianBlur(f, (7, 7), 0),
# 5, 255,
# cv2.THRESH_BINARY_INV)
h = mm.asf(g, 'CO', mm.sedisk(5))
i = mm.close_holes(h)
res = np.vstack(
[np.hstack([a, b, c, d, e]),
np.hstack([f, g, h, i, a])])
cv2.imshow('Result', res)
cv2.waitKey(0)
cv2.destroyAllWindows()
if outimg:
if not os.path.isdir('outimg'):
os.mkdir('outimg')
def N(x):
y = (ianormalize(x, (0, 255)) + 0.5).astype(np.uint8)
return y
adwrite('outimg/a.png', N(a))
adwrite('outimg/b.png', N(b))
adwrite('outimg/c.png', N(c))
adwrite('outimg/d.png', N(d))
adwrite('outimg/e.png', N(e))
adwrite('outimg/f.png', N(f))
adwrite('outimg/g.png', N(g))
adwrite('outimg/h.png', N(h))
adwrite('outimg/i.png', N(i))
return i
def region_prop(fig, subfig):
# Inspired by:
# http://stackoverflow.com/a/9059648/621449
c = subfig
# set up the 'FilledImage' bit of regionprops.
FilledImage = np.zeros(fig.shape[0:2]).astype('uint8')
# set up the 'ConvexImage' bit of regionprops.
ConvexImage = np.zeros(fig.shape[0:2]).astype('uint8')
# calculate some things useful later:
m = cv2.moments(c)
# ** regionprops **
Area = m['m00']
Perimeter = cv2.arcLength(c,True)
# bounding box: x,y,width,height
BoundingBox = cv2.boundingRect(c)
# centroid = m10/m00, m01/m00 (x,y)
Centroid = ( m['m10']/m['m00'],m['m01']/m['m00'] )
# EquivDiameter: diameter of circle with same area as region
EquivDiameter = np.sqrt(4*Area/np.pi)
# Extent: ratio of area of region to area of bounding box
Extent = Area/(BoundingBox[2]*BoundingBox[3])
# FilledImage: draw the region on in white
cv2.drawContours( FilledImage, [c], 0, color=255, thickness=-1 )
# calculate indices of that region..
regionMask = (FilledImage==255)
# FilledArea: number of pixels filled in FilledImage
FilledArea = np.sum(regionMask)
# PixelIdxList : indices of region.
# (np.array of xvals, np.array of yvals)
PixelIdxList = regionMask.nonzero()
# CONVEX HULL stuff
# convex hull vertices
ConvexHull = cv2.convexHull(c)
ConvexArea = cv2.contourArea(ConvexHull)
# Solidity := Area/ConvexArea
Solidity = Area/ConvexArea
# convexImage -- draw on ConvexImage
cv2.drawContours( ConvexImage, [ConvexHull], -1,
color=255, thickness=-1 )
# ELLIPSE - determine best-fitting ellipse.
centre,axes,angle = cv2.fitEllipse(c)
MAJ = np.argmax(axes) # this is MAJor axis, 1 or 0
MIN = 1-MAJ # 0 or 1, minor axis
# Note: axes length is 2*radius in that dimension
MajorAxisLength = axes[MAJ]
MinorAxisLength = axes[MIN]
Eccentricity = np.sqrt(1-(axes[MIN]/axes[MAJ])**2)
Orientation = angle
EllipseCentre = centre # x,y
Test = FilledImage.astype('uint8')
mf = cv2.moments(Test)
CentroidFilled = ( mf['m10']/mf['m00'],mf['m01']/mf['m00'] )
# # ** if an image is supplied with the fig:
# # Max/Min Intensity (only meaningful for a one-channel img..)
# MaxIntensity = np.max(img[regionMask])
# MinIntensity = np.min(img[regionMask])
# # Mean Intensity
# MeanIntensity = np.mean(img[regionMask],axis=0)
# # pixel value
# PixelValues = img[regionMask]
x0, y0, dx, dy = BoundingBox
x1, y1 = x0 + dx, y0 + dy
Image = fig[y0:y1, x0:x1]
FilledImageFit = FilledImage[y0:y1, x0:x1]
OImage = fig[y0-1:y1+1, x0-1:x1+1]
NumPixels = Image.sum()
Fillity = (NumPixels+0.0)/FilledArea
crx, cry = (CentroidFilled[0]-x0, CentroidFilled[1]-y0)
dxc = crx-(x1-x0)/2.0
dyc = cry-(y1-y0)/2.0
CentLength = math.sqrt(dxc*dxc + dyc*dyc)
e = lambda fig: pymorph.erode(fig)
d = lambda fig: pymorph.dilate(fig)
o = lambda fig: pymorph.open(fig)
c = lambda fig: pymorph.close(fig)
a = lambda fun, n: reduce(lambda f1, f2: lambda x: f1(f2(x)), [fun]*n, lambda x: x)
Thin = pymorph.thin(OImage)
if num_holes(Image) >= 2:
Inner = removeOuter(Thin)
Inner = (a(d,7))(Inner>0)
Outer = OImage > Inner
ret = dict((k,v) for k, v in locals().iteritems() if k[0].isupper())
return ret