class PrepareConnection(QWidget, Ui_Prepare):
def __init__(self, parent=None):
super(PrepareConnection, self).__init__(parent)
self.setupUi(self)
self.data_container = DataContainer()
self.buttonLoad.clicked.connect(self.LoadData)
self.buttonRemove.clicked.connect(self.RemoveNonValidValue)
self.loadTestingReference.clicked.connect(
self.LoadTestingReferenceDataContainer)
self.clearTestingReference.clicked.connect(
self.ClearTestingReferenceDataContainer)
self.__testing_ref_data_container = DataContainer()
self.checkSeparate.clicked.connect(self.SetSeparateStatus)
self.spinBoxSeparate.setEnabled(False)
self.logger = eclog(os.path.split(__file__)[-1]).GetLogger()
self.loadTestingReference.setEnabled(False)
self.clearTestingReference.setEnabled(False)
self.buttonSave.clicked.connect(self.CheckAndSave)
def UpdateTable(self):
if self.data_container.GetArray().size == 0:
return
self.tableFeature.setRowCount(len(self.data_container.GetCaseName()))
header_name = deepcopy(self.data_container.GetFeatureName())
header_name.insert(0, 'Label')
self.tableFeature.setColumnCount(len(header_name))
self.tableFeature.setHorizontalHeaderLabels(header_name)
self.tableFeature.setVerticalHeaderLabels(
list(map(str, self.data_container.GetCaseName())))
for row_index in range(len(self.data_container.GetCaseName())):
for col_index in range(len(header_name)):
if col_index == 0:
self.tableFeature.setItem(
row_index, col_index,
QTableWidgetItem(
str(self.data_container.GetLabel()[row_index])))
else:
self.tableFeature.setItem(
row_index, col_index,
QTableWidgetItem(
str(self.data_container.GetArray()[row_index,
col_index -
1])))
text = "The number of cases: {:d}\n".format(
len(self.data_container.GetCaseName()))
text += "The number of features: {:d}\n".format(
len(self.data_container.GetFeatureName()))
if len(np.unique(self.data_container.GetLabel())) == 2:
positive_number = len(
np.where(self.data_container.GetLabel() == np.max(
self.data_container.GetLabel()))[0])
negative_number = len(
self.data_container.GetLabel()) - positive_number
assert (positive_number + negative_number == len(
self.data_container.GetLabel()))
text += "The number of positive samples: {:d}\n".format(
positive_number)
text += "The number of negative samples: {:d}\n".format(
negative_number)
self.textInformation.setText(text)
def LoadData(self):
dlg = QFileDialog()
file_name, _ = dlg.getOpenFileName(self,
'Open SCV file',
filter="csv files (*.csv)")
try:
self.data_container.Load(file_name)
self.logger.info('Open the file ' + file_name + ' Succeed.')
except OSError as reason:
self.logger.log('Open SCV file Error, The reason is ' +
str(reason))
QMessageBox.about(self, 'Load data Error', reason.__str__())
print('Error！' + str(reason))
except ValueError:
self.logger.error('Open SCV file ' + file_name +
' Failed. because of value error.')
QMessageBox.information(self, 'Error',
'The selected data file mismatch.')
self.UpdateTable()
self.buttonRemove.setEnabled(True)
self.buttonSave.setEnabled(True)
def LoadTestingReferenceDataContainer(self):
dlg = QFileDialog()
file_name, _ = dlg.getOpenFileName(self,
'Open SCV file',
filter="csv files (*.csv)")
try:
self.__testing_ref_data_container.Load(file_name)
self.loadTestingReference.setEnabled(False)
self.clearTestingReference.setEnabled(True)
self.spinBoxSeparate.setEnabled(False)
except OSError as reason:
self.logger.log('Load Testing Reference Error: ' + str(reason))
print('Error！' + str(reason))
except ValueError:
self.logger.error('Open SCV file ' + file_name +
' Failed. because of value error.')
QMessageBox.information(self, 'Error',
'The selected data file mismatch.')
def ClearTestingReferenceDataContainer(self):
del self.__testing_ref_data_container
self.__testing_ref_data_container = DataContainer()
self.loadTestingReference.setEnabled(True)
self.clearTestingReference.setEnabled(False)
self.spinBoxSeparate.setEnabled(False)
def RemoveNonValidValue(self):
if self.radioRemoveNonvalidCases.isChecked():
self.data_container.RemoveUneffectiveCases()
elif self.radioRemoveNonvalidFeatures.isChecked():
self.data_container.RemoveUneffectiveFeatures()
self.UpdateTable()
def SetSeparateStatus(self):
if self.checkSeparate.isChecked():
self.spinBoxSeparate.setEnabled(True)
self.loadTestingReference.setEnabled(True)
self.clearTestingReference.setEnabled(False)
else:
self.spinBoxSeparate.setEnabled(False)
self.loadTestingReference.setEnabled(False)
self.clearTestingReference.setEnabled(False)
def CheckAndSave(self):
if self.data_container.IsEmpty():
QMessageBox.warning(self, "Warning", "There is no data",
QMessageBox.Ok)
elif not self.data_container.IsBinaryLabel():
QMessageBox.warning(self, "Warning", "There are not 2 Labels",
QMessageBox.Ok)
non_valid_number_Index = self.data_container.FindNonValidLabelIndex(
)
old_edit_triggers = self.tableFeature.editTriggers()
self.tableFeature.setEditTriggers(QAbstractItemView.CurrentChanged)
self.tableFeature.setCurrentCell(non_valid_number_Index, 0)
self.tableFeature.setEditTriggers(old_edit_triggers)
elif self.data_container.HasNonValidNumber():
QMessageBox.warning(self, "Warning", "There are nan items",
QMessageBox.Ok)
non_valid_number_Index = self.data_container.FindNonValidNumberIndex(
)
old_edit_triggers = self.tableFeature.editTriggers()
self.tableFeature.setEditTriggers(QAbstractItemView.CurrentChanged)
self.tableFeature.setCurrentCell(non_valid_number_Index[0],
non_valid_number_Index[1] + 1)
self.tableFeature.setEditTriggers(old_edit_triggers)
else:
remove_features_with_same_value = RemoveSameFeatures()
self.data_container = remove_features_with_same_value.Run(
self.data_container)
data_balance = DataBalance()
if self.radioDownSampling.isChecked():
data_balance = DownSampling()
elif self.radioUpSampling.isChecked():
data_balance = UpSampling()
elif self.radioSmote.isChecked():
data_balance = SmoteSampling()
if self.checkSeparate.isChecked():
folder_name = QFileDialog.getExistingDirectory(
self, "Save data")
if folder_name != '':
data_separate = DataSeparate.DataSeparate()
try:
if self.__testing_ref_data_container.IsEmpty():
testing_data_percentage = self.spinBoxSeparate.value(
)
training_data_container, _, = data_separate.RunByTestingPercentage(
self.data_container, testing_data_percentage,
folder_name)
else:
training_data_container, _, = data_separate.RunByTestingReference(
self.data_container,
self.__testing_ref_data_container, folder_name)
if training_data_container.IsEmpty():
QMessageBox.information(
self, 'Error',
'The testing data does not mismatch, please check the testing data '
'really exists in current data')
return None
data_balance.Run(training_data_container,
store_path=folder_name)
except Exception as e:
content = 'PrepareConnection, splitting failed: '
self.logger.error('{}{}'.format(content, str(e)))
QMessageBox.about(self, content, e.__str__())
else:
file_name, _ = QFileDialog.getSaveFileName(
self, "Save data", filter="csv files (*.csv)")
if file_name != '':
data_balance.Run(self.data_container, store_path=file_name)
class PrepareConnection(QWidget, Ui_Prepare):
close_signal = pyqtSignal(bool)
def __init__(self, parent=None):
super(PrepareConnection, self).__init__(parent)
self.setupUi(self)
self.data_container = DataContainer()
self._filename = os.path.split(__file__)[-1]
self.buttonLoad.clicked.connect(self.LoadData)
self.buttonRemoveAndExport.clicked.connect(self.RemoveInvalidValue)
self.__testing_ref_data_container = DataContainer()
self.__clinical_ref = pd.DataFrame()
self.radioSplitRandom.clicked.connect(self.ChangeSeparateMethod)
self.radioSplitRef.clicked.connect(self.ChangeSeparateMethod)
self.checkUseClinicRef.clicked.connect(
self.RandomSeparateButtonUpdates)
self.loadTestingReference.clicked.connect(
self.LoadTestingReferenceDataContainer)
self.clearTestingReference.clicked.connect(
self.ClearTestingReferenceDataContainer)
self.loadClinicRef.clicked.connect(self.LoadClinicalRef)
self.clearClinicRef.clicked.connect(self.ClearClinicalRef)
self.buttonSave.clicked.connect(self.CheckAndSave)
def closeEvent(self, QCloseEvent):
self.close_signal.emit(True)
QCloseEvent.accept()
def UpdateTable(self):
self.tableFeature.setRowCount(self.data_container.GetFrame().shape[0])
header_name = deepcopy(list(self.data_container.GetFrame().columns))
min_col = np.min([len(header_name), 100])
if min_col == 100:
header_name = header_name[:100]
header_name[-1] = '...'
