Add SmileGAN Plugin

NiBAx/plugins/SmileGAN/SmileGAN.py

@@ -0,0 +1,215 @@
+from PyQt5.QtGui import *
+from matplotlib.backends.backend_qt5 import FigureCanvasQT
+from PyQt5 import QtGui, QtCore, QtWidgets, uic
+import joblib
+import sys, os, time
+import seaborn as sns
+import numpy as np
+import pandas as pd
+from NiBAx.core.plotcanvas import PlotCanvas
+from NiBAx.core.baseplugin import BasePlugin
+from NiBAx.core.gui.SearchableQComboBox import SearchableQComboBox
+from SmileGAN.Smile_GAN_clustering import clustering_result
+
+class computeSmileGANs(QtWidgets.QWidget,BasePlugin):
+
+    #constructor
+    def __init__(self):
+        super(computeSmileGANs,self).__init__()
+        self.model = []
+        root = os.path.dirname(__file__)
+        self.readAdditionalInformation(root)
+        self.ui = uic.loadUi(os.path.join(root, 'SmileGAN.ui'),self)
+        self.ui.comboBoxHue = SearchableQComboBox(self.ui)
+        self.ui.horizontalLayout_3.addWidget(self.comboBoxHue)
+        self.plotCanvas = PlotCanvas(self.ui.page_2)
+        self.ui.verticalLayout.addWidget(self.plotCanvas)
+        self.plotCanvas.axes = self.plotCanvas.fig.add_subplot(111)
+        self.SmileGANpatterns = None
+        self.ui.stackedWidget.setCurrentIndex(0)
+
+        # Initialize thread
+        self.thread = QtCore.QThread()
+
+
+    def getUI(self):
+        return self.ui
+
+
+    def SetupConnections(self):
+        #pass
+        self.ui.load_SmileGAN_model_Btn.clicked.connect(lambda: self.OnLoadSmileGANModel())
+        self.ui.load_other_model_Btn.clicked.connect(lambda: self.OnLoadSmileGANModel())
+        self.ui.add_to_dataframe_Btn.clicked.connect(lambda: self.OnAddToDataFrame())
+        self.ui.compute_SmileGAN_Btn.clicked.connect(lambda check: self.OnComputePatterns(check))
+        self.ui.show_SmileGAN_prob_from_data_Btn.clicked.connect(lambda: self.OnShowPatterns())
+        self.datamodel.data_changed.connect(lambda: self.OnDataChanged())
+        self.ui.comboBoxHue.currentIndexChanged.connect(self.plotPattern)
+
+        self.ui.add_to_dataframe_Btn.setStyleSheet("background-color: green; color: white")
+        # Set `Show SmileGAN patterns from data` button to visible when SmileGAN_Pattern column
+        # are present in data frame
+        if ('SmileGAN_Pattern' in self.datamodel.GetColumnHeaderNames()):
+            self.ui.show_SmileGAN_prob_from_data_Btn.setStyleSheet("background-color: rgb(230,230,255)")
+            self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(True)
+            self.ui.show_SmileGAN_prob_from_data_Btn.setToolTip('The data frame has variables `SmileGAN patterns` so these can be plotted.')
+        else:
+            self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
+
+        # Allow loading of SmileGAN-* model always, even when residuals are not
+        # calculated yet
+        self.ui.load_SmileGAN_model_Btn.setEnabled(True)
+
+
+    def OnLoadSmileGANModel(self):
+        fileNames, _ = QtWidgets.QFileDialog.getOpenFileNames(None,
+            'Open SmileGAN model file',
+            QtCore.QDir().homePath(),
+            "")
+        if len(fileNames) > 0:
+            self.model = fileNames
+            self.ui.compute_SmileGAN_Btn.setEnabled(True)
+            model_info = 'File:'
+            for file in fileNames:
+                model_info += file + '\n'
+            self.ui.SmileGAN_model_info.setText(model_info)
+        else:
+            return
+
+        self.ui.stackedWidget.setCurrentIndex(0)
+
+        if 'RES_ICV_Sex_MUSE_Volume_47' in self.datamodel.GetColumnHeaderNames():
+            self.ui.compute_SmileGAN_Btn.setStyleSheet("QPushButton"
+                             "{"
+                             "background-color : rgb(230,255,230);"
+                             "}"
+                             "QPushButton::checked"
+                             "{"
+                             "background-color : rgb(255,230,230);"
+                             "border: none;"
+                             "}"
+                             )
+            self.ui.compute_SmileGAN_Btn.setEnabled(True)
+            self.ui.compute_SmileGAN_Btn.setChecked(False)
+            self.ui.compute_SmileGAN_Btn.setToolTip('Model loaded and `RES_ICV_Sex_MUSE_Volmue_*` available so the MUSE volumes can be harmonized.')
+        else:
+            self.ui.compute_SmileGAN_Btn.setStyleSheet("background-color: rgb(255,230,230)")
+            self.ui.compute_SmileGAN_Btn.setEnabled(False)
+            self.ui.compute_SmileGAN_Btn.setToolTip('Model loaded but `RES_ICV_Sex_MUSE_Volmue_*` not available so the MUSE volumes can not be harmonized.')
+
+
+            print('No field `RES_ICV_Sex_MUSE_Volume_47` found. ' +
