I have the following image: mask
I'm trying separate each white piece into its own image. My approach is to find the contours, iterate over them and fill each one with white color then save the new image.
So far, I've found the contours after using Canny Edge Detection: contours
But I can't seem to fill them all on the inside, since the edges are not fully connected:contours filled
Is there a way to fill in the contours without using dilation/erosion? I intend to preserve the image as it is, not altering it more than needed.
I've used the following code.
import cv2
import numpy as np
def get_blank_image(image):
return np.zeros((image.shape[0], image.shape[1], 3), np.uint8)
# Let's load a simple image with 3 black squares
image = cv2.imread('img.png')
cv2.waitKey(0)
blank_image = get_blank_image(image)
# cv2.imshow('blank', blank_image)
# Grayscale
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
# Find Canny edges
edged = cv2.Canny(gray, 30, 50)
cv2.waitKey(0)
# Finding Contours
# Use a copy of the image e.g. edged.copy()
# since findContours alters the image
contours, hierarchy = cv2.findContours(edged, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
good_contours = []
for con in contours:
area = cv2.contourArea(con)
if area > 10:
good_contours.append(con)
cv2.drawContours(blank_image, [con], 0, (255, 255, 255), thickness=cv2.FILLED)
# cv2.fillPoly(blank_image, pts=[con], color=(255, 255, 255))
# cv2.imshow('blank', blank_image)
# cv2.waitKey(0)
# good_contours.remove(con)
# cv2.imshow('Canny Edges After Contouring', edged)
cv2.waitKey(0)
cv2.imshow('blank', blank_image)
print("Number of Contours found = " + str(len(good_contours)))
# Draw all contours
# -1 signifies drawing all contours
cv2.drawContours(image, good_contours, -1, (0, 255, 0), 3)
cv2.imshow('Contours', image)
cv2.waitKey(0)
cv2.destroyAllWindows()
Related
Problem Summary: I have got many complex histopathology images with different dimensions. Complex means a single image having multiple images in it as shown in below input image examples. I need to separate out or crop each single image only and not the text/label/caption of it from that input complex image and further save each of them individually. For the bounding boxes I have gone through the white boundaries (separation) along the single images.
Complex Input Image Example 1:
Complex Input Image Example 2:
Complex Input Image Example 3:
Code I have tried:
import cv2
import numpy as np
# reading the input image
img = cv2.imread('cmp.jpg')
cv2.imshow("histology image", img)
# defining border color
lower = (0, 80, 110)
upper = (0, 120, 150)
# applying thresholding on border color
mask = cv2.inRange(img, lower, upper)
cv2.imshow("masked", mask)
# Using dilate threshold
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (15, 15))
mask = cv2.morphologyEx(mask, cv2.MORPH_DILATE, kernel)
# coloring border to white for other images
img[mask==255] = (255,255,255)
cv2.imshow("white_border", img)
# converting image to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# applying otsu threshold
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_OTSU )[1]
cv2.imshow("thresholded", thresh)
# applying 'Open' morphological operation
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (17,17))
morph = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
morph = 255 - morph
cv2.imshow("morphed", morph)
# finding contours and bounding boxes
bboxes = []
bboxes_img = img.copy()
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
for cntr in contours:
x,y,w,h = cv2.boundingRect(cntr)
cv2.rectangle(bboxes_img, (x, y), (x+w, y+h), (0, 0, 255), 1)
bboxes.append((x,y,w,h))
cv2.imshow("boundingboxes", bboxes_img)
cv2.waitKey(0)
cv2.destroyAllWindows()
I am not getting exact bounding boxes for each of single images present in the input complex image and further I need to save each cropped image individually. Any kind of help will be much appreciated.
I have gray scale image and want to convert to intensity contour with isotherm lines, in my code I am getting only one contour and how to apply the isotherm lines?
