Add SPARE-* plugin

QtBrainChartGUI/core/model/datamodel.py

@@ -160,7 +160,11 @@ def IsValidSPARE(self):
 
     def GetColumnHeaderNames(self):
         """Returns all header names for all columns in the dataset."""
-        k = self.data.keys()
+        if self.data is not None:
+            k = self.data.keys()
+        else:
+            k = []
+
         return k
 
 

QtBrainChartGUI/mainwindow.py

@@ -12,6 +12,8 @@
 #from BrainChart.dataio import DataIO
 from QtBrainChartGUI.core.model.datamodel import DataModel
 
+import pandas as pd
+
 class MainWindow(QtWidgets.QMainWindow):
     def __init__(self, dataFile=None, harmonizationModelFile=None, SPAREModelFile=None):
         super(MainWindow,self).__init__()
@@ -45,9 +47,10 @@ def __init__(self, dataFile=None, harmonizationModelFile=None, SPAREModelFile=No
             self.ui.tabWidget.addTab(po,plugin.name)
 
         if dataFile is not None:
-            pass
             # if datafile provided on cmd line, load it
-            #self.OnDataFileOpenClicked(dataFile)
+            self.OnDataFile(dataFile)
+
+
         if harmonizationModelFile is not None:
             pass
             #if harmonization model file provided on cmd line, load it
@@ -64,7 +67,7 @@ def SetupUi(self):
         print("in setup")
         root = os.path.dirname(__file__)
         self.ui = uic.loadUi(os.path.join(root, 'mainwindow.ui'), self)
-        self.ui.setWindowTitle('Qt BrainChart')
+        self.ui.setWindowTitle('Neuro-imaging brain aging chart')
 
     def OnAboutClicked(self):
         #quit application
@@ -76,6 +79,11 @@ def OnCloseClicked(self):
         QtWidgets.QApplication.quit()
 
 
+    def OnDataFile(self, dataFile):
+        self.datamodel.SetDataFilePath(dataFile)
+        self.datamodel.SetData(pd.read_pickle(dataFile))
+
+
     def ResetUI(self):
         #reset all UI
         pass

QtBrainChartGUI/mainwindow.ui

@@ -11,12 +11,15 @@
    </rect>
   </property>
   <property name="windowTitle">
-   <string>Qt BrainChart</string>
+   <string>NiBAX</string>
   </property>
   <widget class="QWidget" name="centralwidget">
    <layout class="QHBoxLayout" name="horizontalLayout">
     <item>
      <widget class="QTabWidget" name="tabWidget">
+      <property name="currentIndex">
+       <number>1</number>
+      </property>
       <widget class="QWidget" name="tab">
        <attribute name="title">
         <string>Tab 1</string>
@@ -37,7 +40,7 @@
      <x>0</x>
      <y>0</y>
      <width>800</width>
-     <height>22</height>
+     <height>21</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuAbout">

