I have a segmented image using SLIC from scipy and for every superpixel i get an image where only that superpixel is colored and the rest of the image is black. I want to iterate ONLY on the colored pixels from that one superpixel.
I have tried using for loop like this:
for i in range(0,mask.shape[0]):
for j in range(0,mask.shape[1]):
x,y,z = each_segment[i][j] #gets the pixel RGB value
unique_pixel_array = [x,y,z] #creates a vector that holds those values for each pixel
if (unique_pixel_array != [0,0,0]):
print(unique_pixel_array)
This method is working however it is very inefficient considerin it is iterating over the entire image, and if i have a big image it will take a very long time to process for every superpixel.
Is there a faster and more efficient way to do this?
I will attach the whole code below , maybe you will get a better sense of the whole thing.
from skimage.segmentation import slic
from skimage.segmentation import mark_boundaries
from skimage.util import img_as_float
import matplotlib.pyplot as plt
import numpy as np
import cv2
img = cv2.imread("image.png")
segments = slic(img_as_float(img),n_segments= 7 ,slic_zero=True,sigma =5)
fig = plt.figure("Superpixels -- %d segments" % (22))
ax = fig.add_subplot(1, 1, 1)
ax.imshow(mark_boundaries(img, segments))
plt.axis("off")
plt.show()
for (sp,segVal) in enumerate (np.unique(segments)):
mask = np.zeros(img.shape[:2],dtype = "uint8")
mask[segments == segVal] = 255
each_segment = cv2.bitwise_and(img,img,mask=mask)
for i in range(0,mask.shape[0]):
for j in range(0,mask.shape[1]):
x,y,z = each_segment[i][j]
unique_pixel_array = [x,y,z]
print(unique_pixel_array)
cv2.imshow("Mask", mask)
cv2.imshow("Applied", cv2.bitwise_and(img, img, mask = mask))
cv2.waitKey(0)
Related
I have an image:
I have to detect the white space in between and basically partition it into two parts like this-
This is what I have coded so far... but it does detect only the black lines and not the middle white region.
import numpy as np
import cv2
img = cv2.imread('12.png')
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
edges = cv2.Canny(gray,50,150,apertureSize = 3)
median = cv2.medianBlur(gray,5)
minLineLength = 250
maxLineGap = 100
lines = cv2.HoughLinesP(edges,0.3,np.pi/180,250,minLineLength,maxLineGap)
for line in lines:
x1,y1,x2,y2 =line[0]
cv2.line(img,(x1,y1),(x2,y2),(0,255,0),2)
cv2.imwrite('newwhite.png',img)
I have a simple solution based on mean values along axis. I prefer scikit-image against opencv but you can use cv2.
import matplotlib.pyplot
import numpy as np
import skimage.io
import skimage.color
import skimage.morphology
import scipy.signal
img = skimage.io.imread('12.png')
gray = skimage.color.rgb2gray(img)
# Create some large dark area with the text, 10 is quite big!
eroded = skimage.morphology.erosion(gray, skimage.morphology.square(5))
# Compute mean values along axis 0 or 1
hist = np.mean(eroded, axis=0)
# Search large (here 3% of dimension size) and distant (here 20% of dimension size) peaks
scipy.signal.find_peaks(hist, width=len(hist)*3//100, distance=len(hist)*20//100)
Then each peak represents a white line in one dimension of your image
OK so newbie here that has been working on a set of homework problems with the original post here: How do I make a mask from one image and then transfer it to another?
. The original idea was to take the DAPI image (grey image) and apply it as a mask to the NPM1 (green) image. After implementing the suggested code from HansHirse (thanks!) along with some other code I had been making for the homework problem I finally got a working histogram of all compatible cells in the image. The "compatibility" bit is that any cells touching the border weren't supposed to be counted. However, I still need to find a way to get histograms of each individual cell as well. I've attached the original images from the post too:
To do this, I tried blob_doh and one other method to get segmented regions of each cell but have no idea as to how I can apply these coordinates to an image for the histogram.
PS. The code is a bit messy. I segmented the code such that the blob_doh is near the bottom and the other method is also its own separate piece at the very bottom. Sorry!
%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
from PIL import Image
from skimage.feature import blob_dog, blob_log, blob_doh
from skimage.color import rgb2gray
import cv2
import mahotas as mh
import scipy
from scipy import ndimage
import matplotlib.patches as mpatches
from skimage import data
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label, regionprops
from skimage.morphology import closing, square
from skimage.color import label2rgb
# Read image into numpy array
image = cv2.imread("NOTREATDAPI.jpg",0)
dna = np.array(image) # must be gray-scale image
plt.show()
# Remove extraneous artifacts from image; set the threshold
dnaf = ndimage.gaussian_filter(dna, 8) #gaussian filter for general image
T = mh.thresholding.otsu(dnaf) # set threshold via mahotas otsu thresholding
theta=np.array(dnaf > T) #setting mask of values in image to calculated otsu threshold
cleared = clear_border(theta) #removes all cells that are in contact with the image border
epsilon = np.array(cleared) #final masked DAPI product
print("DAPI MASK USING GAUSSIAN FILTER AND OTSU THRESHOLDING");
plt.imshow(epsilon)
plt.show()
# Load and reset original images
image = cv2.imread("NOTREATDAPI.jpg",0) #The DAPI Image
image1 = cv2.imread("NOTREATNPM1.jpg",0) #The NPM1 Image
print("Original DAPI Image");plt.imshow(image);plt.show() #The DAPI Image
print("Original NPM1 Image");plt.imshow(image1);plt.show() #The NPM1 Image
# Create an array of bool of same shape as image
maskAboveThreshold = epsilon > 0 #Use mask array from above - include only values above non-masked zeros
print("Final Masked Image of NPM1"); plt.imshow(image1 *
maskAboveThreshold, cmap='gray')
plt.show()
True_NPM1= image1 * maskAboveThreshold # Final masked version of NPM1 set back to grayscale
# Create a mask using the DAPI image and binary thresholding at 25
_, mask = cv2.threshold(True_NPM1, 1, 255, cv2.THRESH_BINARY)
# Do some morphological opening to get rid of small artifacts
mask = cv2.morphologyEx(mask, cv2.MORPH_OPEN,
cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (15, 15)))
# Calculate the histogram using the NPM1 image and the obtained binary
mask
hist = cv2.calcHist([image1], [0], mask, [256], [0, 256])
# Show bar plot of calculated histogram
plt.bar(np.arange(256), np.squeeze(hist))
plt.show()
# Show mask image
plt.imshow(mask)
plt.show()
#blob_doh way of segmenting the cells ------
import cv2 as cv
from PIL import Image, ImageDraw
image10 = np.array(Image.open("OXALIDAPI.jpg"))
plt.imshow(image10)
#Convert to gaussian image with thresholds
image10 = cv2.imread("OXALIDAPI.jpg",0)
dna = np.array(image10) # gray-scale image
plt.show()
# Remove extraneous artifacts from image; set the threshold
dnaf = ndimage.gaussian_filter(dna, 8) #gaussian filter for general image
T = mh.thresholding.otsu(dnaf) # set threshold via mahotas otsu thresholding
theta=np.array(dnaf > T) #setting mask of values in image to calculated otsu threshold
cleared = clear_border(theta) #removes all cells that are in contact with the image border
image = np.array(cleared) #final masked DAPI product
#print("DAPI MASK USING GAUSSIAN FILTER AND OTSU THRESHOLDING");
plt.imshow(epsilon)
plt.show()
# Convert image to grayscale
image_gray = rgb2gray(image)
plt.imshow(image_gray,cmap="gray")
def plot_blobs(img,blobs):
fig = plt.figure()
ax = fig.add_subplot(1,1,1)
ax.imshow(img, interpolation='nearest')
for blob in blobs:
y, x, r = blob
c = plt.Circle((x, y), r*1.25, color="red", linewidth=1, fill=False)
ax.add_patch(c)
# blob_doh
blobs_doh = blob_doh(image_gray, min_sigma=10, max_sigma=256,
threshold=.025)
plot_blobs(image,blobs_doh)
#get blob coordinates
def filter_blobs(blobs,r_cutoff=5):
new_blobs = []
for b in blobs:
if b[2] > r_cutoff:
new_blobs.append(b)
return new_blobs
new_blobs = filter_blobs(blobs_doh)
#plot_blobs(image,new_blobs)
print(new_blobs)
#Other method of segmenting cells. maybe useful?
