Original question
I have about 80-100 images such as (A). Each image is composed of shapes that were filled with black color after marking the outline in ImageJ. I need to extract each individual shape as in (B). I then need to find the angle of the longest axis as in (C).
And I then need to calculate all the possible widths at regular points within the black shape and return a .csv file containing these values.
I have been doing this manually and there must be a quicker way to do it. Any idea how I can go about doing this?
Partial solution
Solution (partial) as per Epsi's answer:
import matplotlib.pyplot as plt
import cv2
import numpy as np
image = cv2.imread("Image.tif")
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY_INV cv2.THRESH_OTSU)[1]
# Find contours, find rotated rectangle, obtain four verticies, and draw
cnts = cv2.findContours(thresh, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[0] if len(cnts) > 0 else cnts[1]
rect = cv2.minAreaRect(cnts[0])
box = np.int0(cv2.boxPoints(rect))
image_contours = np.zeros(image.shape)
# draw the contours on the empty image
cv2.drawContours(image, [box], 0, (36,255,12), 3)
plt.imshow(image)
The above code gives me the following result D. I need some more help, how do I get the code to calculate the rectangles for all the contours and not just one?
CodePudding user response：
As I'm not that good with python, I wont post code, but will post links to explanations and documentary.
How I would do it is as follows:
Invert the image, so that all the white becomes black and black becomes white. https://www.delftstack.com/howto/python/opencv-invert-image/#invert-images-using-numpy.invert-method-in-python
Use findContours to find all the (now) white contours. https://pythonexamples.org/python-opencv-cv2-find-contours-in-image/
use minAreaRect to create bounding boxes around the contours that is positioned in a way that the area of the box is as small as possible. https://theailearner.com/tag/cv2-minarearect/
from the created bounding boxes, take the longest side, this will represent the length of your contour.
You can also get the angle of rotation from the bounding boxes