I want to cut the MRI by using the respective reference mask. I applied contour operation to crop the mask into 100*100. After that, I am trying to cut the MRI using the cropped mask in the same orientation and extract the mask location in the MRI. But it can't crop the same place as the MRI. Anyone can help, please. Thanks in advance. Here I attach the expected output.
output
```
#crop the mask into 100*100
def crop_brain_contour(image):
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY) # grayscale
cnts = cv2.findContours(gray, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[0] if len(cnts) == 2 else cnts[1]
for c in cnts:
x,y,w,h = cv2.boundingRect(c)
ROI = image[y:y+h, x:x+w]
return ROI
cv_mask = cv2.imread('./input data/442_mask.bmp')
desired_width, desired_height = (100, 100)
final_crop_mask = np.zeros((desired_height, desired_width, 3), dtype="uint8")
mask_crop = crop_brain_contour(cv_mask)
h,w = mask_crop.shape[:2]
x1 = int(desired_width/2 - w/2)
y1 = int(desired_height/2 - h/2)
x2 = x1 + w
y2 = y1 + h
final_crop_mask[y1:y2, x1:x2, :] = mask_crop
cv2.imwrite("crop_mask.bmp",final_crop_mask)
# crop the MRI using reference crop mask in the same orientation
# read image
img = cv2.imread('input_1.bmp')
ht, wd, cc = img.shape
# read mask as grayscale
mask = cv2.imread('crop_mask.bmp', cv2.IMREAD_GRAYSCALE)
# threshold mask and invert
mask = cv2.threshold(mask,0,255,cv2.THRESH_BINARY)[1]
mask = 255 - mask
hh, ww = mask.shape
# make mask 3 channel
mask = cv2.merge([mask,mask,mask])
x1 = int(512 / 2 - ww / 2)
y1 = int(512 / 2 - hh / 2)
x2 = x1 + ww
y2 = y1 + hh
# put mask into black background image
mask2 = np.zeros_like(img)
mask2[y1:y2, x1:x2] = mask
# apply mask to image
img_masked = cv2.bitwise_and(img, mask2)
# crop region
img_masked_cropped = img_masked[y1:y2, x1:x2]
# ALTERNATE just crop input
img_cropped = img[y1:y2, x1:x2]
# save results
cv2.imwrite('./output/mask_inserted.bmp', mask2)
cv2.imwrite('./output/masked_image.bmp', img_masked)
cv2.imwrite('./output/masked_cropped.bmp', img_masked_cropped)
cv2.imwrite('./output/img_cropped.bmp', img_cropped)
```