def BrainExtractFast(input,output):
'''
:param input:
:param output:
:return:
use FSL . bet2 ， faster than HD-BET
'''
# is the input is dir? or file?
import subprocess
images = []
outputImages = []
if os.path.isdir(input):
if not os.path.exists(output):
os.mkdir(output)
images = utils.checkDir(input)
if(len(images) == 0):
print("there is no images in the input dir")
return
for image in images:
outputImages.append(os.path.join(output,"Bet_"+os.path.basename(image)))
else:
images.append(input)
outputImages.append(output)
exPath = os.path.join(setting.path, "bet", "bet2.exe")
for image,outputImage in zip(images,outputImages):
task = subprocess.Popen('%s %s %s' % (exPath, image, outputImage), shell=True,
stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
msg = ''
for line in task.stdout.readlines():
msg += line.decode("gb2312")
status = task.wait()
print(msg)
def runCal(self):
from Core.utils import checkFile, checkDir
self.pbar.setValue(1)
if (self.fileRadiobtn.isChecked()):
if checkFile(self.imageFile) == 1:
QMessageBox.information(self, "Warning",
"The image path is not valid!",
QMessageBox.Yes)
return
self.thread = RunThread(self.imageFile,
self.maskFile,
self.fileName,
type='singleFile')
else:
if len(checkDir(self.directory1)) == 0:
QMessageBox.information(self, "Warning",
"The directory path is not valid!",
QMessageBox.Yes)
return
self.thread = RunThread(self.directory1,
self.directory2,
self.fileName,
type="dir")
self.thread.start()
# self.thread2 = procThread()
# self.thread2.start()
self.thread.trigger.connect(self.process)
self.btnStart.setText("Calculating...")
self.btnStart.setDisabled(True)
def cal(self):
from Core.utils import checkFile, checkDir, checkOutputDir, checkOutputFile
if ((not self.CheckNorm) and (not self.CheckBFC)):
QMessageBox.information(self, "Warning",
"Please Choose at least one function!",
QMessageBox.Yes)
return
if self.RadioSingle.isChecked():
if checkFile(self.imageFile) == 1 or checkOutputFile(
self.outputPath) == 1:
QMessageBox.information(self, "Warning",
"The image path is not valid!",
QMessageBox.Yes)
return
else:
if len(checkDir(self.imageFile)) == 0 or checkOutputDir(
self.outputPath) == 1:
QMessageBox.information(self, "Warning",
"The image path is not valid!",
QMessageBox.Yes)
return
self.thread = calThread(self.imageFile, self.outputPath,
self.CheckBFC.isChecked(),
self.CheckNorm.isChecked(),
self.RadioSingle.isChecked())
self.thread.signal.connect(self.process)
self.thread.start()
self.BtnStart.setDisabled(True)
self.BtnStart.setText("Calculating...")
def segment(filename_input, directory_output, Type=False):
'''
:param filename_input: input dir or filename
:param directory_output: output dir name
:param Type: True ,use dir mode / False use file mode
:return:
'''
inipath = setting.LiviaNet_iniPath
modelname = setting.LiviaNet_modelPath
print(inipath)
print(modelname)
print(filename_input)
filepath = filename_input
iniFile = resini(inipath)
# True THE Whole dir
try:
if Type:
num = str([i for i in range(len(os.listdir(filename_input)))])
iniFile.write(filepath, "imagesFolder")
images = checkDir(filepath)
for image in images:
idata = nib.load(image)
data = idata.get_fdata()
affine = idata.affine
data = (data - np.mean(data.flatten())) / np.std(
data.flatten())
nib.save(nib.Nifti1Image(data, affine).to_filename(image))
else:
idata = nib.load(filepath)
data = idata.get_fdata()
affine = idata.affine
data = (data - np.mean(data.flatten())) / np.std(data.flatten())
nib.save(nib.Nifti1Image(data, affine), filepath)
getNum = lambda file_path, file_name: os.listdir(file_path).index(
file_name)
num = [
getNum(os.path.dirname(filepath), os.path.basename(filepath))
] # 获得文件的索引值
iniFile.write(os.path.dirname(filepath), "imagesFolder")
# resindex = resini(inipath) # 实例化resindex
iniFile.write(str(num),
"indexestosegment") # 将 indexestosegment 写入ini文件
roiPath = os.path.join(path, "hippoSeg", "roi")
iniFile.write(roiPath, "roifolder")
net.startTesting(modelname, inipath, directory_output)
except Exception as e:
print(e)
return 1
return 0
def cal(self):
if self.RadioSingle.isChecked():
if checkFile(self.imageFile) == 1 or checkOutputFile(self.outputPath) == 1:
QMessageBox.information(self, "Warning", "The image path is not valid!", QMessageBox.Yes)
return
else:
if len(checkDir(self.imageFile)) == 0 or checkOutputDir(self.outputPath) == 1:
QMessageBox.information(self, "Warning", "The image path is not valid!", QMessageBox.Yes)
return
if((self.imageFile is None) and (self.outputPath is None)):
QMessageBox.information(self, "Warning", "Please Choose the path!", QMessageBox.Yes)
return
self.thread = calThread(self.imageFile, self.outputPath,self.RadioSingle.isChecked())
self.thread.signal.connect(self.process)
self.thread.start()
self.BtnStart.setDisabled(True)
self.BtnStart.setText("Calculating...")