yeta = cv2.imread("NOTREATDAPI.jpg",0)
image = np.array(yeta)
# apply threshold
dnaf = ndimage.gaussian_filter(image, 8)
T = mh.thresholding.otsu(dnaf) # set threshold
plt.imshow(dnaf > T)
epsilon=np.array(dnaf > T)
plt.show()
# remove artifacts connected to image border
cleared = clear_border(epsilon)
# label image regions
label_image = label(cleared)
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(figsize=(6, 6))
ax.imshow(image_label_overlay)
for region in regionprops(label_image):
# take regions with large enough areas
if region.area >= 50:
# draw rectangle around individual cells
minr, minc, maxr, maxc = region.bbox
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='red', linewidth=0.5)
ax.add_patch(rect)
#ax.set_axis_off()
#plt.tight_layout()
plt.show()
howzer=np.array(image_label_overlay)
What you are looking for is cv2.connectedComponents. Basically, once you have the binary mask that separate the cells, you try to label each connected component of the mask as one cell:
# I choose OTSU instead of binary, but they are not much different in this case
_, mask = cv2.threshold(dapi, 25, 255, cv2.THRESH_OTSU)
# compute the connected component
labels, markers = cv2.connectedComponents(mask)
# load 2nd image in grayscale
# as your 2nd image is only green/black
npm1 = cv2.imread('npm1.jpg', cv2.IMREAD_GRAYSCALE)
# for you image (and usually), labels[0] is the background
for label in labels[1:]:
# compute the histogram over the entire 256 levels of intensity
hist, bins = np.histogram(npm1[markers==label], bins=range(256))
# do whatever you like to hist
# note that bins=range(256) and hist only have 255 values
plt.bar(bins[1:], hist)
plt.title('cell number: {:}'.format(label))
So for example the histogram of the first and second cells:
And the cell markers are:
I am trying to use Python along with opencv, numpy and matplotlib to do some computer vision for a robot which will use a railing to navigate. I am currently extremely stuck have run out of places to look. My current code is:
import cv2
import numpy as np
import matplotlib.pyplot as plt
image = cv2.imread('railings.jpg')
railing_image = np.copy(image)
resized_image = cv2.resize(railing_image,(881,565))
gray = cv2.cvtColor(resized_image, cv2.COLOR_BGR2GRAY)
blur = cv2.GaussianBlur(gray, (5, 5), 0)
canny = cv2.Canny(blur, 85, 255)
cv2.imshow('test',canny)
image_array = np.array(canny)
ncols, nrows = image_array.shape
count = 0
scan = np.array
for x in range(0,image_array.shape[1]):
for y in range(0,image_array.shape[0]):
if image_array[y, x] == 0:
count += 1
scan = [scan, count]
print(scan)
plt.plot([0, count])
plt.axis([0, nrows, 0, ncols])
plt.show()
cv2.waitKey(0)
I am using a canny image which is stored in an array of 1's and 0's, the image I need represented is
The final result should look something like the following image.
I've tried using a histogram function but I've only managed to get that to output essentially a count of the number of times a 1 or 0 appears.
If anyone could help me or point me in the right direction that would produce a graph that represents the image pixels within a graph of height and width dimensions.
Thank you
I'm not sure how general this is but you could just use numpy argmax to get location of the maximum (like this) in your case. You should avoid loops as this will be very slow, better to use numpy functions. I've imported your image and used the cutoff criterion that 200 or more in the yellow channel is railing,
import cv2
import numpy as np
import matplotlib.pyplot as plt
#This loads the canny image you uploaded
image = cv2.imread('uojHJ.jpg')
#Trim off the top taskbar
trimimage = image[100:, :,0]
#Use argmax with 200 cutoff colour in one channel
maxindex = np.argmax(trimimage[:,:]>200, axis=0)
#Plot graph
plt.plot(trimimage.shape[0] - maxindex)
plt.show()
Where this looks as follows:
Just want to retain the lettuce, I have hundreds of image like this and would be comparing the size of lettuce, so to began with I tried the canny edge detection but it doesn't seems to work, any idea how shall move ahead with this
A possible approach is by using the Graph Segmentation method (cv::ximgproc::segmentation::GraphSegmentation), that you apply to the image converted to HSV or HSL, where you set the V or L plane to a constant to flatten illumination.
