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I am trying to segment lung CT images using Kmeans by using code below:
def process_mask(mask):
convex_mask = np.copy(mask)
for i_layer in range(convex_mask.shape[0]):
mask1 = np.ascontiguousarray(mask[i_layer])
if np.sum(mask1)>0:
mask2 = convex_hull_image(mask1)
if np.sum(mask2)>2*np.sum(mask1):
mask2 = mask1
else:
mask2 = mask1
convex_mask[i_layer] = mask2
struct = generate_binary_structure(3,1)
dilatedMask = binary_dilation(convex_mask,structure=struct,iterations=10)
return dilatedMask
def lumTrans(img):
lungwin = np.array([-1200.,600.])
newimg = (img-lungwin[0])/(lungwin[1]-lungwin[0])
newimg[newimg<0]=0
newimg[newimg>1]=1
newimg = (newimg*255).astype('uint8')
return newimg
def lungSeg(imgs_to_process,output,name):
if os.path.exists(output+'/'+name+'_clean.npy') : return
imgs_to_process = Image.open(imgs_to_process)
img_to_save = imgs_to_process.copy()
img_to_save = np.asarray(img_to_save).astype('uint8')
imgs_to_process = lumTrans(imgs_to_process)
imgs_to_process = np.expand_dims(imgs_to_process, axis=0)
x,y,z = imgs_to_process.shape
img_array = imgs_to_process.copy()
A1 = int(y/(512./100))
A2 = int(y/(512./400))
A3 = int(y/(512./475))
A4 = int(y/(512./40))
A5 = int(y/(512./470))
for i in range(len(imgs_to_process)):
img = imgs_to_process[i]
print(img.shape)
x,y = img.shape
#Standardize the pixel values
allmean = np.mean(img)
allstd = np.std(img)
img = img-allmean
img = img/allstd
# Find the average pixel value near the lungs
# to renormalize washed out images
middle = img[A1:A2,A1:A2]
mean = np.mean(middle)
max = np.max(img)
min = np.min(img)
kmeans = KMeans(n_clusters=2).fit(np.reshape(middle,[np.prod(middle.shape),1]))
centers = sorted(kmeans.cluster_centers_.flatten())
threshold = np.mean(centers)
thresh_img = np.where(img<threshold,1.0,0.0) # threshold the image
eroded = morphology.erosion(thresh_img,np.ones([4,4]))
dilation = morphology.dilation(eroded,np.ones([10,10]))
labels = measure.label(dilation)
label_vals = np.unique(labels)
regions = measure.regionprops(labels)
good_labels = []
for prop in regions:
B = prop.bbox
if B[2]-B[0]<A3 and B[3]-B[1]<A3 and B[0]>A4 and B[2]<A5:
good_labels.append(prop.label)
mask = np.ndarray([x,y],dtype=np.int8)
mask[:] = 0
for N in good_labels:
mask = mask + np.where(labels==N,1,0)
mask = morphology.dilation(mask,np.ones([10,10])) # one last dilation
imgs_to_process[i] = mask
m1 = imgs_to_process
convex_mask = m1
dm1 = process_mask(m1)
dilatedMask = dm1
Mask = m1
extramask = dilatedMask ^ Mask
bone_thresh = 180
pad_value = 0
img_array[np.isnan(img_array)]=-2000
sliceim = img_array
sliceim = sliceim*dilatedMask+pad_value*(1-dilatedMask).astype('uint8')
bones = sliceim*extramask>bone_thresh
sliceim[bones] = pad_value
x,y,z = sliceim.shape
if not os.path.exists(output):
os.makedirs(output)
img_to_save[sliceim.squeeze()==0] = 0
im = Image.fromarray(img_to_save)
im.save(output + name + '.png', 'PNG')
The problem is the segmented lung still contains white borderers like this:
Segmented lung (output):
Unsegmented lung (input):
The full code can be found in Google Colab Notebook. code.
And sample of the dataset is here.
For this problem, I don't recommend using Kmeans color quantization since this technique is usually reserved for a situation where there are various colors and you want to segment them into dominant color blocks. Take a look at this previous answer for a typical use case. Since your CT scan images are grayscale, Kmeans would not perform very well. Here's a potential solution using simple image processing with OpenCV:
Obtain binary image. Load input image, convert to grayscale, Otsu's threshold, and find contours.