def cal(self):
'''
这里hd-bet内部自动会判断输入的是文件夹/文件，故没有判断
:return:
'''
from Core.utils import checkDir,checkFile,checkOutputFile,checkOutputDir
if self.RadioSingle.isChecked():
if (checkFile(self.imageFile) == 1 or checkOutputFile(self.outputPath) == 1):
QMessageBox.information(self, "Warning", "The image path is not valid!", QMessageBox.Yes)
return
else:
if (len(checkDir(self.imageFile)) == 0 or checkOutputDir(self.outputPath) == 1):
QMessageBox.information(self, "Warning", "The image path is not valid!", QMessageBox.Yes)
return
self.thread = calThread(self.imageFile,self.outputPath,self.RadioFast.isChecked())
self.thread.signal.connect(self.process)
self.thread.start()
self.BtnStart.setDisabled(True)
self.BtnStart.setText("Calculating...")
def slot_run0(self): # 避免UI堵塞，开启新线程
# self.pb = ProgressBar() # 进度条显示
# self.pb.show()
from Core.utils import checkDir, checkFile
if self.ui.RadioBtn_Dir.isChecked():
if len(checkDir(self.filename_input)) == 0:
QMessageBox.information(self, "Warning",
"The directory path is not valid!",
QMessageBox.Yes)
return
else:
if checkFile(self.filename_input) == 1:
QMessageBox.information(self, "Warning",
"The image path is not valid!",
QMessageBox.Yes)
return
self.ui.run_pushButton.setDisabled(True)
self.thread = RunThread(self.filename_input,
self.directory_output,
Type=self.ui.RadioBtn_Dir.isChecked())
self.thread.trigger.connect(self.process)
self.thread.start()
def run(self):
if (self.refImage == None):
self.refImage = ""
if (self.type == 0):
self.signal.emit(0.5)
p = registration(flo=self.image,
res=self.resImage,
ref=self.refImage)
self.signal.emit(1)
#batch mode
else:
self.signal.emit(0.01)
images = checkDir(self.image)
i = 1
for image in images:
registration(flo=image,
res=os.path.join(self.resImage,
"Reg" + os.path.basename(image)),
ref=self.refImage)
self.signal.emit(i / len(images))
i += 1
self.signal.emit(1)
def Cal(self):
from Core.utils import checkFile, checkDir
if self.RdioSingleFile.isChecked():
if checkFile(self.Image) == 1:
QMessageBox.information(self, "Warning",
"The image path is not valid!",
QMessageBox.Yes)
return
self.thread = calculate(self.Image, self.RefImage, self.ResImage)
else:
if len(checkDir(self.directory1)) == 0:
QMessageBox.information(self, "Warning",
"The directory path is not valid!",
QMessageBox.Yes)
return
self.thread = calculate(self.directory1,
self.RefImage,
self.directory2,
type=1)
self.BtnStart.setDisabled(True)
self.thread.start()
self.thread.signal.connect(self.process)
def calData(self):
from Core.utils import checkDir,checkFile
if len(checkDir(self.brainDIR)) == 0:
QMessageBox.information(self, "Warning", "The image path is not valid!", QMessageBox.Yes)
return
brains = os.listdir(self.brainDIR)
wmPath = ""
gmPath =""
csfPath=""
for brain in brains:
if(brain.find('wm')!=-1):
wmPath = os.path.join(self.brainDIR,brain)
elif(brain.find("csf")!=-1):
csfPath = os.path.join(self.brainDIR,brain)
elif(brain.find("gm")!=-1):
gmPath = os.path.join(self.brainDIR,brain)
if(wmPath == "" or gmPath == "" or csfPath== ""):
QMessageBox.information(self, "Warning", "The brain segmentation path is not valid!", QMessageBox.Yes)
return
self.thread = calThread(self.FeaturePath,wmPath,gmPath,csfPath,self.HippoPath,self.imageFile,self.outputPath)
self.thread.signal.connect(self.precess)
self.thread.start()
self.BtnStart.setDisabled(True)
