Add capability to plot model trends without data

Author: melhemr

niCHART/core/model/datamodel.py

@@ -21,6 +21,7 @@ class DataModel(QObject):
     """This class holds the data model."""
 
     data_changed = QtCore.pyqtSignal()
+    model_changed = QtCore.pyqtSignal()
 
     def __init__(self):
         QObject.__init__(self)
@@ -90,7 +91,8 @@ def SetData(self,d):
     def SetHarmonizationModel(self,m):
         """Setter for neuroHarmonize model"""
         self.harmonization_model = m
-        logger.info('neuroHarmonize model set.')
+        logger.info('neuroHarmonize model set. Signal emmitted')
+        self.model_changed.emit()
 
 
     def SetSPAREModel(self,BrainAgeModel, ADModel):
@@ -190,6 +192,8 @@ def GetColumnHeaderNames(self):
         """Returns all header names for all columns in the dataset."""
         if self.data is not None:
             k = self.data.keys()
+        elif self.harmonization_model is not None:
+            k = self.harmonization_model['ROIs']
         else:
             k = []
 

niCHART/plugins/agetrends/agetrends.py

@@ -8,6 +8,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+from niCHART.plugins.loadsave.dataio import DataIO
 from niCHART.core.plotcanvas import PlotCanvas
 from niCHART.core.gui.SearchableQComboBox import SearchableQComboBox
 
@@ -33,13 +34,24 @@ def getUI(self):
 
     def SetupConnections(self):
         self.datamodel.data_changed.connect(lambda: self.OnDataChanged())
+        self.datamodel.model_changed.connect(lambda: self.OnModelChanged())
         self.ui.comboBoxROI.currentIndexChanged.connect(self.UpdatePlot)
         self.ui.comboBoxHue.currentIndexChanged.connect(self.UpdatePlot)
 
     def OnDataChanged(self):
         self.PopulateROI()
         self.PopulateHue()
 
+    def OnModelChanged(self):
+        self.GetMUSEROIDict()
+        self.PopulateROI()
+
+    def GetMUSEROIDict(self):
+        dio = DataIO()
+        #also read MUSE dictionary
+        MUSEDictNAMEtoID, MUSEDictIDtoNAME, MUSEDictDataFrame = dio.ReadMUSEDictionary()
+        self.datamodel.SetMUSEDictionaries(MUSEDictNAMEtoID, MUSEDictIDtoNAME,MUSEDictDataFrame)
+
     def PopulateROI(self):
         #get data column header names
         datakeys = self.datamodel.GetColumnHeaderNames()
@@ -58,7 +70,6 @@ def PopulateROI(self):
             if invalid_ROI in roiList:
                 roiList.remove(invalid_ROI)
 
-
         _, MUSEDictIDtoNAME = self.datamodel.GetMUSEDictionaries()
         roiList = list(set(roiList).intersection(set(datakeys)))
         roiList.sort()
@@ -131,16 +142,16 @@ def PlotAgeTrends(self,plotOptions):
         self.plotCanvas.axes.clear()
 
         # seaborn plot on axis
-        a = sns.scatterplot(x='Age', y=currentROI,  hue=currentHue,ax=self.plotCanvas.axes, s=5,
-            data=self.datamodel.GetData(currentROI,currentHue))
-        self.plotCanvas.axes.yaxis.set_ticks_position('left')
-        self.plotCanvas.axes.xaxis.set_ticks_position('bottom')
-        sns.despine(fig=self.plotCanvas.axes.get_figure(), trim=True)
-        self.plotCanvas.axes.get_figure().set_tight_layout(True)
-
-        # Plot normative range if according GAM model is available
-        if (self.datamodel.harmonization_model is not None) and (currentROI in ['H_' + x for x in self.datamodel.harmonization_model['ROIs']]):
-            x,y,z = self.datamodel.GetNormativeRange(currentROI[2:])
+        if self.datamodel.data is not None:
+            a = sns.scatterplot(x='Age', y=currentROI,  hue=currentHue,ax=self.plotCanvas.axes, s=5,
+                data=self.datamodel.GetData(currentROI,currentHue))
+            self.plotCanvas.axes.yaxis.set_ticks_position('left')
+            self.plotCanvas.axes.xaxis.set_ticks_position('bottom')
+            sns.despine(fig=self.plotCanvas.axes.get_figure(), trim=True)
+            self.plotCanvas.axes.get_figure().set_tight_layout(True)
+
+        if (self.datamodel.harmonization_model is not None) and (currentROI in [x for x in self.datamodel.harmonization_model['ROIs']]):
+            x,y,z = self.datamodel.GetNormativeRange(currentROI)
             #print('Pooled variance: %f' % (z))
             # Plot three lines as expected mean and +/- 2 times standard deviation
             sns.lineplot(x=x, y=y, ax=self.plotCanvas.axes, linestyle='-', markers=False, color='k')

niCHART/plugins/harmonizationplugin/harmonization.py

@@ -35,7 +35,8 @@ def DoHarmonization(self):
 
         covars = self.datamodel.data[['SITE','Age','Sex','DLICV_baseline']].reset_index(drop=True).copy()
         covars.loc[:,'Sex'] = covars['Sex'].map({'M':1,'F':0})
-        covars.loc[covars.Age>100, 'Age']=100
+        covars.loc[covars.Age>102, 'Age']=102
+        covars.loc[covars.Age<20, 'Age']=20
 
