metadataextractor.py

metadataextractor.py

import hashlib
import time
import openslide

class MetadataExtractor:
    PROPERTIES = [
        "objective",
        "mpp-x",
        "mpp-y",
        "vendor",
        "width",
        "height",
        "level_count",
        "timestamp",
        "md5sum",
        "file-location", #From CSV
        "case_id",
        "study_id"
    ]
    fileMetadata = {}
    def __init__(self, fileMetadata):
        self.fileMetadata = fileMetadata
        self.imageMetadata = self.extractImageMetadata()
        if(self.imageMetadata == []):
            print("Couldn't fetch image metadaa")
    def extractImageMetadata(self):
        fileMetadata = self.fileMetadata
        fileLocation = fileMetadata['file-location']
        try:
            openslideF = openslide.OpenSlide(fileLocation)
            payLoad = openslideF

            return payLoad
        except:
            print("Couldn't read "+fileLocation)

        return []

    def generateMD5Checksum(self,fileName):
        m = hashlib.md5()
        blocksize = 2**20
        with open(fileName, "rb") as f:
            while True:
                buf = f.read(blocksize)
                if not buf:
                    break
                m.update(buf)
        return m.hexdigest()



    def createPayLoad(self):
        payLoad = {}
        fileMetadata = self.fileMetadata
        imageMetadata = self.imageMetadata
        #print(imageMetadata.properties)
        
        if(imageMetadata):
            for prop in self.PROPERTIES:
                #print(prop)
                if prop == "file-location" or prop == "filename":
                    payLoad[prop] = fileMetadata['file-location']
                elif prop == 'study_id':
                    payLoad[prop] = fileMetadata['study_id']
                elif prop == "case_id":
                    payLoad["case_id"] = fileMetadata['id']
                elif prop in ["mpp-x", "mpp-y", "objective"]:

                    '''
                    Tiff specific
                    '''
                    if prop == "mpp-x":
                        if("tiff.XResolution" in imageMetadata.properties):
                            payLoad[prop] = float(imageMetadata.properties["tiff.XResolution"])

                    if prop == "mpp-y":
                        if("tiff.YResolution" in imageMetadata.properties):
                            payLoad[prop] = float(imageMetadata.properties["tiff.YResolution"])


                    
                    '''
                    (SVS) Generic
                    '''
                    property_ = 'openslide.'+str(prop)
                    
                    if(property_ in imageMetadata.properties):
                     
                        payLoad[prop] = float(imageMetadata.properties['openslide.'+str(prop)])
                    else:

                        if(prop == "objective"):
                            if("aperio.AppMag" in imageMetadata.properties):
                                payLoad[prop] = float(imageMetadata.properties["aperio.AppMag"])
                            else:
                                print(imageMetadata.properties)

                elif prop in ["height", "width"]:
                    hw = "openslide.level[0]."+str(prop)
                    payLoad[prop] = int(imageMetadata.properties[hw])
                elif prop == "vendor":
                    payLoad[prop] = imageMetadata.properties['openslide.'+str(prop)]
                elif prop == "md5sum":
                    payLoad[prop] = self.generateMD5Checksum(fileMetadata['file-location'])
                elif prop == "level_count":
                    payLoad[prop] = int(imageMetadata.level_count)
                elif prop == "timestamp":
                    payLoad[prop] = time.time() 
                else:
                    print("Couldn't handle: "+ prop)
       	''' 
        #Check nothing is missing
        for prop in self.PROPERTIES:
            #print(payLoad)
            if prop not in payLoad:
                payLoad
            if not payLoad[prop]:
                payLoad = {}
        '''
        if("mpp-x" in payLoad):
            payLoad["mpp_x"] = payLoad["mpp-x"]
            payLoad["mpp_y"] = payLoad["mpp-y"]
        else:
            payLoad["mpp_x"] = 0.25
            payLoad["mpp_y"] = 0.25
        payLoad["subject_id"] = payLoad["case_id"]
        payLoad["filename"] = payLoad["file-location"]
        return payLoad