Add logging capability

QtBrainChartGUI/__init__.py

@@ -10,9 +10,7 @@
 import os, sys
 from QtBrainChartGUI.mainwindow import MainWindow
 
-
 def main():
-    print("inside main")
     parser = argparse.ArgumentParser(description='iSTAGING Data Visualization and Preparation')
     parser.add_argument('--data_file', type=str, help='Data file containing data frame.', default=None, required=False)
     parser.add_argument('--harmonization_model_file', type=str, help='Harmonization model file.', default=None, required=False)
@@ -29,6 +27,7 @@ def main():
                     harmonizationModelFile=harmonization_model_file,
                     SPAREModelFile=SPARE_model_file)
     mw.show()
+
     sys.exit(app.exec_())
 
 if __name__ == '__main__':

QtBrainChartGUI/core/iStagingLogger.py

@@ -0,0 +1,34 @@
+# This Python file uses the following encoding: utf-8
+"""
+contact: software@cbica.upenn.edu
+Author: Ashish Singh
+Copyright (c) 2018 University of Pennsylvania. All rights reserved.
+Use of this source code is governed by license located in license file: https://github.com/CBICA/iSTAGING-Tools/blob/main/LICENSE
+"""
+
+import logging
+import sys, os
+from logging.handlers import TimedRotatingFileHandler
+#FORMATTER = logging.Formatter("%(asctime)s — %(name)s — %(levelname)s — %(message)s")
+FORMATTER = logging.Formatter("[%(asctime)s — %(name)s — %(filename)s: Line:%(lineno)s — %(funcName)20s() ] — %(levelname)s — %(message)s")
+LOG_FILE = os.path.expanduser(os.path.join('~', '.NiBAx','NiBAx.log'))
+
+def get_console_handler():
+    console_handler = logging.StreamHandler(sys.stdout)
+    console_handler.setFormatter(FORMATTER)
+    return console_handler
+
+def get_file_handler():
+    if not os.path.exists(os.path.dirname(LOG_FILE)):
+        os.makedirs(os.path.dirname(LOG_FILE))
+    file_handler = TimedRotatingFileHandler(LOG_FILE, when='midnight')
+    file_handler.setFormatter(FORMATTER)
+    return file_handler
+
+def get_logger(logger_name):
+    logger = logging.getLogger(logger_name)
+    logger.setLevel(logging.DEBUG) # better to have too much log than not enough
+    logger.addHandler(get_console_handler())
+    logger.addHandler(get_file_handler())
+    logger.propagate = False
+    return logger

QtBrainChartGUI/core/model/datamodel.py

@@ -14,6 +14,9 @@
 import joblib
 from PyQt5.QtCore import QObject, pyqtSignal
 from PyQt5 import QtCore
+from QtBrainChartGUI.core import iStagingLogger
+
+logger = iStagingLogger.get_logger(__name__)
 
 class DataModel(QObject):
     """This class holds the data model."""
@@ -68,6 +71,7 @@ def GetMUSEDictionaries(self):
     def SetData(self,d):
         """Setter for data"""
         self.data = d
+        logger.info('Data changed in datamodel')
         self.data_changed.emit()
 
 

QtBrainChartGUI/mainwindow.py

@@ -16,10 +16,17 @@
 from PyQt5.QtWidgets import QAction
 import pandas as pd
 from QtBrainChartGUI.core.baseplugin import BasePlugin
+from QtBrainChartGUI.core import iStagingLogger
+
+logger = iStagingLogger.get_logger(__name__)
 
 class MainWindow(QtWidgets.QMainWindow):
     def __init__(self, dataFile=None, harmonizationModelFile=None, SPAREModelFile=None):
         super(MainWindow,self).__init__()
+
+        #log
+        logger.info('New NiBAx session starting...')
+
         self.SetupUi()
         self.SetupConnections()
 
@@ -43,7 +50,8 @@ def __init__(self, dataFile=None, harmonizationModelFile=None, SPAREModelFile=No
             po.datamodel = self.datamodel
             po.SetupConnections()
             self.Plugins[plugin.name] = po
-            print("plugins: ", plugin.name)
+
+        logger.info("Loaded Plugins: %s", self.Plugins.keys())
 
         #organize plugins in order:Data -> Characteristics -> Age Trends -> Harmonization -> SPARE-*
         for num in range(len(self.Plugins)):
@@ -71,6 +79,9 @@ def __init__(self, dataFile=None, harmonizationModelFile=None, SPAREModelFile=No
         self.ui.actionHelp.setMenuRole(QAction.NoRole)
         self.ui.actionAbout.setMenuRole(QAction.NoRole)
 
+    def __del__(self):
+        logger.info('NiBAx session ending...')
+
     def SetupConnections(self):
         self.actionAbout.triggered.connect(self.OnAboutClicked)
         self.actionHelp.triggered.connect(self.OnHelpClicked)

QtBrainChartGUI/plugins/data/data.py

@@ -5,6 +5,9 @@
 from QtBrainChartGUI.plugins.data.dataio import DataIO
 import dtale
 from QtBrainChartGUI.core.baseplugin import BasePlugin
+from QtBrainChartGUI.core import iStagingLogger
+
+logger = iStagingLogger.get_logger(__name__)
 
 class PandasModel(QtCore.QAbstractTableModel):
     def __init__(self, data, parent=None):
@@ -89,17 +92,16 @@ def PopulateTable(self):
         model = PandasModel(self.datamodel.data.head(20))
         self.dataView.setModel(model)
 
-
-
     def OnDataChanged(self):
         self.PopulateTable()
 
-
     def ReadData(self,filename):
         #read input data
         dio = DataIO()
         d = dio.ReadPickleFile(filename)
 
+        logger.info('New data read from file: %s', filename)
+
         #also read MUSE dictionary
         MUSEDictNAMEtoID, MUSEDictIDtoNAME = dio.ReadMUSEDictionary()
         self.datamodel.SetMUSEDictionaries(MUSEDictNAMEtoID, MUSEDictIDtoNAME)

QtBrainChartGUI/plugins/data/dataio.py

@@ -8,6 +8,9 @@
 import pandas as pd
 import joblib
 import os, sys
+from QtBrainChartGUI.core import iStagingLogger
+
+logger = iStagingLogger.get_logger(__name__)
 
 class DataIO:
     def __init__(self):
@@ -24,15 +27,17 @@ def SavePickleFile(self,data,filename):
 
     def ReadMUSEDictionary(self):
         # Load MUSE dictionary file
-        MUSEDict = os.path.join(os.path.dirname(__file__), 'MUSE_ROI_Dictionary.csv')
-        MUSEDict = pd.read_csv(MUSEDict)
+        MUSEDictfile = os.path.join(os.path.dirname(__file__), 'MUSE_ROI_Dictionary.csv')
+        MUSEDict = pd.read_csv(MUSEDictfile)
 
         # Create lookup from name to ID and vice-versa
         # e.g. name to ID: Hippocampus right -> MUSE_Volume_48
         MUSEDictNAMEtoID = dict(zip(MUSEDict['ROI_NAME'], MUSEDict['ROI_COL']))
         # e.g. ID to name; MUSE_Volume_48 -> Hippocampus right
         MUSEDictIDtoNAME = dict(zip(MUSEDict['ROI_COL'], MUSEDict['ROI_NAME']))
 
+        logger.info('MUSE dictionary read from file: %s', MUSEDictfile)
+
         return MUSEDictNAMEtoID, MUSEDictIDtoNAME