         # Parameter table for plotting 
         gamma_ROIs = ['gamma_'+ x for x in self.datamodel.harmonization_model['ROIs']]
@@ -73,9 +74,11 @@ def DoHarmonization(self):
                 model_delta = pd.DataFrame(self.datamodel.harmonization_model['delta_star'],columns=delta_ROIs,index=[x for x in self.datamodel.harmonization_model['SITE_labels']])
                 parameters = pd.concat([model_gamma,model_delta],axis=1).sort_index()                     
             else:
-                oos_data = self.datamodel.data[self.datamodel.data['SITE'].isin(sites_to_harmonize)].dropna(subset=covariates)[[x for x in self.datamodel.harmonization_model['ROIs']]].values
-                oos_covars = self.datamodel.data[self.datamodel.data.SITE.isin(sites_to_harmonize)].dropna(subset=covariates)[covariates]
+                oos_data = self.datamodel.data[(self.datamodel.data['SITE'].isin(sites_to_harmonize))&(self.datamodel.data['UseForComBatGAMHarmonization'].notnull())].dropna(subset=covariates)[[x for x in self.datamodel.harmonization_model['ROIs']]].values
+                oos_covars = self.datamodel.data[(self.datamodel.data['SITE'].isin(sites_to_harmonize))&(self.datamodel.data['UseForComBatGAMHarmonization'].notnull())].dropna(subset=covariates)[covariates]
                 oos_covars.loc[:,'Sex'] = oos_covars['Sex'].map({'M':1,'F':0})
+                oos_covars.loc[oos_covars.Age>102, 'Age']=102
+                oos_covars.loc[oos_covars.Age<20, 'Age']=20
                 self.model, _ = nh.harmonizationLearn(oos_data, oos_covars,
                                                 smooth_terms=['Age'],
                                                 smooth_term_bounds=(np.floor(np.min(self.datamodel.data.Age)),np.ceil(np.max(self.datamodel.data.Age))),
@@ -122,7 +125,7 @@ def DoHarmonization(self):
             MUSEDictDataFrame= self.datamodel.GetMUSEDictDataFrame()
             muse_mappings = self.datamodel.GetDerivedMUSEMap()
             for ROI in MUSEDictDataFrame[MUSEDictDataFrame['ROI_LEVEL']=='DERIVED']['ROI_INDEX']:
-                single_ROIs = muse_mappings.loc[ROI].replace('NaN',np.nan).dropna().astype(np.float)
+                single_ROIs = muse_mappings.loc[ROI].replace('NaN',np.nan).dropna().astype(np.float64)
                 single_ROIs = ['H_MUSE_Volume_%0d' % x for x in single_ROIs]
                 muse['H_MUSE_Volume_%d' % ROI] = muse[single_ROIs].sum(axis=1,skipna=False)
             muse.drop(columns=['H_MUSE_Volume_702'], inplace=True)

niCHART/plugins/harmonizationplugin/harmonizationplugin.py

@@ -42,9 +42,6 @@ def getUI(self):
 
     def SetupConnections(self):
         self.ui.load_harmonization_model_Btn.clicked.connect(lambda: self.OnLoadHarmonizationModelBtnClicked())
-        if self.datamodel.data is None:
-            self.ui.load_harmonization_model_Btn.setEnabled(False)
-            self.ui.Harmonized_Data_Information_Lbl.setText('Data must be loaded before model selection.\nReturn to Load and Save Data tab to select data.')
         self.ui.load_other_model_Btn.clicked.connect(lambda: self.OnLoadHarmonizationModelBtnClicked())
         self.ui.show_data_Btn.clicked.connect(lambda: self.OnShowDataBtnClicked())
         self.ui.apply_model_to_dataset_Btn.clicked.connect(lambda: self.OnApplyModelToDatasetBtnClicked())
@@ -98,13 +95,17 @@ def LoadHarmonizationModel(self, filename):
                 age_min = self.datamodel.harmonization_model['smooth_model']['bsplines_constructor'].knot_kwds[0]['lower_bound']
                 model_text4 = ('Valid Age Range: [' + str(age_min) + ', ' + str(age_max) + ']')
                 model_text1 += '\n'+model_text4
-                self.ui.Harmonized_Data_Information_Lbl.setText(model_text1)
                 if self.datamodel.data is None:
                     self.ui.apply_model_to_dataset_Btn.setEnabled(False)
-                    self.ui.Harmonized_Data_Information_Lbl.setText('Data must be loaded before model selection or application.\nReturn to Load and Save Data tab to select data.')
+                    model_text5 = 'Data must be loaded before model application.\nReturn to Load and Save Data tab to select data.'
+                    model_text1 += '\n'+model_text5
+                    self.ui.Harmonized_Data_Information_Lbl.setText(model_text1)
                 else:
+                    self.ui.Harmonized_Data_Information_Lbl.setText(model_text1)
                     self.ui.apply_model_to_dataset_Btn.setEnabled(True)
                     self.ui.apply_model_to_dataset_Btn.setStyleSheet("background-color: rgb(230,255,230); color: black")
+                self.datamodel.SetDataFilePath(filename)
+                self.datamodel.SetHarmonizationModel(self.datamodel.harmonization_model)
         self.ui.stackedWidget.setCurrentIndex(0)
 
     def OnLoadHarmonizationModelBtnClicked(self):
@@ -339,9 +340,8 @@ def OnDataChanged(self):
             self.ui.show_data_Btn.setEnabled(False)
 
         if self.datamodel.data is None:
-            self.ui.load_harmonization_model_Btn.setEnabled(False)
             self.ui.apply_model_to_dataset_Btn.setEnabled(False)
-            self.ui.Harmonized_Data_Information_Lbl.setText('Data must be loaded before model selection.\nReturn to Load and Save Data tab to select data.')
+            self.ui.Harmonized_Data_Information_Lbl.setText('Data must be loaded before model application.\nReturn to Load and Save Data tab to select data.')
         else:
             self.ui.load_harmonization_model_Btn.setEnabled(True)
             if self.datamodel.harmonization_model is None: