def __init__(self):
super(FeatureExtractionForm, self).__init__()
self.ui = Ui_FeatureExtraction()
self._root_folder = ''
self._patterns = 0
self._image_patten_list = []
self._roi_patten_list = []
self.radiomics_params = RadiomicsParamsConfig('RadiomicsParams.yaml')
self.ui.setupUi(self)
self.ui.tableFilePattern.setColumnCount(4)
self.ui.tableFilePattern.setHorizontalHeaderLabels(
["Type", "Name", "Include", "Exclude"])
self.ui.tableFilePattern.setEditTriggers(
QAbstractItemView.NoEditTriggers)
self.ui.tableFilePattern.setSelectionBehavior(
QAbstractItemView.SelectRows)
self.ui.buttonBrowseSourceFolder.clicked.connect(
self.BrowseSourceFolder)
self.ui.buttonAddOne.clicked.connect(self.AddOnePattern)
self.ui.buttonRemoveOne.clicked.connect(self.RemoveOnePattern)
self.ui.buttonRun.clicked.connect(self.Run)
self.ui.UseExistConfigcheckBox.clicked.connect(self.UseExitingConfig)
self.ui.ConfigPushButton.clicked.connect(
self.BrowseRadiomicsFeatureCofigFile)
self.ui.CofnigLineEdit.setText(
r'D:\research\exampleMR_NoResampling.yaml')
self.ui.CofnigLineEdit.setEnabled(False)
self.ui.ConfigPushButton.setEnabled(False)
def __init__(self):
super(FeatureExtractionForm, self).__init__()
self.ui = Ui_FeatureExtraction()
self._root_folder = ''
self._patterns = 0
self._image_patten_list = []
self._roi_patten_list = []
self.radiomics_params = RadiomicsParamsConfig('RadiomicsParams.yaml')
self.ui.setupUi(self)
self.ui.tableFilePattern.setColumnCount(4)
self.ui.tableFilePattern.setHorizontalHeaderLabels(["Type", "Name", "Include", "Exclude"])
self.ui.tableFilePattern.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.ui.tableFilePattern.setSelectionBehavior(QAbstractItemView.SelectRows)
self.ui.buttonBrowseSourceFolder.clicked.connect(self.BrowseSourceFolder)
self.ui.buttonAddOne.clicked.connect(self.AddOnePattern)
self.ui.buttonRemoveOne.clicked.connect(self.RemoveOnePattern)
self.ui.buttonRun.clicked.connect(self.Run)
class FeatureExtractionForm(QWidget):
close_signal = QtCore.pyqtSignal(bool)
def __init__(self):
super(FeatureExtractionForm, self).__init__()
self.ui = Ui_FeatureExtraction()
self._root_folder = ''
self._patterns = 0
self._image_patten_list = []
self._roi_patten_list = []
self.radiomics_params = RadiomicsParamsConfig('RadiomicsParams.yaml')
self.ui.setupUi(self)
self.ui.tableFilePattern.setColumnCount(4)
self.ui.tableFilePattern.setHorizontalHeaderLabels(["Type", "Name", "Include", "Exclude"])
self.ui.tableFilePattern.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.ui.tableFilePattern.setSelectionBehavior(QAbstractItemView.SelectRows)
self.ui.buttonBrowseSourceFolder.clicked.connect(self.BrowseSourceFolder)
self.ui.buttonAddOne.clicked.connect(self.AddOnePattern)
self.ui.buttonRemoveOne.clicked.connect(self.RemoveOnePattern)
self.ui.buttonRun.clicked.connect(self.Run)
def closeEvent(self, event):
self.close_signal.emit(True)
event.accept()
def BrowseSourceFolder(self):
dlg = QFileDialog()
dlg.setFileMode(QFileDialog.DirectoryOnly)
dlg.setOption(QFileDialog.ShowDirsOnly)
if dlg.exec_():
self._root_folder = dlg.selectedFiles()[0]
self.ui.lineEditSourceFolder.setText(self._root_folder)
def _PatternNameExist(self, one_name):
exist_name_list = [item['name'] for item in self._image_patten_list]
if one_name in exist_name_list:
return True
else:
return False
def AddOnePattern(self):
message = QMessageBox()
if self.ui.lineEditkeyInclude.text() == '':
message.about(self, 'Include can not be empty',
'Include patterns are used to identify the file')
return
if self.ui.lineEditkeyShowName.text() == '':
message.about(self, 'ShowName can not be empty',
'ShowName patterns are used to add pre-name in the feature matrix')
return
one_pattern = {'name': self.ui.lineEditkeyShowName.text().split(','),
'include': self.ui.lineEditkeyInclude.text().split(','),
'exclude': self.ui.lineEditkeyExclude.text().split(',')}
if self.ui.radioImagePattern.isChecked() and self._PatternNameExist(one_pattern['name']):
message.about(self, '', 'Same image pattern exists')
return
elif self.ui.radioRoiPattern.isChecked() and self._roi_patten_list:
message.about(self, '', 'There should only one ROI pattern')
return
self.ui.tableFilePattern.insertRow(self._patterns)
if self.ui.radioImagePattern.isChecked():
self.ui.tableFilePattern.setItem(self._patterns, 0, QTableWidgetItem('Image'))
self._image_patten_list.append(one_pattern)
elif self.ui.radioRoiPattern.isChecked():
self.ui.tableFilePattern.setItem(self._patterns, 0, QTableWidgetItem('ROI'))
self._roi_patten_list.append(one_pattern)
self.ui.tableFilePattern.setItem(self._patterns, 1, QTableWidgetItem(','.join(one_pattern['name'])))
self.ui.tableFilePattern.setItem(self._patterns, 2, QTableWidgetItem(','.join(one_pattern['include'])))