Goal:
import numpy as np
import cv2 as cv
img = cv2.imread(path)
imgray = cv.cvtColor(img, cv.COLOR_BGR2GRAY)
ret, thresh = cv.threshold(imgray, 127, 255, 0)
contours, hierarchy = cv.findContours(thresh, cv.RETR_TREE, cv.CHAIN_APPROX_SIMPLE)
cv.drawContours(img, contours, -1, (0,255,0), 3)
plt.imshow(img)
You're on the right track, all you have to do is just take that 127 that you hard-coded into the code, and iterate over a couple of different values. So take what you have and just add a few things (including a plug for the viridis colormap):
import numpy as np
import cv2
# I don't have your image, so I will just create a similar one.
H, W = 480, 640
img = np.zeros([H, W, 3], dtype=np.uint8)
cv2.circle(img, (W//2, H//2), 200, (255,255,255), -1)
img = cv2.GaussianBlur(img, (551, 551), 0)
imgray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# The viridis colormap is better than the jet one you have used.
img_viridis = cv2.applyColorMap(imgray, cv2.COLORMAP_VIRIDIS)
# This for-loop allows you to draw isotherm lines at any value you want.
THRESHES = [30, 90, 170]
for val in THRESHES:
ret, thresh = cv2.threshold(imgray, val, 255, 0)
contours, hierarchy = cv2.findContours(thresh, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(img_viridis, contours, -1, (0, 0, 255), 2)
cv2.imshow('img', img_viridis)
k = cv2.waitKey(0)
output:
Here is another approach in Python/OpenCV by quantizing the gray image and then getting the contours.
Read the input
Convert it to gray
Quantize it
Get Canny edge
Apply morphology close to ensure they are closed
Get the contours
Filter the contours by perimeter to remove small extraneous ones
Draw the contours on the input
Save the results
Input:
import numpy as np
import cv2
# read input
img = cv2.imread('bright_blob.png')
# convert to gray
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# do color quantization
gray = 64*((gray/64).astype(np.uint8))
# get canny edges
edges = cv2.Canny(gray, 10, 250)
# apply morphology closed to ensure they are closed
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3,3))
edges = cv2.morphologyEx(edges, cv2.MORPH_CLOSE, kernel)
# get contours
contours = cv2.findContours(edges, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)
contours = contours[0] if len(contours) == 2 else contours[1]
# filter contours to keep only large ones
result = img.copy()
for c in contours:
perimeter = cv2.arcLength(c, True)
if perimeter > 200:
cv2.drawContours(result, c, -1, (0,0,255), 1)
# save results
cv2.imwrite("bright_blob_gray.jpg", gray)
cv2.imwrite("bright_blob_edges.jpg", edges)
cv2.imwrite("bright_blob_isotherms.jpg", result)
# show images
cv2.imshow("gray", gray)
cv2.imshow("edges", edges)
cv2.imshow("result", result)
cv2.waitKey(0)
Quantized gray image:
Edge image:
Result:
i have this binary image (numpy array) that represents an approximation of a rectangle :
I'm trying to extract the real shape of the rectangle but can't seem to find a way.
The expected result is the following:
I'm using this code
contours,_ = cv2.findContours(numpymask.copy(), 1, 1) # not copying here will throw an error
rect = cv2.minAreaRect(contours[0]) # basically you can feed this rect into your classifier
(x,y),(w,h), a = rect # a - angle
box = cv2.boxPoints(rect)
box = np.int0(box) #turn into ints
rect2 = cv2.drawContours(img.copy(),[box],0,(0,0,255),10)
plt.imshow(rect2)
plt.show()
But the resut i'm getting is the following, which i not what i need :
For this i'm using Python with opencv.
This is something i played around with before. It should work with your image.
import imutils
import cv2
# load the image, convert it to grayscale, and blur it slightly
image = cv2.imread("test.jpg")
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
gray = cv2.GaussianBlur(gray, (5, 5), 0)
# threshold the image,
thresh = cv2.threshold(gray, 200, 255, cv2.THRESH_BINARY)[1]
# find contours in thresholded image, then grab the largest
# one
cnts = cv2.findContours(thresh.copy(), cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_SIMPLE)
cnts = imutils.grab_contours(cnts)
c = max(cnts, key=cv2.contourArea)
# draw the contours of c
cv2.drawContours(image, [c], -1, (0, 0, 255), 2)
# show the output image
cv2.imshow("Image", image)
cv2.waitKey(0)
I am trying to develop a OCR system. I am trying to use MSER in order to extract character from an image and then passing the characters into a CNN to recognize those characters. Here is my code for character extraction:
import cv2
import numpy as np
# create MSER object
mser = cv2.MSER_create()
# read the image
img = cv2.imread('textArea01.png')
# convert to gray scale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# store copy of the image
vis = img.copy()
# detect regions in the image
regions,_ = mser.detectRegions(gray)
# find convex hulls of the regions and draw them onto the original image
hulls = [cv2.convexHull(p.reshape(-1, 1, 2)) for p in regions]
cv2.polylines(vis, hulls, 1, (0, 255, 0))
# create mask for the detected region
mask = np.zeros((img.shape[0], img.shape[1], 1), dtype=np.uint8)
mask = cv2.dilate(mask, np.ones((150, 150), np.uint8))
for contour in hulls:
cv2.drawContours(mask, [contour], -1, (255, 255, 255), -1)
#this is used to find only text regions, remaining are ignored
text_only = cv2.bitwise_and(img, img, mask=mask)
cv2.imshow('img', vis)
cv2.waitKey(0)
cv2.imshow('mask', mask)
cv2.waitKey(0)
cv2.imshow('text', text_only)
cv2.waitKey(0)
This is working fine for most images, but for some images like this:
The outer border is also detected as a region and the contour is drawn in the mask such that all area inside the border is detected as text region. So, the contours inside have no effect. How do I prevent this so that only the text is detected?
