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| from __future__ import print_function
import sys
import pandas as pd
from PyQt5.QtCore import pyqtSignal
from radiomics import featureextractor as FEE
import yaml
from PyQt5 import uic
from PyQt5.QtWidgets import QDialog, QFileDialog, QApplication
from DataProsessing import child
class RadiomicsFunc(QDialog):
isChecked = pyqtSignal(int)
def __init__(self):
super().__init__()
self.dia = uic.loadUi("New_UI.ui", self)
def setupParaFile(self):
self.para_path = './ParaFile/Param.yml'
def ImgType_init(self,tag):
self.para_path = './ParaFile/Param.yml'
settingData = {
}
with open(self.para_path, 'w', encoding='utf-8') as f:
if tag == 1:
self.displayOri()
elif tag == 2:
self.displayCT()
elif tag == 3:
self.displayMR3()
elif tag == 4:
self.displayMR5()
elif tag == 5:
self.displayMR()
yaml.dump(data=settingData, stream=f, allow_unicode=True)
def featureSet(self):
featureData = {
}
with open(self.para_path, 'w', encoding='utf-8') as f:
if self.checkBox_First.isChecked():
featureData["featureClass"] = {"firstorder": [] }
if self.checkBox_shape.isChecked():
featureData["featureClass"] = {"shape": [] }
if self.checkBox_glcm.isChecked():
featureData["featureClass"] = {"glcm": [] }
if self.checkBox_glrlm.isChecked():
featureData["featureClass"] = {"glrlm": []}
if self.checkBox_glszm.isChecked():
featureData["featureClass"] = {"glszm": [] }
if self.checkBox_gldm.isChecked():
featureData["featureClass"] = {"gldm": [] }
if self.checkBox_ngtdm.isChecked():
featureData["featureClass"] = {"ngtdm": [] }
yaml.dump(data=featureData, stream=f, allow_unicode=True)
def outPuts(self,place,name,nii_path,ifsave,ori_path,label_path):
self.ori_path = ori_path
self.label_path = label_path
extractor = FEE.RadiomicsFeatureExtractor(parameter_file=self.para_path)
save_path = name + '.csv'
try:
result = extractor.execute(ori_path, nii_path)
except ValueError:
result = extractor.execute(ori_path, nii_path, label=2)
type(result)
df = pd.DataFrame()
for key, value in result.items():
df = df.append({'Feature': key, 'Value': value}, ignore_index=True)
ori_path = None
lab_path = None
if ifsave == True :
df.to_csv(save_path, index=False)
RadiomicsFunc.invokeDialog_1(self, save_path)
def invokeDialog_1(self,path):
dialog = child(path,self.ori_path,self.label_path)
dialog.exec()
def displayOri(self):
with open('./ParaFile/exampleCT.yaml', "rb") as ff:
content = ff.read()
with open(self.para_path, "ab") as f2:
f2.write(content)
def displayCT(self):
with open('./ParaFile/exampleCT.yaml', "rb") as ff:
content = ff.read()
with open(self.para_path, "ab") as f2:
f2.write(content)
def displayMR3(self):
with open('./ParaFile/exampleMR_3mm.yaml', "rb") as ff:
content = ff.read()
with open(self.para_path, "ab") as f2:
f2.write(content)
def displayMR5(self):
with open('./ParaFile/exampleMR_5mm.yaml', "rb") as ff:
content = ff.read()
with open(self.para_path, "ab") as f2:
f2.write(content)
def displayMR(self):
with open('./ParaFile/exampleMR_NoResampling.yaml.yaml', "rb") as ff:
content = ff.read()
with open(self.para_path, "ab") as f2:
f2.write(content)
def Add_Nor(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"normalize": "True", "normalizeScale": 500}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_Mask(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"minimumROIDimensions": "2", "minimumROISize": "50"}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_Bin(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"minimumROISize": "50"}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_Misc(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"label": 1}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_FirstSpe(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"voxelArrayShift": "1000"}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_FirstSpe2(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"voxelArrayShift": "300"}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_Resampling(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"interpolator ": "'sitkBSpline'", "resampledPixelSpacing": " [2, 2, 2]"}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_Resampling2(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"preCrop ": "true"}
yaml.dump(data=data, stream=f, allow_unicode=True)
"""
if self.dia.checkBox_4.isChecked():
data["setting"] = {"minimumROIDimensions": "2","minimumROISize": "50"}
elif self.dia.checkBox_5.isChecked(): #可以改成binwidth的输入项
data["setting"] = {"minimumROISize": "50"}
elif self.dia.checkBox_6.isChecked():
data["setting"] = {"voxelArrayShift": "1000"}
elif self.dia.checkBox.isChecked():#label数的输入项
data["setting"] = {"label": 1}
"""
def Add_2D(self, state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["setting"] = {"force2D ": "true"}
yaml.dump(data=data, stream=f, allow_unicode=True)
def Add_Voxel(self,state):
data = {
}
with open(self.para_path, 'a', encoding='utf-8') as f:
if state:
data["voxelSetting"] = {"kernelRadius ": 2,"maskedKernel":"true","initValue":"nan","voxelBatch":10000}
yaml.dump(data=data, stream=f, allow_unicode=True)
def cusParaSet(self,place):
file_name = QFileDialog.getOpenFileName(None, "Open File", "./", "yaml(*.yml;*.yaml)")
self.para_path = file_name[0]
place.setText(self.para_path)
"""
if tag == 1: #Original
settingData["imageType"] = {"Original": {}} #写入参数设定文件
self.displayOri(settingData)
elif tag == 2:
settingData["imageType"] = {"Original": {}}
self.displayCT(settingData)
elif tag == 3:
settingData["imageType"] = {"LoG": {}}
elif tag == 4:
settingData["imageType"] = {"Square": {}}
elif tag == 5:
settingData["imageType"] = {"SquareRoot": {}}
elif tag == 6:
settingData["imageType"] = {"Logarithm": {}}
elif tag == 7:
settingData["imageType"] = {"Exponential": {}}
elif tag == 8:
settingData["imageType"] = {"Gradient": {}}
elif tag == 9:
settingData["imageType"] = {"LocalBinaryPattern2D": {}}
else :
settingData["imageType"] = {"LocalBinaryPattern3D": {}}
"""
|