Create a blank mask to extract desired objects. We can use np.zeros() to create a empty mask with the same size as the input image.
Filter contours using contour area and aspect ratio. We search for the lung objects by ensuring that contours are within a specified area threshold as well as aspect ratio. We use cv2.contourArea(), cv2.arcLength(), and cv2.approxPolyDP() for contour perimeter and contour shape approximation. If we have have found our lung object, we utilize cv2.drawContours() to fill in our mask with white to represent the objects that we want to extract.
Bitwise-and mask with original image. Finally we convert the mask to grayscale and bitwise-and with cv2.bitwise_and() to obtain our result.
Here is our image processing pipeline visualized step-by-step:
Grayscale -> Otsu's threshold
Detected objects to extract highlighted in green -> Filled mask
Bitwise-and to get our result -> Optional result with white background instead
Code
import cv2
import numpy as np
image = cv2.imread('1.png')
highlight = image.copy()
original = image.copy()
# Convert image to grayscale, Otsu's threshold, and find contours
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY_INV | cv2.THRESH_OTSU)[1]
contours = cv2.findContours(thresh.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
# Create black mask to extract desired objects
mask = np.zeros(image.shape, dtype=np.uint8)
# Search for objects by filtering using contour area and aspect ratio
for c in contours:
# Contour area
area = cv2.contourArea(c)
# Contour perimeter
peri = cv2.arcLength(c, True)
# Contour approximation
approx = cv2.approxPolyDP(c, 0.035 * peri, True)
(x, y, w, h) = cv2.boundingRect(approx)
aspect_ratio = w / float(h)
# Draw filled contour onto mask if passes filter
# These are arbitary values, may need to change depending on input image
if aspect_ratio <= 1.2 or area < 5000:
cv2.drawContours(highlight, [c], 0, (0,255,0), -1)
cv2.drawContours(mask, [c], 0, (255,255,255), -1)
# Convert 3-channel mask to grayscale then bitwise-and with original image for result
mask = cv2.cvtColor(mask, cv2.COLOR_BGR2GRAY)
result = cv2.bitwise_and(original, original, mask=mask)
# Uncomment if you want background to be white instead of black
# result[mask==0] = (255,255,255)
# Display
cv2.imshow('gray', gray)
cv2.imshow('thresh', thresh)
cv2.imshow('highlight', highlight)
cv2.imshow('mask', mask)
cv2.imshow('result', result)
# Save images
# cv2.imwrite('gray.png', gray)
# cv2.imwrite('thresh.png', thresh)
# cv2.imwrite('highlight.png', highlight)
# cv2.imwrite('mask.png', mask)
# cv2.imwrite('result.png', result)
cv2.waitKey(0)
A simpler approach to solve this problem is using morphological erosion. Its just that than you will have to tune in threshold values
I searched for image recognition using python. It seems there is no tutorial about Extracting Numbers from colored background so I followed THIS TUTORIAL
import cv2
import matplotlib.pyplot as plt
def detect_edge(image):
''' function Detecting Edges '''
image_with_edges = cv2.Canny(image , 100, 200)
images = [image , image_with_edges]
location = [121, 122]
for loc, img in zip(location, images):
plt.subplot(loc)
plt.imshow(img, cmap='gray')
plt.savefig('edge.png')
plt.show()
image = cv2.imread('myscreenshot.png', 0)
detect_edge(image)
This is my image:
This is the result:
Any solution to print out these numbers?
Here is some code for getting clean canny edges for this image.
import cv2
import numpy as np
# load image
img = cv2.imread("numbers.png");
# change to hue colorspace
hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV);
h,s,v = cv2.split(hsv);
# use clahe to improve contrast
# (the contrast is pretty good already, so not much change, but good habit to have here)
clahe = cv2.createCLAHE(clipLimit = 10)
contrast = clahe.apply(v);
# use canny
canny = cv2.Canny(contrast, 20, 110);
# show
cv2.imshow('i', img);
cv2.imshow('v', v);
cv2.imshow('c', contrast);
cv2.imshow("canny", canny);
cv2.waitKey(0);
# save
cv2.imwrite("edges.png", canny);
Without using any OCR like pytesseract or something, I don't see an obvious way to be able to consistently turn this image into "text" numbers. I'll leave that for someone else who might know how to solve that without any pattern recognition stuff because I don't even know where to begin without that. If you're willing to forgo that restriction then pytessaract should have no problem with this; possibly even without doing processing like this.
Ok, I filled in the numbers for the image. OpenCV's findContours' hierarchy wasn't cooperating for some reason so I had to manually do it which makes this code pretty janky. Honestly, if I were to try this again from scratch, I'd try to find colors that contribute to a small number of total pixels and threshold on each and combine the masks.
import cv2
import numpy as np
# check if small box is in big box
def contained(big, small):
# big corners
x,y,w,h = big;
big_tl = [x, y];
big_br = [x+w, y+h];
# small corners
x,y,w,h = small;
small_tl = [x, y];
small_br = [x+w, y+h];
# check
if small_tl[0] > big_tl[0] and small_br[0] < big_br[0]:
if small_tl[1] > big_tl[1] and small_br[1] < big_br[1]:
return True;
return False;
# load image
img = cv2.imread("numbers.png");
# change to hue colorspace
hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV);
h,s,v = cv2.split(hsv);
# use clahe to improve contrast
# (the contrast is pretty good already, so not much change, but good habit to have here)
clahe = cv2.createCLAHE(clipLimit = 10)
contrast = clahe.apply(v);
# rescale
scale = 2.0;
h, w = img.shape[:2];
h = int(h * scale);
w = int(w * scale);
contrast = cv2.resize(contrast, (w,h), cv2.INTER_LINEAR);
img = cv2.resize(img, (w,h), cv2.INTER_LINEAR);
# use canny
canny = cv2.Canny(contrast, 10, 60);
# show
cv2.imshow('i', img);
cv2.imshow('v', v);
cv2.imshow('c', contrast);
cv2.imshow("canny", canny);
cv2.waitKey(0);
# try to fill in contours
# contours
_, contours, hierarchy = cv2.findContours(canny, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE);
# filter contours by size
# filter out noisy bits and the big grid boxes
filtered = [];
for contour in contours:
perimeter = cv2.arcLength(contour, True);
if 50 < perimeter and perimeter < 750:
filtered.append(contour);
# draw contours again
# create a mask of the contoured image
mask = np.zeros_like(contrast);
mask = cv2.drawContours(mask, filtered, -1, 255, -1);
# close to get rid of annoying little gaps
kernel = np.ones((3,3),np.uint8)
mask = cv2.dilate(mask,kernel,iterations = 1);
mask = cv2.erode(mask,kernel, iterations = 1);
# contours
_, contours, hierarchy = cv2.findContours(mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE);
# alright, hierarchy is being stupid, plan B
# SUUUUUPEEERRR JAAAANK
outer_cntrs = [a for a in range(len(contours))];
children = [];
for a in range(len(contours)):
if a in outer_cntrs:
# get current box
big_box = cv2.boundingRect(contours[a]);
# check against all other boxes
for b in range(0, len(contours)):
if b in outer_cntrs:
small_box = cv2.boundingRect(contours[b]);
# remove any children
if contained(big_box, small_box):
outer_cntrs.remove(b);
children.append(contours[b]);
# # select by hierarchy
top_cntrs = [];
for a in range(len(contours)):
if a in outer_cntrs:
top_cntrs.append(contours[a]);
# create a mask of the contoured image
mask = np.zeros_like(contrast);
mask = cv2.drawContours(mask, top_cntrs, -1, 255, -1);
mask = cv2.drawContours(mask, children, -1, 255, -1);
# close
kernel = np.ones((3,3),np.uint8)
mask = cv2.dilate(mask,kernel,iterations = 1);
mask = cv2.erode(mask,kernel, iterations = 1);
# do contours agains because opencv is being super difficult
# honestly, at this point, a fill method would've been better
# contours
_, contours, hierarchy = cv2.findContours(mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE);
# fill in
for con in contours:
cv2.fillPoly(mask, pts = [con], color=(255));
for con in children:
cv2.fillPoly(mask, pts = [con], color=(0));
# resize back down
h, w = mask.shape;
h = int(h / scale);
w = int(w / scale);
mask = cv2.resize(mask, (w,h));
# show
cv2.imshow("mask", mask);
cv2.waitKey(0);
# save
cv2.imwrite("filled.png", mask);
You can find the digits in three-steps
Applying Adaptive-threshold
Applying erosion
Read using pytesseract
Adaptive-threshold result:
Here we see 9 and 0 is different from rest of the digits. We need to remove the boundaries of the 9.