self.tableFeature.setColumnCount(min_col)
self.tableFeature.setHorizontalHeaderLabels(header_name)
self.tableFeature.setVerticalHeaderLabels(
list(map(str,
self.data_container.GetFrame().index)))
for row_index in range(self.data_container.GetFrame().shape[0]):
for col_index in range(min_col):
if col_index < 99:
self.tableFeature.setItem(
row_index, col_index,
QTableWidgetItem(
str(self.data_container.GetFrame().iloc[
row_index, col_index])))
else:
self.tableFeature.setItem(row_index, col_index,
QTableWidgetItem('...'))
text = "The number of cases: {:d}\n".format(
self.data_container.GetFrame().shape[0])
# To process Label temporally
if 'label' in self.data_container.GetFrame().columns:
label_name = 'label'
text += "The number of features: {:d}\n".format(
self.data_container.GetFrame().shape[1] - 1)
elif 'Label' in self.data_container.GetFrame().columns:
label_name = 'Label'
text += "The number of features: {:d}\n".format(
self.data_container.GetFrame().shape[1] - 1)
else:
label_name = ''
text += "The number of features: {:d}\n".format(
self.data_container.GetFrame().shape[1])
if label_name:
labels = np.asarray(
self.data_container.GetFrame()[label_name].values,
dtype=np.int)
if len(np.unique(labels)) == 2:
positive_number = len(np.where(labels == np.max(labels))[0])
negative_number = len(labels) - positive_number
assert (positive_number + negative_number == len(labels))
text += "The number of positive samples: {:d}\n".format(
positive_number)
text += "The number of negative samples: {:d}\n".format(
negative_number)
self.textInformation.setText(text)
def SetButtonsState(self, state):
self.buttonRemoveAndExport.setEnabled(state)
self.buttonSave.setEnabled(state)
self.checkExport.setEnabled(state)
self.radioRemoveNone.setEnabled(state)
self.radioRemoveNonvalidCases.setEnabled(state)
self.radioRemoveNonvalidFeatures.setEnabled(state)
self.radioSplitRandom.setEnabled(state)
self.radioSplitRef.setEnabled(state)
def LoadData(self):
dlg = QFileDialog()
file_name, _ = dlg.getOpenFileName(self,
'Open SCV file',
filter="csv files (*.csv)")
if file_name:
try:
if self.data_container.Load(file_name, is_update=True):
self.UpdateTable()
self.SetButtonsState(True)
except OSError as reason:
eclog(self._filename).GetLogger().error(
'Load CSV Error: {}'.format(reason))
QMessageBox.about(self, 'Load data Error', reason.__str__())
print('Error！' + str(reason))
except ValueError:
eclog(self._filename).GetLogger().error(
'Open CSV Error: {}'.format(file_name))
QMessageBox.information(self, 'Error',
'The selected data file mismatch.')
def LoadTestingReferenceDataContainer(self):
dlg = QFileDialog()
file_name, _ = dlg.getOpenFileName(self,
'Open SCV file',
filter="csv files (*.csv)")
if file_name:
try:
self.__testing_ref_data_container.Load(file_name)
self.loadTestingReference.setEnabled(False)
self.clearTestingReference.setEnabled(True)
self.spinBoxSeparate.setEnabled(False)
except OSError as reason:
eclog(self._filename).GetLogger().error(
'Load Testing Ref Error: {}'.format(reason))
print('Error！' + str(reason))
except ValueError:
eclog(self._filename).GetLogger().error(
'Open CSV Error: {}'.format(file_name))
QMessageBox.information(self, 'Error',
'The selected data file mismatch.')
def ClearTestingReferenceDataContainer(self):
del self.__testing_ref_data_container
self.__testing_ref_data_container = DataContainer()
self.loadTestingReference.setEnabled(True)
self.clearTestingReference.setEnabled(False)
self.spinBoxSeparate.setEnabled(False)
def LoadClinicalRef(self):
dlg = QFileDialog()
file_name, _ = dlg.getOpenFileName(self,
'Open SCV file',
filter="csv files (*.csv)")
if file_name:
try:
self.__clinical_ref = pd.read_csv(file_name, index_col=0)
if list(self.__clinical_ref.index
) != self.data_container.GetCaseName():
QMessageBox.information(
self, 'Error',
'The index of clinical features is not consistent to the data'
)
return None
self.loadClinicRef.setEnabled(False)
self.clearClinicRef.setEnabled(True)
except OSError as reason:
eclog(self._filename).GetLogger().error(
'Load Clinical Ref Error: {}'.format(reason))
QMessageBox.information(self, 'Error',
'Can not Open the Files')
except ValueError:
eclog(self._filename).GetLogger().error(
'OpenCSV Error: {}'.format(file_name))
QMessageBox.information(self, 'Error',
'The selected data file mismatch.')
