def findHvalue(_rawImageFile="E:\workspace\jinyoung\CancerImageAnalyzer\img\BF_position020100_time0001.tif"): _outputPath = '/ppimg'+datetime.datetime.today().strftime('%y%m%d%H%M')+'/' rawImgFloat = cia.loadRawImage(_rawImageFile) filteredImg1st = cia.execGaussianFiltering(rawImgFloat) for hVal in np.arange(0.1,1.0,0.1): dilatedImg = cia.execMorphologicalDilation(filteredImg1st,h=hVal) cia.savePreprocessingImage(dilatedImg,outputPath=_outputPath,h=hVal)
def findThresholdValue(_ppImageFile="E:\workspace\jinyoung\CancerImageAnalyzer\img\ppimg1601101615\BF_position020100_time0001hVal0.4.png"): _thOutputPath = '/thimg'+datetime.datetime.today().strftime('%y%m%d%H%M')+'/' ppImageFileName = os.path.basename(_ppImageFile) ppImageFilePath = os.path.dirname(_ppImageFile) biImageFilePath = ppImageFilePath + _thOutputPath ppImg = cia.loadRawImage(_ppImageFile) for thVal in np.arange(0.1,1.0,0.1): filledImg = cia.convertBinaryImage(ppImg,threshold=thVal) if not os.path.exists(biImageFilePath): os.mkdir(biImageFilePath) biImageFileName = ppImageFileName[:ppImageFileName.rfind('.')]+'thVal'+str(thVal)+'.png' imsave(biImageFilePath+biImageFileName, filledImg)
def startProcess(currentDir = "E:/workspace/jinyoung/img/expr1"): resArr = [] for i in os.listdir(currentDir): i = currentDir + '/'+i if os.path.isdir(i): resArrSub = [] for j in os.listdir(i): j = i + '/' + j res = cia.testCancerAnalyzer(os.path.abspath(j)) resArrSub.append(res) resArr.append(resArrSub) return resArr
def findRemSmObjValue(_biImageFile="E:/workspace/jinyoung/CancerImageAnalyzer/img/ppimg1601101508/thimg1601101511/BF_position020100_time0001hVal0.4thVal0.9.png"): _remSmObjOutputPath = '/remSmObjImg'+datetime.datetime.today().strftime('%y%m%d%H%M')+'/' remSmObjImageFileName = os.path.basename(_biImageFile) biImageFilePath = os.path.dirname(_biImageFile) reSmObjImageFilePath = biImageFilePath + _remSmObjOutputPath biImg = imread(_biImageFile) biImgRsize = biImg.shape[0] * 0.1 biImgCsize = biImg.shape[1] * 0.1 biImg = biImg[biImgRsize:-biImgRsize, biImgCsize:-biImgCsize] biImg = ndimage.binary_fill_holes(biImg) for smObjVal in np.arange(0,100000,10000): filledImg = cia.removeSmallObject(biImg, minSize=smObjVal) if not os.path.exists(reSmObjImageFilePath): os.mkdir(reSmObjImageFilePath) biImageFileName = remSmObjImageFileName[:remSmObjImageFileName.rfind('.')]+'smObjVal'+str(smObjVal)+'.png' imsave(reSmObjImageFilePath+biImageFileName, filledImg)