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metadataextractor.py
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| 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 | |
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