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zhijian-yang
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Add SmileGAN Plugin
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‎NiBAx/plugins/SmileGAN/SmileGAN.py‎

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from PyQt5.QtGui import *
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from matplotlib.backends.backend_qt5 import FigureCanvasQT
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from PyQt5 import QtGui, QtCore, QtWidgets, uic
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import joblib
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import sys, os, time
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import seaborn as sns
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import numpy as np
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import pandas as pd
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from NiBAx.core.plotcanvas import PlotCanvas
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from NiBAx.core.baseplugin import BasePlugin
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from NiBAx.core.gui.SearchableQComboBox import SearchableQComboBox
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from SmileGAN2.Smile_GAN_clustering import clustering_result
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class computeSmileGANs(QtWidgets.QWidget,BasePlugin):
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#constructor
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def __init__(self):
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super(computeSmileGANs,self).__init__()
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self.model = []
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root = os.path.dirname(__file__)
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self.readAdditionalInformation(root)
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self.ui = uic.loadUi(os.path.join(root, 'SmileGAN.ui'),self)
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self.ui.comboBoxHue = SearchableQComboBox(self.ui)
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self.ui.horizontalLayout_3.addWidget(self.comboBoxHue)
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self.plotCanvas = PlotCanvas(self.ui.page_2)
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self.ui.verticalLayout.addWidget(self.plotCanvas)
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self.plotCanvas.axes = self.plotCanvas.fig.add_subplot(111)
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self.SmileGANpatterns = None
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self.ui.stackedWidget.setCurrentIndex(0)
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# Initialize thread
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self.thread = QtCore.QThread()
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def getUI(self):
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return self.ui
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def SetupConnections(self):
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#pass
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self.ui.load_SmileGAN_model_Btn.clicked.connect(lambda: self.OnLoadSmileGANModel())
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self.ui.load_other_model_Btn.clicked.connect(lambda: self.OnLoadSmileGANModel())
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self.ui.add_to_dataframe_Btn.clicked.connect(lambda: self.OnAddToDataFrame())
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self.ui.compute_SmileGAN_Btn.clicked.connect(lambda check: self.OnComputePatterns(check))
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self.ui.show_SmileGAN_prob_from_data_Btn.clicked.connect(lambda: self.OnShowPatterns())
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self.datamodel.data_changed.connect(lambda: self.OnDataChanged())
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self.ui.comboBoxHue.currentIndexChanged.connect(self.plotPattern)
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self.ui.add_to_dataframe_Btn.setStyleSheet("background-color: green; color: white")
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# Set `Show SmileGAN patterns from data` button to visible when SmileGAN_Pattern column
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# are present in data frame
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if ('SmileGAN_Pattern' in self.datamodel.GetColumnHeaderNames()):
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self.ui.show_SmileGAN_prob_from_data_Btn.setStyleSheet("background-color: rgb(230,230,255)")
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self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(True)
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self.ui.show_SmileGAN_prob_from_data_Btn.setToolTip('The data frame has variables `SmileGAN patterns` so these can be plotted.')
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else:
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self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
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# Allow loading of SmileGAN-* model always, even when residuals are not
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# calculated yet
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self.ui.load_SmileGAN_model_Btn.setEnabled(True)
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def OnLoadSmileGANModel(self):
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fileNames, _ = QtWidgets.QFileDialog.getOpenFileNames(None,
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'Open SmileGAN model file',
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QtCore.QDir().homePath(),
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"")
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if len(fileNames) > 0:
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self.model = fileNames
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self.ui.compute_SmileGAN_Btn.setEnabled(True)
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model_info = 'File:'
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for file in fileNames:
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model_info += file + '\n'
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self.ui.SmileGAN_model_info.setText(model_info)
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else:
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return
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self.ui.stackedWidget.setCurrentIndex(0)
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if 'RES_ICV_Sex_MUSE_Volume_47' in self.datamodel.GetColumnHeaderNames():
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self.ui.compute_SmileGAN_Btn.setStyleSheet("QPushButton"
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"{"
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"background-color : rgb(230,255,230);"
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"}"
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"QPushButton::checked"
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"{"
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"background-color : rgb(255,230,230);"
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"border: none;"
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"}"
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)
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self.ui.compute_SmileGAN_Btn.setEnabled(True)
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self.ui.compute_SmileGAN_Btn.setChecked(False)
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self.ui.compute_SmileGAN_Btn.setToolTip('Model loaded and `RES_ICV_Sex_MUSE_Volmue_*` available so the MUSE volumes can be harmonized.')
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else:
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self.ui.compute_SmileGAN_Btn.setStyleSheet("background-color: rgb(255,230,230)")
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self.ui.compute_SmileGAN_Btn.setEnabled(False)
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self.ui.compute_SmileGAN_Btn.setToolTip('Model loaded but `RES_ICV_Sex_MUSE_Volmue_*` not available so the MUSE volumes can not be harmonized.')
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print('No field `RES_ICV_Sex_MUSE_Volume_47` found. ' +