Erosion result:
Pytesseract result:
8 | 1
5 9
4 #
3 | 3
6 | 1
There are multiple page-segmentation-modes are available for pytesseract
If you want to remove | from the output you can use re.sub
text = re.sub('[^A-Za-z0-9]+', ',', text)
Result will be:
8
1
5
9
4
3
3
6
1
Code:
import cv2
import pytesseract
import re
import numpy as np
image = cv2.imread("7UUGYHw.png")
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
thresh = cv2.adaptiveThreshold(gray, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY, 13, 2)
erode = cv2.erode(thresh, np.array((7, 7)), iterations=1)
text = pytesseract.image_to_string(erode, config="--psm 6")
text = re.sub('[^A-Za-z0-9]+', '\n', text)
print(text)
I am attempting to find the area inside an arbitrarily-shaped closed curve plotted in python (example image below). So far, I have tried to use both the alphashape and polygon methods to acheive this, but both have failed. I am now attempting to use OpenCV and the floodfill method to count the number of pixels inside the curve and then I will later convert that to an area given the area that a single pixel encloses on the plot.
Example image:
testplot.jpg
In order to do this, I am doing the following, which I adapted from another post about OpenCV.
import cv2
import numpy as np
# Input image
img = cv2.imread('testplot.jpg', cv2.IMREAD_GRAYSCALE)
# Dilate to better detect contours
temp = cv2.dilate(temp, cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3)))
# Find largest contour
cnts, _ = cv2.findContours(255-temp, cv2.RETR_TREE , cv2.CHAIN_APPROX_NONE) #255-img and cv2.RETR_TREE is to account for how cv2 expects the background to be black, not white, so I convert the background to black.
largestCnt = [] #I expect this to yield the blue contour
for cnt in cnts:
if (len(cnt) > len(largestCnt)):
largestCnt = cnt
# Determine center of area of largest contour
M = cv2.moments(largestCnt)
x = int(M["m10"] / M["m00"])
y = int(M["m01"] / M["m00"])
# Initial mask for flood filling, should cover entire figure
width, height = temp.shape
mask = img2 = np.ones((width + 2, height + 2), np.uint8) * 255
mask[1:width, 1:height] = 0
# Generate intermediate image, draw largest contour onto it, flood fill this contour
temp = np.zeros(temp.shape, np.uint8)
temp = cv2.drawContours(temp, largestCnt, -1, 255, cv2.FILLED)
_, temp, mask, _ = cv2.floodFill(temp, mask, (x, y), 255)
temp = cv2.morphologyEx(temp, cv2.MORPH_OPEN, cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3)))
area = cv2.countNonZero(temp) #Number of pixels encircled by blue line
I expect from this to get to a place where I have the same image as above, but with the center of the contour filled in white and the background and original blue contour in black. I end up with this:
result.jpg
While this at first glance appears to have accurately turned the area inside the contour white, the white area is actually larger than the area inside the contour and so the result I get is overestimating the number of pixels inside it.
Any input on this would be greatly appreciated. I am fairly new to OpenCV so I may have misunderstood something.
EDIT:
Thanks to a comment below, I made some edits and this is now my code, with edits noted:
import cv2
import numpy as np
# EDITED INPUT IMAGE: Input image
img = cv2.imread('testplot2.jpg', cv2.IMREAD_GRAYSCALE)
# EDIT: threshold
_, temp = cv2.threshold(img, 250, 255, cv2.THRESH_BINARY_INV)
# EDIT, REMOVED: Dilate to better detect contours
# Find largest contour
cnts, _ = cv2.findContours(temp, cv2.RETR_EXTERNAL , cv2.CHAIN_APPROX_NONE)
largestCnt = [] #I expect this to yield the blue contour
for cnt in cnts:
if (len(cnt) > len(largestCnt)):
largestCnt = cnt
# Determine center of area of largest contour
M = cv2.moments(largestCnt)
x = int(M["m10"] / M["m00"])
y = int(M["m01"] / M["m00"])
# Initial mask for flood filling, should cover entire figure
width, height = temp.shape
mask = img2 = np.ones((width + 2, height + 2), np.uint8) * 255
mask[1:width, 1:height] = 0
# Generate intermediate image, draw largest contour, flood filled
temp = np.zeros(temp.shape, np.uint8)
temp = cv2.drawContours(temp, largestCnt, -1, 255, cv2.FILLED)
_, temp, mask, _ = cv2.floodFill(temp, mask, (x, y), 255)
temp = cv2.morphologyEx(temp, cv2.MORPH_OPEN, cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3, 3)))
area = cv2.countNonZero(temp) #Number of pixels encircled by blue line
I input a different image with the axes and the frame that python adds by default removed for ease. I get what I expect at the second step, so this image. However, in the enter image description here both the original contour and the area it encircles appear to have been made white, whereas I want the original contour to be black and only the area it encircles to be white. How might I acheive this?
The problem is your opening operation at the end. This morphological operation includes a dilation at the end that expands the white contour, increasing its area. Let’s try a different approach where no morphology is involved. These are the steps:
Convert your image to grayscale
Apply Otsu’s thresholding to get a binary image, let’s work with black and white pixels only.
Apply a first flood-fill operation at image location (0,0) to get rid of the outer white space.
Filter small blobs using an area filter
Find the “Curve Canvas” (The white space that encloses the curve) and locate and store its starting point at (targetX, targetY)
Apply a second flood-fill al location (targetX, targetY)
Get the area of the isolated blob with cv2.countNonZero
Let’s take a look at the code:
import cv2
import numpy as np
# Set image path
path = "C:/opencvImages/"
fileName = "cLIjM.jpg"
# Read Input image
inputImage = cv2.imread(path+fileName)
inputCopy = inputImage.copy()
# Convert BGR to grayscale:
grayscaleImage = cv2.cvtColor(inputImage, cv2.COLOR_BGR2GRAY)
# Threshold via Otsu + bias adjustment:
threshValue, binaryImage = cv2.threshold(grayscaleImage, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
This is the binary image you get:
Now, let’s flood-fill at the corner located at (0,0) with a black color to get rid of the first white space. This step is very straightforward:
# Flood-fill background, seed at (0,0) and use black color:
cv2.floodFill(binaryImage, None, (0, 0), 0)
This is the result, note how the first big white area is gone:
Let’s get rid of the small blobs applying an area filter. Everything below an area of 100 is gonna be deleted:
# Perform an area filter on the binary blobs:
componentsNumber, labeledImage, componentStats, componentCentroids = \
cv2.connectedComponentsWithStats(binaryImage, connectivity=4)
# Set the minimum pixels for the area filter:
minArea = 100
# Get the indices/labels of the remaining components based on the area stat
# (skip the background component at index 0)
remainingComponentLabels = [i for i in range(1, componentsNumber) if componentStats[i][4] >= minArea]
# Filter the labeled pixels based on the remaining labels,
# assign pixel intensity to 255 (uint8) for the remaining pixels
filteredImage = np.where(np.isin(labeledImage, remainingComponentLabels) == True, 255, 0).astype('uint8')
This is the result of the filter:
Now, what remains is the second white area, I need to locate its starting point because I want to apply a second flood-fill operation at this location. I’ll traverse the image to find the first white pixel. Like this:
# Get Image dimensions:
height, width = filteredImage.shape
# Store the flood-fill point here:
targetX = -1
targetY = -1
for i in range(0, width):
for j in range(0, height):
# Get current binary pixel:
currentPixel = filteredImage[j, i]
# Check if it is the first white pixel:
if targetX == -1 and targetY == -1 and currentPixel == 255:
targetX = i
targetY = j
print("Flooding in X = "+str(targetX)+" Y: "+str(targetY))
There’s probably a more elegant, Python-oriented way of doing this, but I’m still learning the language. Feel free to improve the script (and share it here). The loop, however, gets me the location of the first white pixel, so I can now apply a second flood-fill at this exact location:
# Flood-fill background, seed at (targetX, targetY) and use black color:
cv2.floodFill(filteredImage, None, (targetX, targetY), 0)
You end up with this:
As you see, just count the number of non-zero pixels:
# Get the area of the target curve:
area = cv2.countNonZero(filteredImage)
print("Curve Area is: "+str(area))
The result is:
Curve Area is: 1510
Here is another approach using Python/OpenCV.