+                  'Make sure to compute and add harmonized residuals first.')
+
+    def OnComputationDone(self, p):
+        self.SmileGANpatterns = p
+        self.ui.compute_SmileGAN_Btn.setText('Compute SmileGAN Patterns-*')
+        if self.SmileGANpatterns.empty:
+            return
+        self.ui.compute_SmileGAN_Btn.setChecked(False)
+        self.ui.stackedWidget.setCurrentIndex(1)
+        self.ui.comboBoxHue.setVisible(False)
+        self.plotPattern()
+
+        # Activate buttons
+        self.ui.compute_SmileGAN_Btn.setEnabled(False)
+        if ('SmileGAN_Pattern' in self.datamodel.GetColumnHeaderNames()):
+            self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(True)
+        else:
+            self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
+        self.ui.load_SmileGAN_model_Btn.setEnabled(True)
+
+
+
+    def OnComputePatterns(self, checked):
+        # Setup tasks for long running jobs
+        # Using this example: https://realpython.com/python-pyqt-qthread/
+        # Disable buttons
+        if checked is not True:
+            self.thread.requestInterruption()
+        else:
+            self.ui.compute_SmileGAN_Btn.setStyleSheet("QPushButton"
+                             "{"
+                             "background-color : rgb(230,255,230);"
+                             "}"
+                             "QPushButton::checked"
+                             "{"
+                             "background-color : rgb(255,230,230);"
+                             "}"
+                             )
+            self.ui.compute_SmileGAN_Btn.setText('Cancel computation')
+            self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
+            self.ui.load_SmileGAN_model_Btn.setEnabled(False)
+            self.thread = QtCore.QThread()
+            self.worker = PatternWorker(self.datamodel.data, self.model)
+            self.worker.moveToThread(self.thread)
+            self.thread.started.connect(self.worker.run)
+            self.worker.done.connect(self.thread.quit)
+            self.worker.done.connect(self.worker.deleteLater)
+            self.thread.finished.connect(self.thread.deleteLater)
+            self.worker.done.connect(lambda p: self.OnComputationDone(p))
+            self.thread.start()
+
+
+    def plotPattern(self):
+        # Plot data
+        if self.ui.stackedWidget.currentIndex() == 0:
+            return
+        self.plotCanvas.axes.clear()
+
+        sns.countplot(x='Pattern', data=self.SmileGANpatterns,
+                        ax=self.plotCanvas.axes) 
+
+        sns.despine(ax=self.plotCanvas.axes, trim=True)
+        self.plotCanvas.axes.set(ylabel='Count', xlabel='Patterns')
+        self.plotCanvas.axes.get_figure().set_tight_layout(True)
+        self.plotCanvas.draw()
+
+
+    def OnAddToDataFrame(self):
+        print('Adding SmileGAN patterns to data frame...')
+        for col in self.SmileGANpatterns.columns:
+            self.datamodel.data.loc[:,'SmileGAN_'+col] = self.SmileGANpatterns[col]
+        self.datamodel.data_changed.emit()
+        self.OnShowPatterns()
+
+
+    def OnShowPatterns(self):
+        self.ui.stackedWidget.setCurrentIndex(1)
+        self.plotPattern()
+
+
+    def OnDataChanged(self):
+        # Set `Show SmileGAN patterns from data` button to visible when SmileGAN_Pattern column
+        # are present in data frame
+        self.ui.stackedWidget.setCurrentIndex(0)
+        if ('SmileGAN_Pattern' in self.datamodel.GetColumnHeaderNames()):
+            self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(True)
+            self.ui.show_SmileGAN_prob_from_data_Btn.setStyleSheet("background-color: rgb(230,230,255)")
+        else:
+            self.ui.show_SmileGAN_prob_from_data_Btn.setEnabled(False)
+
+
+class PatternWorker(QtCore.QObject):
+
+    done = QtCore.pyqtSignal(pd.DataFrame)
+    progress = QtCore.pyqtSignal(str, int)
+
+    #constructor
+    def __init__(self, data, model_list):
+        super(PatternWorker, self).__init__()
+        self.data = data
+        self.model = model_list
+
+    def run(self):
+        train_data = self.data[['participant_id']+[ name for name in self.data.columns if ('H_MUSE_Volume' in name and int(name[14:])<300)] ]
+        covariate = self.data[['participant_id','Age','Sex']]
+        covariate['Sex'] = covariate['Sex'].map({'M':1,'F':0})
+        train_data['diagnosis'] = 1
+        covariate['diagnosis'] = 1
+        cluster_label, cluster_prob, _, _ = clustering_result(self.model, 'highest_matching_clustering', train_data, covariate)
+        p = pd.DataFrame(data = cluster_prob, columns = ['P'+str(_) for _ in range(1,cluster_prob.shape[1]+1)])
+        p['Pattern'] = cluster_label
+
+        # Emit the result
+        self.done.emit(p)

