get annotation overlay with images by using python

gistfile1.txt

#!/usr/bin/env python3

import multiresolutionimageinterface as mir
import matplotlib.pyplot as plt
import cv2
import numpy as np

reader = mir.MultiResolutionImageReader()
mr_image = reader.open('/home/wli/Downloads/tumor_036.tif')
Ximageorg, Yimageorg = mr_image.getDimensions()
dims = mr_image.getLevelDimensions(4)
#Ximage = (Ximage+240//2)//240
#Ximage = 4000
#Yimage = (Yimage+240//2)//240 
#Yimage = 2000
import xml.etree.ElementTree as et
import pandas as pd
import math

def convert_xml_df (file):
    parseXML = et.parse(file)
    root = parseXML.getroot()
    dfcols = ['Name', 'Order', 'X', 'Y']
    df_xml = pd.DataFrame(columns=dfcols)
    for child in root.iter('Annotation'):
        for coordinate in child.iter('Coordinate'):
            Name = child.attrib.get('Name')
            Order = coordinate.attrib.get('Order')
            X_coord = float(coordinate.attrib.get('X'))
           # X_coord = X_coord - 30000
            X_coord = ((X_coord)*dims[0])/Ximageorg
            Y_coord = float(coordinate.attrib.get('Y'))
           # Y_coord = Y_coord - 155000
            Y_coord = ((Y_coord)*dims[1])/Yimageorg
            df_xml = df_xml.append(pd.Series([Name, Order, X_coord, Y_coord], index = dfcols), ignore_index=True)
            df_xml = pd.DataFrame(df_xml)
        return (df_xml)  

annotations = convert_xml_df('/home/wli/Downloads/tumor_036.xml')

x_values = list(annotations['X'].get_values())
y_values = list(annotations['Y'].get_values())
xy = list(zip(x_values,y_values))


#image = cv2.imread('/home/wli/Downloads/tumor_036.xml', -1)
tile =mr_image.getUCharPatch(0, 0, dims[0], dims[1], 4)
#canvas = np.zeros((Ximage, Yimage, 3), np.uint8) # fix the division
coords = np.array([xy], dtype=np.int32)

#cv2.drawContours(canvas, [coords],-1, (0,255,0), -1)
cv2.polylines(tile, [coords], isClosed=True, color=(0,0,255), thickness=5)
cv2.imshow("tile", tile);cv2.waitKey();cv2.destroyAllWindows()

#cv2.fillConvexPoly(mask, coords,1)
#mask = mask.astype(np.bool)

#output = np.zeros_like(image)
#output[mask] = image[mask]

#cv2.imshow('image',output)
#cv2.waitKey(0)
#cv2.destroyAllWindows()

I tried the code in windows. It is working. I find an interesting color problem
(We will not worry about color information now). The left image is from ASAP GUI, and the right one is from python. The colors are opposite: purple in GUI is displayed as pink in python, and pink in GUI is displayed as purpler in python.