Read Input
convert to HSV colorspace
Threshold on color range of blue
Find the largest contour
Get its area and print that
draw the contour as a white filled contour on black background
Save the results
Input:
import cv2
import numpy as np
# read image as grayscale
img = cv2.imread('closed_curve.jpg')
# convert to HSV
hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV)
#select blu color range in hsv
lower = (24,128,115)
upper = (164,255,255)
# threshold on blue in hsv
thresh = cv2.inRange(hsv, lower, upper)
# get largest contour
contours = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
contours = contours[0] if len(contours) == 2 else contours[1]
big_contour = max(contours, key=cv2.contourArea)
area = cv2.contourArea(c)
print("Area =",area)
# draw filled contour on black background
result = np.zeros_like(thresh)
cv2.drawContours(result, [c], -1, 255, cv2.FILLED)
# save result
cv2.imwrite("closed_curve_thresh.jpg", thresh)
cv2.imwrite("closed_curve_result.jpg", result)
# view result
cv2.imshow("threshold", thresh)
cv2.imshow("result", result)
cv2.waitKey(0)
cv2.destroyAllWindows()
Threshold Image:
Result Filled Contour On Black Background:
Area Result:
Area = 2347.0
I'm trying to follow movement of a part using red dots. I tried with white dots and thresholding before, but there is too much reflection from the smartphone I'm using. The plan is to recognize a dot as a contour, find the center and fill the array with the coordinates of all contour centers for further calculation.
The code is posted bellow, it recognizes the correct number of dots, but I get the division by zero error. Does anyone know what I'm doing wrong?
Image:https://imgur.com/a/GLXGCPP
import cv2
import numpy as np
from matplotlib import pyplot as plt
import imutils
#load image
img = cv2.imread('dot4_red.jpg')
#apply median blur, 15 means it's smoothing image 15x15 pixels
blur = cv2.medianBlur(img,15)
#convert to hsv
hsv = cv2.cvtColor(blur, cv2.COLOR_BGR2HSV)
#color definition
red_lower = np.array([0,0,240])
red_upper = np.array([10,10,255])
#red color mask (sort of thresholding, actually segmentation)
mask = cv2.inRange(hsv, red_lower, red_upper)
#copy image for, .findContours distorts the source image
mask_copy = mask.copy()
#find contours
cnts = cv2.findContours(mask_copy,cv2.RETR_LIST,cv2.CHAIN_APPROX_SIMPLE)
#extract contours from the list??
cnts = imutils.grab_contours(cnts)
#count number of conoturs of specific size
s1 = 500
s2 = 10000
xcnts = []
for cnt in cnts:
if s1<cv2.contourArea(cnt)<s2:
xcnts.append(cnt)
n = len(xcnts)
#pre-allocate array for extraction of centers of contours
s = (n,2)
array = np.zeros(s)
#fill array of center coordinates
for i in range(0,n):
cnt = cnts[i]
moment = cv2.moments(cnt)
c_x = int(moment["m10"]/moment["m00"])
c_y = int(moment["m01"]/moment["m00"])
array[i,:] = [c_x, c_y]
#display image
cv2.namedWindow('image', cv2.WINDOW_NORMAL)
cv2.imshow('image', mask)
cv2.waitKey(0) & 0xFF
cv2.destroyAllWindows()
#print results
print ('number of dots, should be 4:',n)
print ('array of dot center coordinates:',array)
The problem was the wrong color range. Because of this, there were holes in the mask of the circles. Due to division by zero. M00. You can choose the correct color range or pre-fill the holes in the mask. Or use this code:
import cv2
import numpy as np
#load image
img = cv2.imread('ZayrMep.jpg')
#apply median blur, 15 means it's smoothing image 15x15 pixels
blur = cv2.medianBlur(img,15)
#convert to hsv
hsv = cv2.cvtColor(blur, cv2.COLOR_BGR2HSV)
#color definition
red_lower = np.array([160,210,230])
red_upper = np.array([180,255,255])
#red color mask (sort of thresholding, actually segmentation)
mask = cv2.inRange(hsv, red_lower, red_upper)
connectivity = 4
# Perform the operation
output = cv2.connectedComponentsWithStats(mask, connectivity, cv2.CV_32S)
# Get the results
num_labels = output[0]-1
centroids = output[3][1:]
#print results
print ('number of dots, should be 4:',num_labels )
print ('array of dot center coordinates:',centroids)
moments00 (area) can be 0 for some shapes according to cv documentation. This is probably what is happening here:
Note Since the contour moments are computed using Green formula, you
may get seemingly odd results for contours with self-intersections,
e.g. a zero area (m00) for butterfly-shaped contours.