NiBAx/plugins/SmileGAN/SmileGAN.ui

@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Form</class>
+ <widget class="QWidget" name="Form">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>891</width>
+    <height>695</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Compute SPAREs</string>
+  </property>
+  <layout class="QGridLayout" name="gridLayout">
+   <item row="0" column="0">
+    <widget class="QStackedWidget" name="stackedWidget">
+     <property name="styleSheet">
+      <string notr="true"/>
+     </property>
+     <property name="currentIndex">
+      <number>0</number>
+     </property>
+     <widget class="QWidget" name="page">
+      <layout class="QVBoxLayout" name="verticalLayout_2">
+       <item>
+        <spacer name="verticalSpacer_2">
+         <property name="orientation">
+          <enum>Qt::Vertical</enum>
+         </property>
+         <property name="sizeHint" stdset="0">
+          <size>
+           <width>338</width>
+           <height>241</height>
+          </size>
+         </property>
+        </spacer>
+       </item>
+       <item>
+        <widget class="QPushButton" name="show_SmileGAN_prob_from_data_Btn">
+         <property name="enabled">
+          <bool>false</bool>
+         </property>
+         <property name="text">
+          <string>Show SmileGAN patterns from data</string>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <widget class="QPushButton" name="load_SmileGAN_model_Btn">
+         <property name="text">
+          <string>Load SmileGAN Model</string>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <widget class="QLabel" name="SmileGAN_model_info">
+         <property name="text">
+          <string>No SmileGAN model loaded</string>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <widget class="QPushButton" name="compute_SmileGAN_Btn">
+         <property name="enabled">
+          <bool>false</bool>
+         </property>
+         <property name="text">
+          <string>Compute SmileGAN patterns</string>
+         </property>
+         <property name="checkable">
+          <bool>true</bool>
+         </property>
+         <property name="checked">
+          <bool>false</bool>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <spacer name="verticalSpacer">
+         <property name="orientation">
+          <enum>Qt::Vertical</enum>
+         </property>
+         <property name="sizeHint" stdset="0">
+          <size>
+           <width>338</width>
+           <height>241</height>
+          </size>
+         </property>
+        </spacer>
+       </item>
+       <item>
+        <widget class="Line" name="line">
+         <property name="orientation">
+          <enum>Qt::Horizontal</enum>
+         </property>
+        </widget>
+       </item>
+      </layout>
+     </widget>
+     <widget class="QWidget" name="page_2">
+      <layout class="QVBoxLayout" name="verticalLayout">
+       <item>
+        <layout class="QHBoxLayout" name="horizontalLayout_3">
+         <item>
+          <widget class="QLabel" name="label">
+           <property name="text">
+            <string>SmileGAN</string>
+           </property>
+          </widget>
+         </item>
+         <item>
+          <widget class="QPushButton" name="load_other_model_Btn">
+           <property name="text">
+            <string>Load other model</string>
+           </property>
+          </widget>
+         </item>
+         <item>
+          <widget class="QPushButton" name="add_to_dataframe_Btn">
+           <property name="text">
+            <string>Add to DataFrame</string>
+           </property>
+          </widget>
+         </item>
+        </layout>
+       </item>
+      </layout>
+     </widget>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

NiBAx/plugins/SmileGAN/SmileGAN.yapsy-plugin

@@ -0,0 +1,13 @@
+[Core]
+Name = SmileGAN
+Module = SmileGAN
+
+[Documentation]
+Author = Zhijian Yang
+Version = 0.1
+Website = 
+Description = Compute SmileGAN patterns from existing model. 
+
+[Tab]
+#tab position starts from 0
+Position = 5 

requirements.txt

@@ -23,3 +23,4 @@ six==1.16.0
 statsmodels==0.13.0
 wheel>=0.37.1
 Yapsy==1.12.2
+SmileGAN==0.1.2