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)