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'Make sure to compute and add harmonized residuals first.')
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def OnComputationDone(self, p):
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self.SmileGANpatterns = p
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self.ui.compute_SmileGAN_Btn.setText('Compute SmileGAN Patterns-*')
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if self.SmileGANpatterns.empty:
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return
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self.ui.compute_SmileGAN_Btn.setChecked(False)
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self.ui.stackedWidget.setCurrentIndex(1)
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self.ui.comboBoxHue.setVisible(False)
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self.plotPattern()
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# Activate buttons
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self.ui.compute_SmileGAN_Btn.setEnabled(False)
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if ('SmileGAN_Pattern' in self.datamodel.GetColumnHeaderNames()):
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self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(True)
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else:
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self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
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self.ui.load_SmileGAN_model_Btn.setEnabled(True)
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def OnComputePatterns(self, checked):
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# Setup tasks for long running jobs
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# Using this example: https://realpython.com/python-pyqt-qthread/
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# Disable buttons
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if checked is not True:
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self.thread.requestInterruption()
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else:
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self.ui.compute_SmileGAN_Btn.setStyleSheet("QPushButton"
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"{"
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"background-color : rgb(230,255,230);"
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"}"
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"QPushButton::checked"
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"{"
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"background-color : rgb(255,230,230);"
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"}"
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)
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self.ui.compute_SmileGAN_Btn.setText('Cancel computation')
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self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
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self.ui.load_SmileGAN_model_Btn.setEnabled(False)
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self.thread = QtCore.QThread()
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self.worker = PatternWorker(self.datamodel.data, self.model)
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self.worker.moveToThread(self.thread)
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self.thread.started.connect(self.worker.run)
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self.worker.done.connect(self.thread.quit)
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self.worker.done.connect(self.worker.deleteLater)
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self.thread.finished.connect(self.thread.deleteLater)
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self.worker.done.connect(lambda p: self.OnComputationDone(p))
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self.thread.start()
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def plotPattern(self):
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# Plot data
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if self.ui.stackedWidget.currentIndex() == 0:
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return
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self.plotCanvas.axes.clear()
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sns.countplot(x='Pattern', data=self.SmileGANpatterns,
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ax=self.plotCanvas.axes)
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sns.despine(ax=self.plotCanvas.axes, trim=True)
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self.plotCanvas.axes.set(ylabel='Count', xlabel='Patterns')
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self.plotCanvas.axes.get_figure().set_tight_layout(True)
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self.plotCanvas.draw()
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def OnAddToDataFrame(self):
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print('Adding SmileGAN patterns to data frame...')
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for col in self.SmileGANpatterns.columns:
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self.datamodel.data.loc[:,'SmileGAN_'+col] = self.SmileGANpatterns[col]
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self.datamodel.data_changed.emit()
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self.OnShowPatterns()
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def OnShowPatterns(self):
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self.ui.stackedWidget.setCurrentIndex(1)
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self.plotPattern()
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def OnDataChanged(self):
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# Set `Show SmileGAN patterns from data` button to visible when SmileGAN_Pattern column
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# are present in data frame
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self.ui.stackedWidget.setCurrentIndex(0)
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if ('SmileGAN_Pattern' in self.datamodel.GetColumnHeaderNames()):
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self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(True)
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self.ui.show_SmileGAN_prob_from_data_Btn.setStyleSheet("background-color: rgb(230,230,255)")
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else:
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self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
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class PatternWorker(QtCore.QObject):
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done = QtCore.pyqtSignal(pd.DataFrame)
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progress = QtCore.pyqtSignal(str, int)
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#constructor
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def __init__(self, data, model_list):
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super(PatternWorker, self).__init__()
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self.data = data
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self.model = model_list
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def run(self):
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train_data = self.data[['participant_id']+[ name for name in self.data.columns if ('H_MUSE_Volume' in name and int(name[14:])<300)] ]
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covariate = self.data[['participant_id','Age','Sex']]
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covariate['Sex'] = covariate['Sex'].map({'M':1,'F':0})
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train_data['diagnosis'] = 1
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covariate['diagnosis'] = 1
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cluster_label, cluster_prob, _, _ = clustering_result(self.model, 'highest_matching_clustering', train_data, covariate)
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p = pd.DataFrame(data = cluster_prob, columns = ['P'+str(_) for _ in range(1,cluster_prob.shape[1]+1)])
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p['Pattern'] = cluster_label
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# Emit the result
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self.done.emit(p)

