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you can easily crop the image in python by using

roi = oriImage[refPoint[0][1]:refPoint[1][1], refPoint[0][0]:refPoint[1][0]]

In order to get the two points you can call cv2.setMouseCallback("image", mouse_crop). The function is something like this

def mouse_crop(event, x, y, flags, param):
    # grab references to the global variables
    global x_start, y_start, x_end, y_end, cropping

    # if the left mouse button was DOWN, start RECORDING
    # (x, y) coordinates and indicate that cropping is being
    if event == cv2.EVENT_LBUTTONDOWN:
        x_start, y_start, x_end, y_end = x, y, x, y
        cropping = True

    # Mouse is Moving
    elif event == cv2.EVENT_MOUSEMOVE:
        if cropping == True:
            x_end, y_end = x, y

    # if the left mouse button was released
    elif event == cv2.EVENT_LBUTTONUP:
        # record the ending (x, y) coordinates
        x_end, y_end = x, y
        cropping = False # cropping is finished

        refPoint = [(x_start, y_start), (x_end, y_end)]

        if len(refPoint) == 2: #when two points were found
            roi = oriImage[refPoint[0][1]:refPoint[1][1], refPoint[0][0]:refPoint[1][0]]
            cv2.imshow("Cropped", roi)

You can get details from here : Mouse Click and Cropping using Python