return None
def ClearClinicalRef(self):
del self.__clinical_ref
self.__clinical_ref = pd.DataFrame()
self.loadClinicRef.setEnabled(True)
self.clearClinicRef.setEnabled(False)
def RemoveInvalidValue(self):
if not self.data_container.IsEmpty():
if self.checkExport.isChecked():
folder_name = QFileDialog.getExistingDirectory(
self, "Save Invalid data")
store_path = os.path.join(folder_name, 'invalid_feature.csv')
else:
store_path = ''
if self.radioRemoveNone.isChecked():
self.data_container.RemoveInvalid(store_path=store_path,
remove_index=REMOVE_NONE)
if self.radioRemoveNonvalidCases.isChecked():
self.data_container.RemoveInvalid(store_path=store_path,
remove_index=REMOVE_CASE)
elif self.radioRemoveNonvalidFeatures.isChecked():
self.data_container.RemoveInvalid(store_path=store_path,
remove_index=REMOVE_FEATURE)
self.UpdateTable()
def ChangeSeparateMethod(self):
if self.radioSplitRandom.isChecked():
self.spinBoxSeparate.setEnabled(True)
self.checkUseClinicRef.setEnabled(True)
self.loadTestingReference.setEnabled(False)
self.clearTestingReference.setEnabled(False)
elif self.radioSplitRef.isChecked():
self.spinBoxSeparate.setEnabled(False)
self.checkUseClinicRef.setEnabled(False)
if self.__testing_ref_data_container.IsEmpty():
self.loadTestingReference.setEnabled(True)
self.clearTestingReference.setEnabled(False)
else:
self.loadTestingReference.setEnabled(False)
self.clearTestingReference.setEnabled(True)
self.RandomSeparateButtonUpdates()
def RandomSeparateButtonUpdates(self):
if self.checkUseClinicRef.isChecked():
if self.__clinical_ref.size > 0:
self.loadClinicRef.setEnabled(False)
self.clearClinicRef.setEnabled(True)
else:
self.loadClinicRef.setEnabled(True)
self.clearClinicRef.setEnabled(False)
else:
self.loadClinicRef.setEnabled(False)
self.clearClinicRef.setEnabled(False)
def CheckAndSave(self):
if self.data_container.IsEmpty():
QMessageBox.warning(self, "Warning", "There is no data",
QMessageBox.Ok)
elif not self.data_container.IsBinaryLabel():
QMessageBox.warning(self, "Warning", "There are not 2 Labels",
QMessageBox.Ok)
non_valid_number_index = self.data_container.FindInvalidLabelIndex(
)
old_edit_triggers = self.tableFeature.editTriggers()
self.tableFeature.setEditTriggers(QAbstractItemView.CurrentChanged)
self.tableFeature.setCurrentCell(non_valid_number_index, 0)
self.tableFeature.setEditTriggers(old_edit_triggers)
elif self.data_container.HasInvalidNumber():
QMessageBox.warning(self, "Warning", "There are nan items",
QMessageBox.Ok)
non_valid_number_index = self.data_container.FindInvalidNumberIndex(
)
old_edit_triggers = self.tableFeature.editTriggers()
self.tableFeature.setEditTriggers(QAbstractItemView.CurrentChanged)
self.tableFeature.setCurrentCell(non_valid_number_index[0],
non_valid_number_index[1] + 1)
self.tableFeature.setEditTriggers(old_edit_triggers)
else:
remove_features_with_same_value = RemoveSameFeatures()
self.data_container = remove_features_with_same_value.Run(
self.data_container)
if self.radioSplitRandom.isChecked(
) or self.radioSplitRef.isChecked():
folder_name = QFileDialog.getExistingDirectory(
self, "Save data")
if folder_name != '':
data_separate = DataSeparate.DataSeparate()
try:
if self.__testing_ref_data_container.IsEmpty():
testing_data_percentage = self.spinBoxSeparate.value(
)
if self.__clinical_ref.size == 0:
training_data_container, _, = \
data_separate.RunByTestingPercentage(self.data_container,
testing_data_percentage,
store_folder=folder_name)
else:
training_data_container, _, = \
data_separate.RunByTestingPercentage(self.data_container,
testing_data_percentage,
clinic_df=self.__clinical_ref,
store_folder=folder_name)
else:
training_data_container, _, = \
data_separate.RunByTestingReference(self.data_container,
self.__testing_ref_data_container,
folder_name)
if training_data_container.IsEmpty():
QMessageBox.information(
self, 'Error',
'The testing data does not mismatch, please check the testing data '
'really exists in current data')
return None
os.system("explorer.exe {:s}".format(
os.path.normpath(folder_name)))
except Exception as e:
content = 'PrepareConnection, splitting failed: '
eclog(self._filename).GetLogger().error(
'Split Error: ' + e.__str__())
QMessageBox.about(self, content, e.__str__())
else:
file_name, _ = QFileDialog.getSaveFileName(
self, "Save data", filter="csv files (*.csv)")
if file_name:
self.data_container.Save(file_name)
