Add harmonization plugin

NiChartGUI/mainwindow.py

@@ -73,12 +73,22 @@ def __init__(self, dataFiles = None, dictFiles = None):
 
         ## Sort plugins based on tab position. Create a dictionary of plugins
         indSort = np.argsort(plIndTmp)
+
+        ## FIXME Select to activate few plugins:
+        ## ['Dataset View', 'Filter View', 'Dist View', 'Plot View', 'Merge View', 'Normalize View', 'Adjust Cov View', 'Harmonize View', 'Spare View']
+        indSort = indSort[[0,3,5,6,7,8]]
+
         plTmp = np.array(plTmp)[indSort]
         plNameTmp = np.array(plNameTmp)[indSort]
+
 
         self.pluginDescriptions = np.array(pluginDescriptions)[indSort]       # A list with plugin descriptions
 
         self.Plugins = dict(zip(plNameTmp, plTmp))                  # A dictionary with plugin name and plugin object
+
+        #logger.info(self.Plugins)
+        #logger.info('AAAAAA')
+
         self.IndexPlugins = dict(zip(plNameTmp, np.arange(0, plNameTmp.shape[0])))  # A dictionary with plugin name and plugin index
 
 
@@ -105,7 +115,7 @@ def __init__(self, dataFiles = None, dictFiles = None):
         for i, [key,value] in enumerate(self.Plugins.items()):
             self.ui.tabWidget.insertTab(i, value, key)
             if i>0:
-                #self.ui.tabWidget.setTabVisible(i, False)
+                self.ui.tabWidget.setTabVisible(i, False)
                 self.ui.tabWidget.setTabVisible(i, True)
 
         if dataFiles is not None:

NiChartGUI/plugins/harmonizeview/harmonizeview.py

@@ -0,0 +1,202 @@
+from PyQt5.QtGui import *
+from PyQt5 import QtGui, QtCore, QtWidgets, uic
+from PyQt5.QtWidgets import QMdiArea, QMdiSubWindow, QLineEdit, QComboBox, QMenu, QAction, QWidgetAction
+import sys, os
+import pandas as pd
+import gzip
+import pickle
+import numpy as np
+from NiChartGUI.core.dataio import DataIO
+# import dtale
+from NiChartGUI.core.baseplugin import BasePlugin
+from NiChartGUI.core import iStagingLogger
+from NiChartGUI.core.gui.SearchableQComboBox import SearchableQComboBox
+from NiChartGUI.core.gui.CheckableQComboBox import CheckableQComboBox
+from NiChartGUI.core.gui.NestedQMenu import NestedQMenu
+from NiChartGUI.core.model.datamodel import PandasModel
+
+import inspect
+
+import sys
+
+from NiChartHarmonize import nh_apply_model as nh_test
+
+logger = iStagingLogger.get_logger(__name__)
+
+class HarmonizeView(QtWidgets.QWidget,BasePlugin):
+
+    def __init__(self):
+        super(HarmonizeView,self).__init__()
+
+        self.data_model_arr = None
+        self.active_index = -1
+
+        self.cmds = None
+
+        self.modelname = None
+        ##self.modelname = '/home/guraylab/AIBIL/Github/TmpPackages/HarmonizeScores/mdl/mdl_SPARE_AD_MUSE_single.pkl.gz'
+
+        ## Status bar of the main window
+        ## Initialized by the mainwindow during loading of plugin
+        self.statusbar = None
+
+
+        ## Status bar of the main window
+        ## Initialized by the mainwindow during loading of plugin
+        self.statusbar = None
+
+        root = os.path.dirname(__file__)
+        self.readAdditionalInformation(root)
+        self.ui = uic.loadUi(os.path.join(root, 'harmonizeview.ui'),self)
+
+        ## Main view panel        
+        self.mdi = self.findChild(QMdiArea, 'mdiArea')       
+        self.mdi.setBackground(QtGui.QColor(245,245,245,255))
+
+        ## Options panel is not shown if there is no dataset loaded
+        self.ui.wOptions.hide()
+
+        self.ui.wOptions.setMaximumWidth(300)
+
+        self.ui.wCalcHarmonize.hide()
+
+
+
+    def SetupConnections(self):
+
+        self.data_model_arr.active_dset_changed.connect(self.OnDataChanged)
+
+        self.ui.selectModelBtn.clicked.connect(self.OnSelectModelBtnClicked)
+        self.ui.calcHarmonizeBtn.clicked.connect(self.OnCalcHarmonizeBtnClicked)
+
+
+    def CheckModel(self, filename):
+        #read input data
+
+        # Load model
+        with gzip.open(filename, 'rb') as f:
+            self.mdl = pickle.load(f)
+
+        # Get columns and check if they exist in dset
+        mdlCol = self.mdl['predictors']
+        dfCol = self.data_model_arr.datasets[self.active_index].data.columns
+
+        dfMdl = pd.DataFrame(columns=['Predictor'], data = mdlCol)
+        dfMdl['Status'] = dfMdl.Predictor.isin(dfCol)
+        dfMdl = dfMdl.replace({True:'FOUND', False:'MISSING'}).sort_values('Status', ascending = False)
+
+        self.PopulateTable(dfMdl)
+
+        ## Set data view to mdi widget
+        sub = QMdiSubWindow()
+        sub.setWidget(self.dataView)
+        sub.setWindowTitle('MODEL: ' + os.path.basename(filename))
+        self.mdi.addSubWindow(sub)        
+        sub.show()
+        self.mdi.tileSubWindows()
+
+        if dfMdl[dfMdl.Status=='MISSING'].shape[0] > 0:
+            self.statusbar.showMessage('WARNING: Model does not match the data!')
+
+        else:
+            self.ui.wCalcHarmonize.show()
+            self.statusbar.showMessage('Model is valid')
+
+
+        logger.critical(dfMdl.head())
+
+    def OnSelectModelBtnClicked(self):
+
+        #if self.dataPathLast == '':
+            #directory = QtCore.QDir().homePath()
+        #else:
+            #directory = self.dataPathLast
+        directory = QtCore.QDir().homePath()
+        directory = '/home/guraylab/AIBIL/Github/TmpPackages/HarmonizeScores/mdl'
+
+        filename = QtWidgets.QFileDialog.getOpenFileName(None,
+            caption = 'Open model file',
+            directory = directory,
+            filter = "Pickle/pickle.gz files (*.pkl *.gz)")
+
+        if filename[0] == "":
+            logger.warning("No file was selected")
+        else:
+            self.modelname = filename[0]
+            self.ui.wCalcHarmonize.show()
+
+
+    def OnCalcHarmonizeBtnClicked(self):
+
+        ## Read data and harmonize options
+        df = self.data_model_arr.datasets[self.active_index].data
+        outVarName = self.ui.edit_outVarName.text()
+        if outVarName == '':
+            outVarName = 'HARM'
+        if outVarName[0] == '_':
+            outVarName = outVarName[1:]
+        outCat = outVarName
+
+        ## Apply Harmonization
+        res_harm = nh_test.nh_harmonize_to_ref(df, self.modelname)
+
+        if len(res_harm) == 1:          ## Model mismatch
+            logger.warning('AAAAAAAAAAAAAAAAAAA')
+
+        else:
+            mdlOut, dfOut = res_harm
+
+        ## Set updated dset
+        df = dfOut
+        self.data_model_arr.datasets[self.active_index].data = df
+
+        ## Create dict with info about new columns
+        outDesc = 'Created by NiChartHarmonize Plugin'
+        outSource = 'NiChartHarmonize Plugin'
+        ##self.data_model_arr.AddNewVarsToDict([outVarName], outCat, outDesc, outSource)
+
+        ## Call signal for change in data
+        ##self.data_model_arr.OnDataChanged()
+
+        ## Load data to data view 
+        self.dataView = QtWidgets.QTableView()
+
+        ## Show only columns involved in application
+
+        #dfOut = dfOut.round(3)
+        self.PopulateTable(dfOut)
+
+        ## Set data view to mdi widget
+        sub = QMdiSubWindow()
+        sub.setWidget(self.dataView)
+        sub.setWindowTitle('Harmonized Values')
+        self.mdi.addSubWindow(sub)        
+        sub.show()
+        self.mdi.tileSubWindows()
+
+
+    def PopulateTable(self, data):
+
+        model = PandasModel(data)
+        self.dataView = QtWidgets.QTableView()
+        self.dataView.setModel(model)
+
+    def OnDataChanged(self):
+
+        if self.data_model_arr.active_index >= 0:
+
+            ## Make options panel visible
+            self.ui.wOptions.show()
+
+            ## Set fields for various options     
+            self.active_index = self.data_model_arr.active_index
+
+            ## Get data variables
+            dataset = self.data_model_arr.datasets[self.active_index]
+
+            ## Set active dset name
+            self.ui.edit_activeDset.setText(self.data_model_arr.dataset_names[self.active_index])
+
+            ### Update selection, sorting and drop duplicates panels
+            #self.UpdatePanels(catNames, colNames)
+