Source code for WSI.readwsi

"""
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Created on Fri Feb  4 11:42:52 2023

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**Title:**        ValidPath Toolbox - WSI Handler module

**Description:**  This is the WSI Handler module for the ValidPath toolbox. It is includes ReadWsi class and several methods
              
**Classes:**      WSIReader
              

**Methods:** There are three methods in the ReadWSI module as follows:
        
        •	Reader: wsi_obj = WSIReader.wsi_reader(path)
        
        
        •	Region Extractor: WSIReader.extract_region(wsi_obj,location,level,size)
        
        
        •	Extract Bounds: WSIReader.extract_bounds(wsi_obj,bounds,level)


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Author: SeyedM.MousaviKahaki (seyed.kahaki@fda.hhs.gov)
Version ='1.0'
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"""

import numpy as np
import cv2
from skimage.io import imsave, imread
from PIL import Image
import os
from glob import glob
#import openslide
#Sfrom openslide.deepzoom import DeepZoomGenerator
import numpy as np
from pathlib import Path
import tifffile as tiff
import random
import matplotlib.pyplot as plt
#from readwsi.TissueSegmentation import TissueSegmentation
from shapely.geometry import Polygon, Point
#from readwsi.normalization import Normalization
#from readwsi import normalization
import PIL



class WSIReader:
    def __init__(self):
        pass  
  


    def extract_region(wsi_obj,location,level,size):
        """
        This method process the WSIs and extract regions.
        
      
        :Parameters:
        wsi_obj : object
            recieve the WSI object
            
        :Returns:
        IMG : Image
            Image data
        """
        # level = The number of levels in the slide.
        #Levels are numbered from 0 (highest resolution) to level_count - 1 (lowest resolution).
        
        return wsi_obj.read_region(location,level,size).convert('RGB')

    


    def extract_bounds(wsi_obj,bounds,level):
        """
        This method process the WSIs and extract image.
        
        :Parameters:
        wsi_obj : object
            recieve the WSI object
        bounds : tuple
            recieve the locations for extracting image from WSI
        level : int
            WSI level to extract image from
            
        :Returns:
        IMG : Image
            Image data
        """

        # Specify the bounds in terms of rectangle (left, top, right, bottom)
        
        size_h = bounds[3] - bounds[1] 
        size_w = bounds[2] - bounds[0] 
        
        if(size_h<0 or size_w<0):
            print("error in bounds , try again")
            return 0
        
        size = (size_w,size_h)
        
        location = ( bounds[0] , bounds[1] )
        
        return wsi_obj.read_region(location,level,size).convert('RGB')

        
    


    def wsi_xml_list (wsis_dir):
        """
        This code process the WSIs and XML list and returns these lists.
        Only WSI are included if there is an XML file with the same name.
      
        :Parameters:
        wsis_dir : string
            Input Directory which has the original WSIs and XML files
            
        :Returns:
        WSIs : list
            List of included WSIs
            
        xml_ : list
            List of XML files associated with included WSIs
        """
        #WSIs_ = glob(wsis_dir+'/*.svs')
        files = os.listdir(wsis_dir)
        WSIs_ = [os.path.join(wsis_dir,f) for f in files]
        
        WSIs = []
        XMLs = []

        for WSI in WSIs_:
            xml_ = str.replace(WSI, 'svs', 'xml')
            xmlexist = os.path.exists(xml_)
            if xmlexist:
                print('including: ' + WSI)
                XMLs.append(xml_)
                WSIs.append(WSI)


        return (WSIs, xml_)





    def wsi_reader(WSI_path):
        """
        This code read a WSI and return the WSI object.
        This code can read the WSIs with the following formats:
        Aperio (.svs, .tif)
        Hamamatsu (.vms, .vmu, .ndpi)
        Leica (.scn)
        MIRAX (.mrxs)
        Philips (.tiff)
        Sakura (.svslide)
        Trestle (.tif)
        Ventana (.bif, .tif)
        Generic tiled TIFF (.tif)
          
        :Parameters:
            WSI_path : string
                The address to the WSI file.
                
        :Returns:
            wsi_obj : object
                WSI object

        """

        wsi_obj = openslide.OpenSlide(WSI_path)

        return (wsi_obj)