From: https://docs.opencv.org/3.4/d8/d23/classcv_1_1Moments.html#a8b1b4917d1123abc3a3c16b007a7319b
You need to ensure the area (m00) is not 0 before using it for division.
I have a problem while getting a binary image from colored images. cv2.inRange() function is used to get mask of an image (simillar with thresholding) and I want to delete unnecessary parts, minimizing erosion of mask images. The biggest problem is that masks are not regularly extracted.
Samples
Crack:
Typical one
Ideal one:
My first object is making second picture as third one. I guess getting contour that has biggest area and deleting other contours(also for the mask) would be work. But can't not find how.
Second probleme is that the idea I described above would not work for the first image(crack). This kind of images could be discarded. But anyway it should be labeled as crack. In so far, I don't have ideas for this.
What I did
Here is input image and codes 42_1.jpg
class Real:
__ex_low=np.array([100,30,60])
__ex_high=np.array([140,80,214])
__ob_low=np.array([25,60,50]) #27,65,100])
__ob_high=np.array([50,255,255]) #[45,255,255])
def __opening(self, mask):
kernel = np.ones((3,3), np.uint8)
op = cv2.morphologyEx(mask, cv2.MORPH_OPEN, kernel)
return op
def __del_ext(self, img_got):
img = img_got[0:300,]
hsv = cv2.cvtColor(img,cv2.COLOR_BGR2HSV)
mask = cv2.inRange(hsv, self.__ex_low, self.__ex_high)
array1 = np.transpose(np.nonzero(mask))
array2 = np.nonzero(mask)
temp=array1.tolist()
xmin=min(array2[0]) #find the highest point covered blue
x,y,channel=img.shape
img=img[xmin:x,]
hsv=hsv[xmin:x,]
return img, hsv
def __init__(self, img_got):
img, hsv = self.__del_ext(img_got)
mask_temp = cv2.inRange(hsv, self.__ob_low, self.__ob_high)
mask = self.__opening(mask_temp)
array1 = np.transpose(np.nonzero(mask))
array2 = np.nonzero(mask)
ymin=min(array2[1])
ymax=max(array2[1])
xmin=min(array2[0])
xmax=max(array2[0])
self.x = xmax-xmin
self.y = ymax-ymin
self.ratio = self.x/self.y
# xmargin = int(self.x*0.05)
#ymargin = int(self.y*0.05)
self.img = img[(xmin):(xmax),(ymin):(ymax)]
self.mask = mask[(xmin):(xmax),(ymin):(ymax)]
#models = glob.glob("D:/Python36/images/motor/*.PNG")
img = cv2.imread("D:/Python36/images/0404/33_1.jpg")#<- input image
#last_size = get_last_size(models[-1])
#m2= Model(models[39],last_size)
r1 = Real(img)
cv2.imshow("2",r1.img)
cv2.imshow("3",r1.mask)
It would be great if codes are written in python3, but anything will be okay.
In general, you method is ok, except the wrong kernel to remove the horizontal lines.
I finish it by in following steps:
(1) Read and convert to HSV
(2) Find the target yellow color region in HSV
(3) morph-op to remove horizone lines
(4) crop the region
This is the result:
The code:
#!/usr/bin/python3
# 2018/04/16 13:20:07
# 2018/04/16 14:13:03
import cv2
import numpy as np
## (1) Read and convert to HSV
img = cv2.imread("euR2X.png")
hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV)
## (2) Find the target yellow color region in HSV
hsv_lower = (25, 100, 50)
hsv_upper = (33, 255, 255)
mask = cv2.inRange(hsv, hsv_lower, hsv_upper)
## (3) morph-op to remove horizone lines
kernel = np.ones((5,1), np.uint8)
mask2 = cv2.morphologyEx(mask, cv2.MORPH_OPEN, kernel)
## (4) crop the region
ys, xs = np.nonzero(mask2)
ymin, ymax = ys.min(), ys.max()
xmin, xmax = xs.min(), xs.max()
croped = img[ymin:ymax, xmin:xmax]
pts = np.int32([[xmin, ymin],[xmin,ymax],[xmax,ymax],[xmax,ymin]])
cv2.drawContours(img, [pts], -1, (0,255,0), 1, cv2.LINE_AA)
cv2.imshow("croped", croped)
cv2.imshow("img", img)
cv2.waitKey()
References:
what are recommended color spaces for detecting orange color in open cv?
Find single color, horizontal spaces in image