QtBrainChartGUI/plugins/computeSPAREs/computeSPAREs.py

@@ -0,0 +1,166 @@
+from PyQt5.QtGui import *
+from yapsy.IPlugin import IPlugin
+from PyQt5 import QtGui, QtCore, QtWidgets, uic
+import joblib
+import sys, os
+
+import seaborn as sns
+import numpy as np
+import pandas as pd
+
+# Plotting with matplotlib
+from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+import matplotlib as mpl
+mpl.use('QT5Agg')
+
+
+class PlotCanvas(FigureCanvas):
+    """ A generic Plotting class that derives from FigureCanvasQTAgg
+    and plots data as per different options"""
+
+    def __init__(self, parent=None, width=5, height=4, dpi=100):
+        """The constructor."""
+
+        # a figure instance to plot on
+        fig = mpl.figure.Figure(figsize=(width, height), dpi=dpi)
+        self.axes = fig.add_subplot(111)
+
+        #super clas
+        FigureCanvas.__init__(self, fig)
+        self.setParent(parent)
+
+        FigureCanvas.setSizePolicy(self,
+                QtWidgets.QSizePolicy.Expanding,
+                QtWidgets.QSizePolicy.Expanding)
+        FigureCanvas.updateGeometry(self)
+
+class computeSPAREs(QtWidgets.QWidget,IPlugin):
+
+    #constructor
+    def __init__(self):
+        super(computeSPAREs,self).__init__()
+        self.model = {'BrainAge': None, 'AD': None}
+        root = os.path.dirname(__file__)
+        self.ui = uic.loadUi(os.path.join(root, 'computeSPAREs.ui'),self)
+        self.plotCanvas = PlotCanvas(self.ui.page_2)
+        self.ui.verticalLayout.addWidget(self.plotCanvas)
+        self.SPAREs = None
+        #TODO: hook up plot functionality
+
+        self.ui.stackedWidget.setCurrentIndex(0)
+
+
+    def getUI(self):
+        return self.ui
+
+
+    def SetupConnections(self):
+        #pass
+        self.ui.load_SPARE_model_Btn.clicked.connect(lambda: self.OnLoadSPAREModel())
+        self.ui.load_other_model_Btn.clicked.connect(lambda: self.OnLoadSPAREModel())
+        self.ui.add_to_dataframe_Btn.clicked.connect(lambda: self.OnAddToDataFrame())
+        self.ui.compute_SPARE_scores_Btn.clicked.connect(lambda: self.OnComputeSPAREs())
+        self.ui.show_SPARE_scores_from_data_Btn.clicked.connect(lambda: self.OnShowSPAREs())
+        self.datamodel.data_changed.connect(lambda: self.OnDataChanged())
+        # Set `Show SPARE-* from data` button to visible when SPARE-* columns
+        # are present in data frame
+        if ('SPARE_BA' in self.datamodel.GetColumnHeaderNames() and
+            'SPARE_AD' in self.datamodel.GetColumnHeaderNames()):
+            self.ui.show_SPARE_scores_from_data_Btn.setEnabled(True)
+        else:
+            self.ui.show_SPARE_scores_from_data_Btn.setEnabled(False)
+
+
+
+    def OnLoadSPAREModel(self):
+        fileName, _ = QtWidgets.QFileDialog.getOpenFileName(None,
+            'Open SPARE-* model file',
+            QtCore.QDir().homePath(),
+            "Pickle files (*.pkl.gz *.pkl)")
+        if fileName != "":
+            self.model['BrainAge'], self.model['AD'] = joblib.load(fileName)
+            self.ui.compute_SPARE_scores_Btn.setEnabled(True)
+
+        self.ui.stackedWidget.setCurrentIndex(0)
+
+
+    def OnComputeSPAREs(self):
+        self.SPAREs = pd.DataFrame.from_dict({
+            'SPARE_BA': predictBrainAge(self.datamodel.data, self.model['BrainAge']),
+            'SPARE_AD': predictAD(self.datamodel.data, self.model['AD'])})
+        self.plotSPAREs()
+        self.ui.stackedWidget.setCurrentIndex(1)
+
+
+    def plotSPAREs(self):
+        sns.scatterplot(x='SPARE_AD', y='SPARE_BA', data=self.SPAREs,
+                        ax=self.plotCanvas.axes)
+
+
+    def OnAddToDataFrame(self):
+        pass
+
+
+    def OnShowSPAREs(self):
+        self.SPAREs = pd.DataFrame.from_dict({
+            'SPARE_BA': self.datamodel.data['SPARE_BA'].values,
+            'SPARE_AD': self.datamodel.data['SPARE_AD'].values})
+        self.plotSPAREs()
+        self.ui.stackedWidget.setCurrentIndex(1)
+
+
+    def OnDataChanged(self):
+        # Set `Show SPARE-* from data` button to visible when SPARE-* columns
+        # are present in data frame
+        if ('SPARE_BA' in self.datamodel.GetColumnHeaderNames() and
+            'SPARE_AD' in self.datamodel.GetColumnHeaderNames()):
+            self.ui.show_SPARE_scores_from_data_Btn.setEnabled(True)
+        else:
+            self.ui.show_SPARE_scores_from_data_Btn.setEnabled(False)
+
+
+
+def predictBrainAge(data,model):
+
+    idx = ~data[model['predictors'][0]].isnull()
+
+    y_hat_test = np.zeros((np.sum(idx),))
+    n_ensembles = np.zeros((np.sum(idx),))
+
+    for i,_ in enumerate(model['scaler']):
+        # Predict validation (fold) and test
+        print('Fold %d' % (i))
+        test = np.logical_not(data[idx]['participant_id'].isin(np.concatenate(model['train']))) | data[idx]['participant_id'].isin(model['validation'][i])
+        X = data[idx].loc[test, model['predictors']].values
+        X = model['scaler'][i].transform(X)
+        y_hat_test[test] += (model['svm'][i].predict(X) - model['bias_ints'][i]) / model['bias_slopes'][i]
+        n_ensembles[test] += 1.
+
+    y_hat_test /= n_ensembles
+    y_hat = np.full((data.shape[0],),np.nan)
+    y_hat[idx] = y_hat_test
+
+    return y_hat
+
+
+def predictAD(data,model):
+
+    idx = ~data[model['predictors'][0]].isnull()
+
+    y_hat_test = np.zeros((np.sum(idx),))
+    n_ensembles = np.zeros((np.sum(idx),))
+
+    for i,_ in enumerate(model['scaler']):
+        # Predict validation (fold) and test
+        print('Fold %d' % (i))
+        test = np.logical_not(data[idx]['participant_id'].isin(np.concatenate(model['train']))) | data[idx]['participant_id'].isin(model['validation'][i])
+        X = data[idx].loc[test, model['predictors']].values
+        X = model['scaler'][i].transform(X)
+        y_hat_test[test] += model['svm'][i].decision_function(X)
+        n_ensembles[test] += 1.
+
+    y_hat_test /= n_ensembles
+    y_hat = np.full((data.shape[0],),np.nan)
+    y_hat[idx] = y_hat_test
+
+    return y_hat