self.ui.tableFilePattern.setItem(self._patterns, 3, QTableWidgetItem(','.join(one_pattern['exclude'])))
self._patterns += 1
def RemoveOnePattern(self):
if not self.ui.tableFilePattern.selectedIndexes():
return None
index = self.ui.tableFilePattern.selectedIndexes()[0].row()
image_type = self.ui.tableFilePattern.item(index, 0).text()
if image_type == 'Image':
one_pattern = {'name': self.ui.tableFilePattern.item(index, 1).text().split(','),
'include': self.ui.tableFilePattern.item(index, 2).text().split(','),
'exclude': self.ui.tableFilePattern.item(index, 3).text().split(',')}
self._image_patten_list.remove(one_pattern)
elif image_type == 'ROI':
self._roi_patten_list = []
self._patterns -= 1
self.ui.tableFilePattern.removeRow(index)
def _GetImageAndRoiMatcher(self):
series_matchers = {}
for one_pattern in self._image_patten_list:
series_matchers[one_pattern['name'][0]] = SeriesStringMatcher(include_key=one_pattern['include'],
exclude_key=one_pattern['exclude'])
roi_matcher = SeriesStringMatcher(include_key=self._roi_patten_list[0]['include'],
exclude_key=self._roi_patten_list[0]['exclude'])
return series_matchers, roi_matcher
def _CheckFiles(self):
if len(self._roi_patten_list) == 0:
self._missing_message += 'Must have 1 Roi Pattern. \n'
return False
if len(self._image_patten_list) == 0:
self._missing_message += 'Must have at least 1 Image Pattern. \n'
return False
all_match = True
series_matchers, roi_matcher = self._GetImageAndRoiMatcher()
for case_name in os.listdir(self._root_folder):
case_folder = os.path.join(self._root_folder, case_name)
if not os.path.isdir(case_folder):
continue
series_list = os.listdir(case_folder)
# Match series according to patterns
for key, one_series_matcher in series_matchers.items():
result = one_series_matcher.Match(series_list)
if len(result) != 1:
self._missing_message += '{} does not match {}\n'.format(case_name, key)
all_match = False
result = roi_matcher.Match(series_list)
if len(result) != 1:
self._missing_message += '{} does not match ROI\n'.format(case_name)
all_match = False
return all_match
def _UpdateImageClassesFeature(self, update_data, image_types):
image_types_ctrl = {self.ui.checkBoxOriginal, self.ui.checkBoxWavelet, self.ui.checkBoxSquare,
self.ui.checkBoxSquareRoot, self.ui.checkBoxLoG, self.ui.checkBoxLogarithm,
self.ui.checkBoxExponential, self.ui.checkBoxGradient, self.ui.checkBoxLocalBinaryPattern2D,
self.ui.checkBoxLocalBinaryPattern3D}
if update_data:
for ctrl in image_types_ctrl:
if ctrl.isChecked():
image_types.append(ctrl.text())
else:
for ctrl in image_types_ctrl:
ctrl.setChecked(ctrl.text() in image_types)
def _UpdateFeatureClasses(self, update_data, feature_classes):
feature_classes_ctrl = {self.ui.checkBoxFirstOrderStatistics, self.ui.checkBoxShapeBased2D,
self.ui.checkBoxGLCM, self.ui.checkBoxGLRLM, self.ui.checkBoxGLSZM,
self.ui.checkBoxGLDM, self.ui.checkBoxNGTDM}
if update_data:
for ctrl in feature_classes_ctrl:
if ctrl.isChecked():
feature_classes.append(ctrl.text())
else:
for ctrl in feature_classes_ctrl:
ctrl.setChecked(ctrl.text() in feature_classes)
def Run(self):
try:
def UpdateRadiomicsConfig():
image_types = list()
self._UpdateImageClassesFeature(True, image_types)
feature_classes = list()
self._UpdateFeatureClasses(True, feature_classes)
self.radiomics_params.SetImageClasses(image_types)
self.radiomics_params.SetFeatureClasses(feature_classes)
self.radiomics_params.SaveConfig()
dlg = QFileDialog()
file_name, _ = dlg.getSaveFileName(self, 'Save CSV feature files', 'features.csv',
filter="CSV files (*.csv)")
if not file_name:
return None
self.ui.plainTextOutput.setPlainText('Checking Files ...')
QApplication.processEvents()
self._missing_message = ''
if not self._CheckFiles():
self.ui.plainTextOutput.appendPlainText(self._missing_message)
self.ui.plainTextOutput.appendPlainText("Please Check the Data")
QApplication.processEvents()
return
self.ui.plainTextOutput.appendPlainText('Done')
QApplication.processEvents()
UpdateRadiomicsConfig()
extractor = MyFeatureExtractor('RadiomicsParams.yaml')
series_matchers, roi_matcher = self._GetImageAndRoiMatcher()
name_list, matcher_list = [], []
for name, matcher in series_matchers.items():
name_list.append(name)
matcher_list.append(matcher)
total_cases = len([temp for temp in os.listdir(self._root_folder) if
os.path.isdir(os.path.join(self._root_folder, temp))])
self.ui.plainTextOutput.appendPlainText("\n\nTotal {} cases are processed:\n".format(total_cases))
for index, case_name in extractor.Execute(self._root_folder,
image_matcher_list=matcher_list,
roi_matcher=roi_matcher,
show_name_list=name_list,
store_path=file_name):
self.ui.plainTextOutput.appendPlainText('{} Done ({}/{})\n'.format(case_name, index, total_cases))
QApplication.processEvents()
except Exception as e:
print(e.__str__())