‎NiBAx/plugins/SmileGAN/SmileGAN.ui‎

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<?xml version="1.0" encoding="UTF-8"?>
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<ui version="4.0">
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<class>Form</class>
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<widget class="QWidget" name="Form">
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<property name="geometry">
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<rect>
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<x>0</x>
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<y>0</y>
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<width>891</width>
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<height>695</height>
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</rect>
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</property>
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<property name="windowTitle">
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<string>Compute SPAREs</string>
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</property>
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<layout class="QGridLayout" name="gridLayout">
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<item row="0" column="0">
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<widget class="QStackedWidget" name="stackedWidget">
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<property name="styleSheet">
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<string notr="true"/>
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</property>
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<property name="currentIndex">
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<number>0</number>
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</property>
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<widget class="QWidget" name="page">
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<layout class="QVBoxLayout" name="verticalLayout_2">
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<item>
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<spacer name="verticalSpacer_2">
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<property name="orientation">
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<enum>Qt::Vertical</enum>
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</property>
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<property name="sizeHint" stdset="0">
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<size>
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<width>338</width>
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<height>241</height>
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</size>
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</property>
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</spacer>
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</item>
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<item>
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<widget class="QPushButton" name="show_SmileGAN_prob_from_data_Btn">
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<property name="enabled">
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<bool>false</bool>
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</property>
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<property name="text">
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<string>Show SmileGAN patterns from data</string>
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</property>
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</widget>
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</item>
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<item>
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<widget class="QPushButton" name="load_SmileGAN_model_Btn">
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<property name="text">
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<string>Load SmileGAN Model</string>
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</property>
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</widget>
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</item>
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<item>
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<widget class="QLabel" name="SmileGAN_model_info">
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<property name="text">
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<string>No SmileGAN model loaded</string>
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</property>
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</widget>
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</item>
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<item>
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<widget class="QPushButton" name="compute_SmileGAN_Btn">
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<property name="enabled">
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<bool>false</bool>
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</property>
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<property name="text">
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<string>Compute SmileGAN patterns</string>
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</property>
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<property name="checkable">
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<bool>true</bool>
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</property>
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<property name="checked">
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<bool>false</bool>
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</property>
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</widget>
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</item>
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<item>
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<spacer name="verticalSpacer">
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<property name="orientation">
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<enum>Qt::Vertical</enum>
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</property>
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<property name="sizeHint" stdset="0">
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<size>
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<width>338</width>
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<height>241</height>
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</size>
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</property>
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</spacer>
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</item>
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<item>
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<widget class="Line" name="line">
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<property name="orientation">
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<enum>Qt::Horizontal</enum>
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</property>
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</widget>
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</item>
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</layout>
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</widget>
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<widget class="QWidget" name="page_2">
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<layout class="QVBoxLayout" name="verticalLayout">
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<item>
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<layout class="QHBoxLayout" name="horizontalLayout_3">
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<item>
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<widget class="QLabel" name="label">
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<property name="text">
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<string>SmileGAN</string>
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</property>
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</widget>
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</item>
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<item>
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<widget class="QPushButton" name="load_other_model_Btn">
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<property name="text">
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<string>Load other model</string>
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</property>
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</widget>
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</item>
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<item>
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<widget class="QPushButton" name="add_to_dataframe_Btn">
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<property name="text">
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<string>Add to DataFrame</string>
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</property>
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</widget>
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</item>
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</layout>
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</item>
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</layout>
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</widget>
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</widget>
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</item>
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</layout>
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</widget>
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<resources/>
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<connections/>
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</ui>

‎NiBAx/plugins/SmileGAN/SmileGAN.yapsy-plugin‎

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[Core]
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Name = SmileGAN
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Module = SmileGAN
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[Documentation]
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Author = Zhijian Yang
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Version = 0.1
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Website =
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Description = Compute SmileGAN patterns from existing model.
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[Tab]
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#tab position starts from 0
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Position = 5

‎NiBAx/plugins/SmileGAN/__init__.py‎

Whitespace-only changes.

‎requirements.txt‎

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statsmodels==0.13.0
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wheel>=0.37.1
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Yapsy==1.12.2
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SmileGAN==0.1.1

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