QtBrainChartGUI/plugins/computeSPAREs/computeSPAREs.ui

@@ -0,0 +1,91 @@
+<?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>400</width>
+    <height>300</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout_2">
+   <item>
+    <widget class="QStackedWidget" name="stackedWidget">
+     <property name="styleSheet">
+      <string notr="true"/>
+     </property>
+     <property name="currentIndex">
+      <number>1</number>
+     </property>
+     <widget class="QWidget" name="page">
+      <layout class="QVBoxLayout" name="verticalLayout_3">
+       <item>
+        <widget class="QPushButton" name="show_SPARE_scores_from_data_Btn">
+         <property name="enabled">
+          <bool>false</bool>
+         </property>
+         <property name="text">
+          <string>Show SPARE-* from data</string>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <widget class="QPushButton" name="load_SPARE_model_Btn">
+         <property name="text">
+          <string>Load SPARE Model</string>
+         </property>
+        </widget>
+       </item>
+       <item>
+        <widget class="QPushButton" name="compute_SPARE_scores_Btn">
+         <property name="enabled">
+          <bool>false</bool>
+         </property>
+         <property name="text">
+          <string>Compute SPARE-*</string>
+         </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>SPARE-* model details</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>

QtBrainChartGUI/plugins/computeSPAREs/computeSPAREs.yapsy-plugin

@@ -0,0 +1,9 @@
+[Core]
+Name = SPARE-*
+Module = computeSPAREs
+
+[Documentation]
+Author = Ahmed Abdulkadir
+Version = 0.1
+Website = 
+Description = Compute SPARE-* scores from existing model.