You can convert the RGB image into HSV image and segment the Green color region.
import cv2
import numpy as np
frame=cv2.imread('a.png')
hsv = cv2.cvtColor(frame, cv2.COLOR_BGR2HSV)
lower = np.array([50,50,50])
upper = np.array([70,255,255])
mask = cv2.inRange(hsv, lower, upper)
res = cv2.bitwise_and(frame,frame, mask= mask)
cv2.imshow('frame',frame)
cv2.imshow('res',res)
cv2.waitKey(0)
cv2.destroyAllWindows()
You may get away with thresholding as long as you fix your lighting (method 1 listed below), if not, you might need a simple classifier method (for example a clustering technique, method 2) in conjunction with connected components and assumption on the location of the plant or color to assign the detected class to the plant.
from scipy.misc import imread
import matplotlib.pyplot as plt
import matplotlib.patches as patches
%matplotlib inline
import matplotlib
import numpy as np
# read the image
img = imread('9v5wv.png')
# show the image
fig,ax = plt.subplots(1)
ax.imshow(img)
ax.grid('off')
# show the r,g,b channels separately.
for n,d in enumerate([('r',0),('g',1),('b',2)]):
k,v = d
plt.figure(n)
plt.subplot(131)
plt.imshow(arr[:,:,v],cmap='gray')
plt.grid('off')
plt.title(k)
plt.subplot(133)
_=plt.hist(arr[:,:,v].ravel(),bins=100)
# method 1, rgb thresholding will not work when lighting changes
arr = img
r_filter = lambda x: x[:,:,0] < 100
g_filter = lambda x: x[:,:,1] > 80
b_filter = lambda x: x[:,:,2] < 200
mask=np.logical_and(np.logical_and(r_filter(arr),g_filter(arr)),b_filter(arr))
plt.imshow(mask,cmap='gray')
plt.grid('off')
# method 2, kmeans clustering
from sklearn.cluster import KMeans
arr = matplotlib.colors.rgb_to_hsv(img[:,:,0:3])
# ignore v per Yves Daoust
data = np.array(arr[:,:,0:2])
x,y,z = data.shape
X = np.reshape(data,(x*y,z))
kmeans = KMeans(n_clusters=6, random_state=420).fit(X)
mask = np.reshape(kmeans.labels_,(x,y,))
plt.imshow(mask==0,cmap='gray')
plt.grid('off')
I am trying to implement adaptive histogram equalization in python. I take an image and split it into smaller regions and then apply the traditional histogram equalization to it. I then combine the smaller images into one and obtain a final resultant image. The final image appears to be very blocky in nature and has different contrast levels for each individual region. Is there a way I could maintain a uniform contrast for each individual image so that it looks like a single image instead of smaller images stitched together.
import cv2
import numpy as np
from matplotlib import pyplot as plt
from scipy.misc import imsave
from scipy import ndimage
from scipy import misc
import scipy.misc
import scipy
import image_slicer
from image_slicer import join
from PIL import Image
img = 'watch.png'
num_tiles = 25
tiles = image_slicer.slice(img, num_tiles)
for tile in tiles:
img = scipy.misc.imread(tile.filename)
hist,bins = np.histogram(img.flatten(),256,[0,256])
cdf = hist.cumsum()
cdf_normalized = cdf *hist.max()/ cdf.max()
plt.plot(cdf_normalized, color = 'g')
plt.hist(img.flatten(),256,[0,256], color = 'g')
plt.xlim([0,256])
plt.legend(('cdf','histogram'), loc = 'upper left')
cdf_m = np.ma.masked_equal(cdf,0)
cdf_o = (cdf_m - cdf_m.min())*255/(cdf_m.max()-cdf_m.min())
cdf = np.ma.filled(cdf_o,0).astype('uint8')
img3 = cdf[img]
cv2.imwrite(tile.filename,img3)
tile.image = Image.open(tile.filename
image = join(tiles)
image.save('watch-join.png')
I reviewed the actual algorithm and came up with the following implementation. I am sure there is a better way to do this. Any suggestions are appreciated.
import numpy as np
import cv2
img = cv2.imread('watch.png',0)
print img
img_size=img.shape
print img_size
img_mod = np.zeros((600, 800))
for i in range(0,img_size[0]-30):
for j in range(0,img_size[1]-30):
kernel = img[i:i+30,j:j+30]
for k in range(0,30):
for l in range(0,30):
element = kernel[k,l]
rank = 0
for m in range(0,30):
for n in range(0,30):
if(kernel[k,l]>kernel[m,n]):
rank = rank + 1
img_mod[i,j] = ((rank * 255 )/900)
im = np.array(img_mod, dtype = np.uint8)
cv2.imwrite('target.png',im)