Hulls detected:
and the mask as a result:
My result using this code:
import cv2
import numpy as np
img = cv2.imread("img.png")
# grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
cv2.imshow('gray', gray)
# binary
# ret, thresh = cv2.threshold(gray, 250, 255, cv2.THRESH_BINARY_INV)
thresh = cv2.adaptiveThreshold(gray, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY_INV, 35, 180)
cv2.imshow('threshold', thresh)
# dilation
kernel = np.ones((1, 1), np.uint8)
img_dilation = cv2.dilate(thresh, kernel, iterations=1)
cv2.imshow('dilated', img_dilation)
# find contours
# cv2.findCountours() function changed from OpenCV3 to OpenCV4: now it have only two parameters instead of 3
cv2MajorVersion = cv2.__version__.split(".")[0]
# check for contours on thresh
if int(cv2MajorVersion) >= 4:
ctrs, hier = cv2.findContours(img_dilation.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
else:
im2, ctrs, hier = cv2.findContours(img_dilation.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
# sort contours
sorted_ctrs = sorted(ctrs, key=lambda ctr: cv2.boundingRect(ctr)[0])
for i, ctr in enumerate(sorted_ctrs):
# Get bounding box
x, y, w, h = cv2.boundingRect(ctr)
# Getting ROI
roi = img[y:y + h, x:x + w]
# show ROI
# cv2.imshow('segment no:'+str(i),roi)
cv2.rectangle(img, (x, y), (x + w, y + h), (0, 255, 0), 1)
# if you want to save the letters without green bounding box, comment the line above
if w > 5:
cv2.imwrite('C:\\Users\\PC\\Desktop\\output\\{}.png'.format(i), roi)
cv2.imshow('marked areas', img)
cv2.waitKey(0)
You can have a threshold on the contour area so that it ignores all shapes that cover more than a certain area in the image.
for contour in hulls:
if cv.contourArea(contour) < ThresholdArea:
continue
cv2.drawContours(mask, [contour], -1, (255, 255, 255), -1)
#this is used to find only text regions, remaining are ignored
text_only = cv2.bitwise_and(img, img, mask=mask)
I am trying to focus on a Region of Interest on the face by using Numpy cropping. For large images, I have no trouble. But for smaller ones, I can find the face and find the matching bounding box, but when I try to crop it and show the image, I get a gray background to the right of the image. I wouldn't mind it, but when I try to apply contours to the image, the bottom and right edges are picked up as contour edges. How do I make sure that the gray padding doesn't affect my contour?
Here is my function:
def head_ratio(self):
face_cascade = cv2.CascadeClassifier('haarcascade_frontalface_default.xml')
faces = face_cascade.detectMultiScale(self.gray, 1.3, 5)
m_height, m_width, channels = self.image.shape
x, y, w, h = faces[0]
ROI = self.image[y:y+h,x:x+w]
kernel = np.ones((5,5), np.float32)/10
blurred = cv2.filter2D(self.gray[y:y+h, x:x+w], -1, kernel)
ret, thresh = cv2.threshold(blurred, 127, 255, cv2.THRESH_BINARY)
_,contours,_ = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(ROI, contours, -1, (255, 255, 255), 3)
cv2.imshow("output", ROI)
cv2.waitKey(0)
cv2.destroyAllWindows()
return 1
Thank you for your help. I have been trying to look for an answer to this but was having trouble with what to search for.